BenchMark XT Service Manual (New)

BenchMark XT / DISCOVERY XT /
BenchMark LT Service Manual
Part Number 2000300 Revision E

BenchMark XT / DISCOVERY XT / Benchmark LT Service Manual
Copyright
Copyright © 2004 - 2012 Ventana Medical Systems, Inc., 1910 E. Innovation Park Drive, Tucson, Arizona
85755 USA. All rights reserved.
Trademark
BENCHMARK, DISCOVERY, NEXES, VENTANA, and the VENTANA logo are trademarks of Roche.
All other trademarks are the property their respective owners. Windows is a registered trademark of
Microsoft Corporation in the United States and other countries. Intel is a trademark of Intel Corporation in
the U.S. and/or other countries. Loctite is a trademark of Henkel AG & Co. KGaA.
Preface
This manual is designed for reference use by trained service personnel of Ventana Medical Systems, Inc.
Hence, a basic level of mechanical and technical skills plus an overall familiarity with Ventana instruments
is assumed.
The manual covers BenchMark XT / DISCOVERY XT / BenchMark LT instruments. The BenchMark LT
and BenchMark XT / DISCOVERY XT instruments are similar, the major difference being slide tray
capacity. The BenchMark LT instrument accommodates 20 slides and the BenchMark XT / DISCOVERY
XT instruments accommodate 30 slides. Therefore, in some areas of this manual, figures or text referring
to only one instrument may be used to illustrate or explain something related to all three instruments.
This manual is designed as a guide for instrument field servicing and doubles as a technical tutorial if
read from front to back. Since the instrument has several hundred individual part numbers, the manual
necessarily concentrates on those components believed to be field serviceable and subject to wear. For
problems beyond the scope of this manual, factory service may be the only alternative.
VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page ii

Table of Contents
1.0 Safety Information .............................................................................................. 1
1.1 Stainer Subassembly .......................................................................................................... 1
1.2 Labels .................................................................................................................................. 1
1.2.1 Caution: Hot Surface—Do Not Touch ............................................................ 1
1.2.2 Caution: Refer to Accompanying Documents ................................................ 1
1.2.3 Caution: Risk of Electric Shock ...................................................................... 2
1.2.4 Caution: Disconnect Power Before Servicing ................................................ 2
1.2.5 Ground Connection ......................................................................................... 2
1.2.6 Caution: LASER ............................................................................................. 3
1.2.7 Caution: LASER ............................................................................................. 3
1.3 Safety Training .................................................................................................................... 3
1.4 Safety Compliance .............................................................................................................. 4
2.0 What the Instrument Does ................................................................................. 5
2.1 Tissue Staining.................................................................................................................... 5
2.2 Tissue Staining Process ..................................................................................................... 5
2.3 How the Instrument Works .................................................................................................. 6
3.0 Major System Modules ....................................................................................... 8
3.1 Stainer Subassembly .......................................................................................................... 8
3.2 Automated Fluidics Module (AFM)...................................................................................... 9
3.3 Waste Subassembly ........................................................................................................... 9
3.4 Personal Computer ........................................................................................................... 10
4.0 Stainer Subassembly ....................................................................................... 12
4.1 Reagent Carousel and Nozzle Plate ................................................................................. 13
4.1.1 Reagent Carousel.......................................................................................... 13
4.1.2 Nozzle Plate .................................................................................................. 14
4.1.3 Home Sensors ............................................................................................... 14
4.2 Slide Tray .......................................................................................................................... 15
4.3 Reagent Dispensers.......................................................................................................... 15
4.4 Barcode Readers .............................................................................................................. 15
4.5 Liquid and Air Nozzles ...................................................................................................... 16
4.5.1 Nozzle Arrangement ...................................................................................... 16
4.5.2 Dual Rinse Nozzles ....................................................................................... 17
4.5.3 Jet Drain Nozzle ............................................................................................ 18
4.5.4 Multispense Nozzles...................................................................................... 18
4.5.5 LCS Nozzles .................................................................................................. 20
4.5.6 Barcode Blowoff/Air Knife .............................................................................. 20
4.5.7 Vortex Mixer Nozzles..................................................................................... 21
4.6 Restrictors and Filters ....................................................................................................... 23
4.7 Fan and Sensor................................................................................................................. 23
4.8 Slide Tray Sensor.............................................................................................................. 23
4.9 Tub and Overflow Sensor ................................................................................................. 24
4.10 Instrument Control Panel .................................................................................................. 24
4.11 Power Supply .................................................................................................................... 24
4.12 Cables and Wiring Harnesses .......................................................................................... 25
4.13 Plumbing ........................................................................................................................... 25
5.0 Microcontroller PCB ......................................................................................... 26
5.1 Serial Port ......................................................................................................................... 28
5.2 Address Switch ................................................................................................................. 28
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5.3 Microcontroller IC .............................................................................................................. 28

5.4 Serial Output Board........................................................................................................... 29
5.5 Motor Controllers............................................................................................................... 30
5.6 Valve, Nozzle Plate, 24 VDC Power, and Cooling Fan Outputs ....................................... 30
5.7 Air Pressure Sensor .......................................................................................................... 30
5.8 Beeper ............................................................................................................................... 31
5.9 Slide Heater Circuit Boards ............................................................................................... 31
5.10 Port Expander Circuit Board ............................................................................................. 31
6.0 Automated Fluidics Module ............................................................................. 33
6.1 Pneumatics Systems of the AFM ...................................................................................... 34
6.1.1 Pressurized Air .............................................................................................. 35
6.1.2 Vacuum ......................................................................................................... 35
6.1.3 Vacuum Assist ............................................................................................... 36
6.1.4 Pneumatic Valve Manifold Assembly ............................................................ 36
6.1.5 Compressor ................................................................................................... 37
6.2 Connectors ........................................................................................................................ 37
6.3 Fluidics Systems of the AFM ............................................................................................ 37
6.3.1 Multi-Chamber Fluid Reservoir ...................................................................... 37
6.3.2 Automated Fluidics Bottles ............................................................................ 38
6.3.3 Waste Collection............................................................................................ 39
7.0 Personal Computer .......................................................................................... 40
7.1 PC Configuration and Accessories ................................................................................... 41
7.2 Connectors and Cables .................................................................................................... 41
7.3 Hardware Key ................................................................................................................... 41
7.4 USB to Serial Adapter ....................................................................................................... 42
7.5 Reagent Read Probe ........................................................................................................ 42
7.5.1 Reagent Read Probe Power Supply ............................................................. 42
8.0 NexES Software ................................................................................................ 43
8.1 Function Tests................................................................................................................... 45
8.2 Service Tests .................................................................................................................... 46
8.2.1 Basic I/O Control Tab .................................................................................... 47
8.2.2 Test Functions Tab ........................................................................................ 48
8.2.3 Instrument Data Tab ...................................................................................... 50
8.2.4 Temperature Chart Tab ................................................................................. 51
8.3 Service Tests with Calibration ........................................................................................... 52
8.4 Command Line Options .................................................................................................... 53
9.0 Voltage Conversion .......................................................................................... 55
10.0 Level One Tests and Adjustments .................................................................. 59
10.1 Inspect Compressor Muffler .............................................................................................. 59
10.2 Verify Reagent Homing Alignment .................................................................................... 59
10.3 Jog Reagent Tray.............................................................................................................. 60
10.4 Verify Nozzle Plate Homing Alignment ............................................................................. 61
10.5 Jog Nozzle Plate ............................................................................................................... 62
10.6 Verify Slide Barcode Read Alignment ............................................................................... 63
10.7 Verify Reagent Barcode Read Alignment ......................................................................... 64
10.8 Verify Dispense Cylinder to Dispenser Alignment ............................................................ 64
10.9 Verify Operation of Barcode Blowoff ................................................................................. 65
10.10 Verify Mixer Height, Alignment, and Performance ............................................................ 66
10.10.1 Vortex Mixer Height ....................................................................................... 66
10.10.2 Vortex Mixer Alignment ................................................................................. 68
10.10.3 Vortex Mixer Performance ............................................................................. 70
10.11 Verify Waste Sensor Performance.................................................................................... 71
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10.12 Verify Instrument Level ..................................................................................................... 71

10.13 High System Pressure ...................................................................................................... 71
10.14 Low System Pressure ....................................................................................................... 72
10.15 Vacuum ............................................................................................................................. 73
10.16 Mixer Flow Rates .............................................................................................................. 73
10.17 Fluid Volumes ................................................................................................................... 74
10.18 Test-Cell Conditioner #1 XT .............................................................................................. 74
10.19 Test-Cell Conditioner #2 XT .............................................................................................. 75
10.20 Test-Coverslip XT ............................................................................................................. 75
10.21 Test-Rinse Mix 1x SSC XT ............................................................................................... 76
10.22 Test-Rinsing (EZ Prep) XT ................................................................................................ 76
10.23 Test-Rinsing (Option) XT (Only needed for SISH)............................................................ 77
10.24 Test-Rinsing (RB) XT ........................................................................................................ 78
10.25 Test-Rinsing (SSC) XT ..................................................................................................... 78
10.26 Test-Volume Adj (EzPrep) XT........................................................................................... 79
10.27 Test-Slide Vol IHC (RB) XT .............................................................................................. 79
10.28 Test-Slide Vol IHC (SSC) XT ............................................................................................ 80
10.29 Test-Slide Vol ISH (Opt) XT (Only needed for SISH) ....................................................... 81
10.30 Test-Slide Vol ISH (RB) XT ............................................................................................... 82
10.31 Test-Slide Vol ISH (SSC) XT ............................................................................................ 83
11.0 Preventive Maintenance Tests and Adjustments .......................................... 85
11.1 Replace Compressor Muffler ............................................................................................ 85
11.2 Check Moisture Trap ......................................................................................................... 85
11.3 Replace All In-Line Filters Between Fluid Reservoirs and Nozzles .................................. 85
11.4 Inspect Reservoir Chambers ............................................................................................ 85
11.5 Inspect Bottle Filters.......................................................................................................... 86
11.6 Inspect Motor Gear Pulleys, Tighten Pulley Set Screws .................................................. 86
11.7 Inspect Reagent Belt ......................................................................................................... 86
11.8 Inspect Nozzle Plate Belt .................................................................................................. 86
11.9 Inspect Tubing to Nozzle Plate Assembly ........................................................................ 86
11.10 Inspect and Clean Tub Drain ............................................................................................ 86
11.11 Inspect Underside of Slide Drawer and Heater PCBs for Fluid Leaks ............................. 87
11.12 Verify Operation of Tub Overflow Sensor ......................................................................... 87
11.13 Verify Operation of Bulk Bottle Sensors............................................................................ 87
11.14 Verify Waste Sensor Performance.................................................................................... 87
11.15 Verify Operation of Vacuum Trap Check Valve ................................................................ 87
11.16 Verify Reagent Homing Alignment .................................................................................... 88
11.17 Jog Reagent Tray.............................................................................................................. 88
11.18 Verify Nozzle Plate Homing Alignment ............................................................................. 88
11.19 Jog Nozzle Plate ............................................................................................................... 88
11.20 Verify Slide Barcode Read Alignment ............................................................................... 88
11.21 Verify Reagent Barcode Read Alignment ......................................................................... 88
11.22 Verify Operation of Fans ................................................................................................... 88
11.23 Verify Dispense Cylinder to Dispenser Alignment ............................................................ 88
11.24 Verify Operation of Barcode Blowoff ................................................................................. 88
11.25 Verify Mixer Height, Alignment, and Performance ............................................................ 89
11.26 Verify All Technical Bulletins Have Been Completed ....................................................... 89
11.27 Verify Instrument Level ..................................................................................................... 89
11.28 High Pressure System Leak Rate ..................................................................................... 89
11.29 Low Pressure System Leak Rate...................................................................................... 91
11.30 Disassemble, Clean, and Calibrate Vacuum Relief Valve, Record Vacuum .................... 92
11.31 Test-Rinse Mix 0.1x SSC XT ............................................................................................ 94
11.32 Test-Rinse Mix 0.5x SSC XT ............................................................................................ 94
11.35 Run Temperature Verification Slides ................................................................................ 95
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12.0 Additional Tests and Adjustments.................................................................. 97

12.1 Motor Test ......................................................................................................................... 97
12.2 Motor Torque Voltages ..................................................................................................... 98
12.3 Continuous Tray Check Tests........................................................................................... 99
12.3.1 Continuous Reagent Carousel ...................................................................... 99
12.3.2 Continuous Nozzle Plate ............................................................................. 100
12.4 Draining the Fluidics System .......................................................................................... 100
12.5 Empty Vacuum Trap ....................................................................................................... 102
12.6 Priming the Fluidics System ............................................................................................ 102
12.7 Reservoir Fill ................................................................................................................... 103
12.8 Slide Drawer Test............................................................................................................ 105
12.9 Jet Drain Test .................................................................................................................. 105
12.10 Purge Tests ..................................................................................................................... 106
12.11 Select Tests .................................................................................................................... 107
12.12 Beeper Volume ............................................................................................................... 108
12.13 Fuses .............................................................................................................................. 108
12.14 Power Supplies, +24 Volt and +5 Volt ............................................................................ 108
12.15 Slide Tray Height and Parallelism ................................................................................... 110
12.16 Slide Tray Centering ....................................................................................................... 111
12.17 Bottle Inlet Check Valve Test .......................................................................................... 113
12.18 Reagent Carousel and Nozzle Plate Belt Inspection ...................................................... 113
12.19 Nozzle Plate Tubing Inspection ...................................................................................... 113
12.20 Cooling and Exhaust Fan Test........................................................................................ 114
12.21 Adjustment of the Slide Tray Up Sensor ......................................................................... 114
12.22 Adjustment of the Slide Tray In Sensor .......................................................................... 115
12.23 Slide Heater Test ............................................................................................................ 115
13.0 Assembly Removal / Installation ................................................................... 118
13.1 AFM Drawer .................................................................................................................... 118
13.2 Bottle Fittings .................................................................................................................. 118
13.3 Compressor..................................................................................................................... 119
13.4 Drive Belt Replacement .................................................................................................. 120
13.4.1 Reagent Carousel Belt Replacement .......................................................... 120
13.4.2 Nozzle Plate Belt Replacement ................................................................... 121
13.5 In-line 250-micron Bottle Filter ........................................................................................ 122
13.6 In-line 65-micron and 25-micron Filters .......................................................................... 122
13.7 Microcontroller PCB, 24V Power Supply, and Associated Electronics Boards .............. 122
13.7.1 Microcontroller PCB with Programmed Microcontroller IC .......................... 123
13.7.2 Microcontroller IC ........................................................................................ 124
13.7.3 Programming the Microcontroller IC............................................................ 124
13.7.3.1 Downloading Operating Code ..................................................................... 125
13.7.3.2 Assigning Instrument Personality ................................................................ 127
13.7.3.3 Inputting the Serial Number ......................................................................... 127
13.8 Nozzle Plate .................................................................................................................... 128
13.9 Nozzle Plate Stepper Motor ............................................................................................ 129
13.10 Power Inlet Module ......................................................................................................... 129
13.11 Reagent Barcode Reader ............................................................................................... 130
13.12 Slide Barcode Reader ..................................................................................................... 130
13.13 Reagent Stepper Motor ................................................................................................... 130
13.14 Reservoir Float Switches ................................................................................................ 131
13.15 Roof Substructure Tubes and Cable............................................................................... 134
13.15.1 Tubes ........................................................................................................... 134
13.15.2 Valve Connector to Slip Cable PCB Cable Assembly ................................. 136
13.15.3 Slip Cable .................................................................................................... 139
13.16 Lift Cylinder ..................................................................................................................... 142
13.17 Slide Drawer.................................................................................................................... 144
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13.18 Slide Heater Assembly .................................................................................................... 145

13.19 Slide Heater PCB ............................................................................................................ 146
13.20 Waste Sensor.................................................................................................................. 147
13.21 Dispense Cylinder ........................................................................................................... 151
13.22 Bottle Sensors ................................................................................................................. 152
13.23 Volume Adjust Block ....................................................................................................... 155
14.0 Common Problems and Solutions ................................................................ 156
14.1 Stainer Subassembly Power-on LED on Front Panel is OFF ......................................... 156
14.2 Valve Associated Function Is Inoperable ........................................................................ 156
14.3 Reagent Carousel or Nozzle Plate Will Not Move .......................................................... 157
14.4 Compressor Not Coming On ........................................................................................... 159
14.5 Homing Input Not Working .............................................................................................. 159
14.6 Slide Tray In Sensor Not Working................................................................................... 160
14.7 Slide Tray Up Sensor Not Working ................................................................................. 161
14.8 Overflow Sensor Not Working ......................................................................................... 162
14.9 No Beep on Power-up ..................................................................................................... 162
14.10 Barcode Reading Problems ............................................................................................ 162
14.11 No “Connected” Light ...................................................................................................... 163
14.12 Drive Belt Slipping ........................................................................................................... 164
14.12.1 Nozzle Plate Belt ......................................................................................... 165
14.12.2 Reagent Carousel Belt ................................................................................ 165
14.13 Port Expander PCB Fuse Check .................................................................................... 165
14.14 Serial Output PCB Failure ............................................................................................... 166
14.15 Vortex Mixer Flow Rate Issues ....................................................................................... 169
15.0 Error Messages............................................................................................... 170
15.1 Misalignment of Nozzle Plate or Reagent Carousel ....................................................... 170
15.2 Recharge Error Messages .............................................................................................. 171
15.3 Priming Error Messages ................................................................................................. 172
15.4 Vacuum Trap Error Messages ........................................................................................ 172
15.5 Slide Heating Error Messages ........................................................................................ 173
15.5.1 Temperature Too High or Too Low ............................................................. 173
15.6 Hardware Error Messages: (Normal Status Reports) ..................................................... 174
15.7 Hardware Error Messages: (Possible Hardware Failure) ............................................... 174
15.8 User Initiated Messages ................................................................................................. 175
15.9 Backup Problems ............................................................................................................ 175
15.10 Run Related Error Messages.......................................................................................... 175
15.11 Reagent Database and Encryption Messages ............................................................... 176
15.12 Communications Between PC and Modules .................................................................. 177
16.0 Appendix A: Assembly Drawings ................................................................ 179
17.0 Appendix B: Wiring Diagrams ...................................................................... 244
18.0 Appendix C: Fluidics and Pneumatics Diagrams ....................................... 248
19.0 Appendix D: Technical Bulletins .................................................................. 252
20.0 Appendix E: Error Codes .............................................................................. 254
VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page vii

Table of Figures
Figure 1. Hot Surface Caution Label ....................................................................................................... 1
Figure 2. Document Reference Caution Label ........................................................................................ 1
Figure 3. Electric Shock Caution Label ................................................................................................... 2
Figure 4. Disconnect Power Caution Label ............................................................................................. 2
Figure 5. Ground Connection Label ........................................................................................................ 2
Figure 6. LASER Caution Label .............................................................................................................. 3
Figure 7. LASER Caution and Information Label .................................................................................... 3
Figure 8. Stainer Subassembly ............................................................................................................. 12
Figure 9. Nozzle Plate Assembly .......................................................................................................... 16
Figure 10. Dual Rinse Nozzles................................................................................................................ 17
Figure 11. Jet Drain Nozzle, Old Configuration and New Configuration (Splash Guard Not Shown) .... 18
Figure 12. Volume Adjust and Stringency Adjust Nozzles ...................................................................... 19
Figure 13. LCS Dispense Nozzles and Barcode Blowoff/Air Knife Nozzles ........................................... 20
Figure 14. Inner Mixer ............................................................................................................................. 21
Figure 15. Outer Mixer ............................................................................................................................ 22
Figure 16. Microcontroller PCB LEDs and Connectors........................................................................... 27
Figure 17. Automated Fluidics Module.................................................................................................... 33
Figure 18. Software Main Screen............................................................................................................ 44
Figure 19. Test Task Menu ..................................................................................................................... 44
Figure 20. Download Tests Screen ......................................................................................................... 45
Figure 21. Service/Test Screen (BASIC I/O CONTROL Tab)................................................................. 46
Figure 22. TEST FUNCTIONS Tab......................................................................................................... 48
Figure 23. INSTRUMENT DATA Tab...................................................................................................... 50
Figure 24. TEMPERATURE CHART Tab ............................................................................................... 51
Figure 25. Fuse Panel Cover Removed .................................................................................................. 56
Figure 26. Domestic Plug ........................................................................................................................ 57
Figure 27. International Plug ................................................................................................................... 57
Figure 28. Old Configuration, Hose Barb Fittings ................................................................................... 90
Figure 29. New Configuration, Push Lock Fittings .................................................................................. 91
Figure 30. Vacuum Relief Valve, Disassembled ..................................................................................... 93
Figure 31. Cap with Teflon Tape and Lock Nut ...................................................................................... 93
Figure 32. Vacuum Trap Relief Valve, Reassembled ............................................................................. 93
Figure 33. Connecting the Tubing Harness .......................................................................................... 101
Figure 34. Kinematic Mounts ................................................................................................................ 111
Figure 35. Posts .................................................................................................................................... 111
Figure 36. Lift Cylinder Arm .................................................................................................................. 112
Figure 37. Proper Routing of Tubing ..................................................................................................... 114
Figure 38. Temperature Chart showing properly functioning slide positions ........................................ 116
Figure 39. Temperature Chart showing slide positions 8 and 9 are problematic ................................. 117
Figure 40. Detail of slide positions 8 and 9 ........................................................................................... 117
Figure 41. Cable Ties ............................................................................................................................ 119
Figure 42. Cable Tie Pad ...................................................................................................................... 120
Figure 43. NexFact Main Screen .......................................................................................................... 126
Figure 44. Float Sensor ......................................................................................................................... 132
Figure 45. Check Valve ......................................................................................................................... 132
Figure 46. Torque pattern for screws .................................................................................................... 133
Figure 47. Swivel Elbows ...................................................................................................................... 133
Figure 48. 90° Fittings ........................................................................................................................... 133
Figure 49. 90° Fittings Can Be Oriented to Within 30° of Direction Shown .......................................... 134
Figure 50. Proper Routing of Tubing ..................................................................................................... 136
Figure 51. Location of Tie Wraps .......................................................................................................... 137
Figure 52. Flex Cable Installation (Slip Cable) ...................................................................................... 140
Figure 53. Flex Cable Routing .............................................................................................................. 141
VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page viii

Figure 54. Flex Cable Installed ............................................................................................................. 141

Figure 55. Lift Cylinder .......................................................................................................................... 143
Figure 56. Lift Cylinder and Washers .................................................................................................... 143
Figure 57. Inverted View of PCB Cover, PCB, and Canopy ................................................................. 147
Figure 58. Waste Sensor Removal ....................................................................................................... 149
Figure 59. Green Light On Waste Sensor ............................................................................................. 149
Figure 60. Bottle Sensor and Bracket (New Configuration) .................................................................. 153
Figure 61. Bottle Sensor Removal (Old Configuration Shown) ............................................................ 153
Figure 62. Bottle Sensor Connection .................................................................................................... 154
Figure 63. Bottle Sensor Assembly (New Configuration Shown) ......................................................... 154
Figure 64. Port Expander PCB Fuse Check ......................................................................................... 166
Figure 65. Ferrite on Microcontroller to Serial Out Cable ..................................................................... 167
Figure 66. Ferrite on Microcontroller to Host Communications Connector Cable ................................ 168
Figure 67. Ferrite on Motor and Homing Cables ................................................................................... 169
Figure 68. Compressor Unit Assembly ................................................................................................. 179
Figure 69. Compressor Unit Assembly, Schematic .............................................................................. 180
Figure 70. Compressor Unit Assembly, BOM ....................................................................................... 181
Figure 71. Compressor with Connector ................................................................................................ 182
Figure 72. Compressor with Connector, Schematic ............................................................................. 183
Figure 73. Compressor with Connector, BOM ...................................................................................... 184
Figure 74. Electrical/PCB, Fan Assembly ............................................................................................. 184
Figure 75. Electrical/PCB, Fan Assembly (View 1) ............................................................................... 185
Figure 81. Electrical/PCB, Fan Assembly, BOM ................................................................................... 188
Figure 82. Fluidics Drawer Assembly (View 1) ..................................................................................... 189
Figure 86. Fluidics Drawer Assembly, BOM ......................................................................................... 192
Figure 87. Fluidics Reservoir Assembly (Exploded) ............................................................................. 193
Figure 88. Fluidics Reservoir Assembly ................................................................................................ 194
Figure 89. Fluidics Reservoir Assembly, BOM ..................................................................................... 194
Figure 90. Left Front Drawer Lift Assembly (View 1) ............................................................................ 195
Figure 91. Left Front Drawer Lift Assembly (View 2) ............................................................................ 195
Figure 92. Left Front Drawer Lift Assembly, BOM ................................................................................ 196
Figure 93. Left Rear Drawer Lift Assembly (View 2) ............................................................................. 196
Figure 94. Left Rear Drawer Lift Assembly (View 1) ............................................................................. 197
Figure 95. Left Rear Drawer Lift Assembly, BOM ................................................................................. 197
Figure 96. Right Front Drawer Lift Assembly ........................................................................................ 198
Figure 97. Right Front Drawer Lift Assembly, BOM .............................................................................. 198
Figure 98. Right Rear Drawer Lift Assembly ......................................................................................... 199
Figure 99. Right Rear Drawer Lift Assembly, BOM .............................................................................. 199
Figure 100. Motor Rotation Assembly ..................................................................................................... 200
Figure 101. Motor Rotation Assembly BOM............................................................................................ 200
Figure 102. Nozzle Plate Assembly (View 1) .......................................................................................... 201
Figure 106. Nozzle Plate Assembly, Schematic ..................................................................................... 204
Figure 107. Nozzle Plate Assembly, BOM (Part 1) ................................................................................. 205
Figure 108. Nozzle Plate Assembly, BOM (Part 2) ................................................................................. 206
Figure 109. Nozzle Plate Power Transmission Assembly ...................................................................... 207
Figure 110. Nozzle Plate Power Transmission Assembly, BOM ............................................................ 207
VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page ix

Figure 111. Motor Rotation Nozzle Plate Assembly ............................................................................... 208

Figure 112. Motor Rotation Nozzle Plate Assembly BOM ...................................................................... 208
Figure 113. Power Entry Assembly ......................................................................................................... 209
Figure 114. Power Entry Assembly, BOM............................................................................................... 210
Figure 115. Reagent Carousel Assembly (View 1) ................................................................................. 211
Figure 118. Reagent Carousel Assembly, BOM ..................................................................................... 213
Figure 119. Reagent Carousel Power Transmission Assembly ............................................................. 214
Figure 120. Reagent Carousel Power Transmission Assembly, BOM ................................................... 215
Figure 121. Roof Substructure Assembly ............................................................................................... 216
Figure 122. Roof Substructure Assembly, BOM ..................................................................................... 216
Figure 123. XT Slide Tray Assembly (View 1) ........................................................................................ 217
Figure 128. XT Slide Tray Assembly, BOM ............................................................................................ 221
Figure 129. LT Slide Tray Assembly (View 1) ......................................................................................... 222
Figure 134. LT Slide Tray Assembly, BOM ............................................................................................. 226
Figure 135. XT Stainer (View 1) .............................................................................................................. 227
Figure 144. XT Stainer (View 10) ............................................................................................................ 232
Figure 145. XT Stainer, BOM .................................................................................................................. 233
Figure 146. XT Bottle Liner Assembly (View 1) ...................................................................................... 234
Figure 151. XT Bottle Liner Assembly, BOM .......................................................................................... 237
Figure 152. XT Complete Assembly (View 1) ......................................................................................... 238
Figure 157. XT Complete Assembly, BOM ............................................................................................. 243
Figure 158. Wiring Diagram #1908200, Sheet 1 ..................................................................................... 244
Figure 162. Nozzle Plate Diagram .......................................................................................................... 248
Figure 163. Pneumatic Components Schematic #1935100.................................................................... 249
Figure 164. XT Bottle Liner Schematic (Part 1) ...................................................................................... 250
Figure 165. XT Bottle Liner Schematic (Part 2) ...................................................................................... 251
VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page x

BenchMark XT / DISCOVERY XT / Benchmark LT Service Manual Safety Information
1.0 Safety Information

1.1 Stainer Subassembly
No operator serviceable parts are inside the stainer
subassembly.
WARNING: UNPLUG THE UNIT BEFORE RELOCATING IT.
WARNING: FOR CONTINUED PROTECTION AGAINST THE

RISK OF FIRE, REPLACE THE FUSE ONLY WITH A FUSE
OF THE SAME TYPE AND RATING.
1.2 Labels
The following labels are affixed to the instrument.
1.2.1 Caution: Hot Surface—Do Not Touch
Figure 1. Hot Surface Caution Label
1.2.2 Caution: Refer to Accompanying Documents
Figure 2. Document Reference Caution Label
VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page 1

1.2.3 Caution: Risk of Electric Shock
Figure 3. Electric Shock Caution Label
1.2.4 Caution: Disconnect Power Before Servicing
Figure 4. Disconnect Power Caution Label
1.2.5 Ground Connection
Figure 5. Ground Connection Label

1.2.6 Caution: LASER
Figure 6. LASER Caution Label
1.2.7 Caution: LASER
Figure 7. LASER Caution and Information Label
1.3 Safety Training

All operators must be trained in the safe use of the instrument.
After such training, operators must understand that
l The instrument must be connected to a grounded outlet
l The instrument must be connected to a voltage source that

is in agreement with the rating label
l Instruments not used in a manner specified by Ventana may
impair protection provided by the equipment
l Replacement of filters and tubing is determined by Ventana
service personnel
l Operators must keep their hands clear of the moving parts of
the instrument

¨ This includes the reagent carousel, dispensers, and

dispenser actuator
l Operators must keep their hands clear of potential pinch
points
¨ This includes the slide drawer and reagent carousel
l Operators must consult the Material Safety Data Sheets for
safe handling and disposal of reagents used with the
instrument
1.4 Safety Compliance

All safety related regulations, local codes, and instructions that
appear in the manual or on equipment must be observed to
ensure personal safety and to prevent damage to either the
instrument or equipment connected to it. If equipment is used
in a manner not specified by the manufacturer, the protection
provided by the equipment may be impaired.

BenchMark XT / DISCOVERY XT / Benchmark LT Service Manual What the Instrument Does
2.0 What the Instrument Does

2.1 Tissue Staining
The BenchMark XT / DISCOVERY XT / BenchMark LT
instrument automates an exacting and somewhat tedious
laboratory procedure used to produce visible stains on
biological tissue samples.
l These stained tissue samples (on glass slides) are used by
a pathologist to diagnose various diseases
l The chemistries involved are called immunohistochemistry
(IHC) or in situ hybridization (ISH)
2.2 Tissue Staining Process

A multi-step process is needed to produce a stain. In each
step, a chemical called a reagent is applied to the tissue
sample.
l The reagent and the tissue sample undergo a biochemical
reaction
¨ The biochemical reaction must be allowed to occur over a
specified amount of time
¨ The biochemical reaction must be allowed to occur at a
precisely controlled temperature
l The process is then repeated with another reagent, which
requires yet another reaction time
l A number of steps spaced over one to four hours is usually
required to produce the desired stain
The BenchMark XT / DISCOVERY XT instrument allows up to
30 slides to be loaded and stained in a single run, while the
BenchMark LT instrument allows up to 20 slides to be loaded
and stained in a single run. All three instruments can use up to
35 different reagents. A laboratory technician can specify the
stain needed for each slide, load the reagents, then start the
instrument and simply walk away until all of the stains have
been completed.

2.3 How the Instrument Works

There are a number of standard staining sequences called
procedures.
l Each procedure specifies the sequence and timing of
reagents needed for a specific kind of stain
¨ A laboratory will modify and supplement the procedure to
suit its own needs and preferences
¨ A procedure, once modified and supplemented,
becomes a protocol
§ The protocol tells the instrument what to do and
when to do it to produce a particular kind of stain for
a particular slide
§ BenchMark XT / DISCOVERY XT / BenchMark LT
instrument uses a computer to accumulate and
manage procedures, protocols, and reagent data
§ The computer also controls the operation of the
instrument
When following a protocol, BenchMark XT / DISCOVERY XT /
BenchMark LT instrument dispenses the correct reagents to the
appropriate slides based on the information in the barcode
labels attached to the reagent dispenser bottles and the
barcode labels on individual slides.
The basic operation of the instrument is quite simple, involving
only six repeated steps:
l RINSING—the slide is rinsed with a solution called a buffer
¨ This cleans off any previous chemical residue
l VOLUME ADJUST—additional buffer is added to the slide
¨ This is to make sure that the amount of buffer solution
remaining on the slide after rinsing will be precisely
known and controlled
l LCS—a solution called LCS is added over the buffer solution
¨ The oil-based LCS solution floats to the top of the buffer,
covering it to prevent evaporation
l CLEANUP—excess solution is removed from the slide using
jets of air to:
¨ Remove liquid from the barcode

¨This is called barcode blow-off

§ Liquid on the barcode label prevents the barcode
reader from reading
¨ Create an LCS puddle separated from the barcode label
¨ A jet of air called an air knife keeps the puddle from
leaking or wicking into the barcode label
§ Once separated, the edge of the barcode label will
act as a dam, forcing the puddle to remain intact on
the slide like a drop of water on a window
l DISPENSING—The specified reagent (identified by its
barcode label) is dispensed into the puddle created in the
previous steps
¨ The LCS solution floats to the top, again covering the
solution, which is now a mixture of buffer and reagent
l MIXING—The instrument uses vortex mixers (air streams)
to mix the solution and distribute it over the tissue sample on
the slide
¨ The mixing action is performed several times
¨ The mixing action helps the biochemical reaction
¨ The mixing action ensures that the reagents come into
contact with the entire tissue sample on the slide
Temperature is an important ingredient in the process.
l BenchMark XT / DISCOVERY XT / BenchMark LT
instrument has slide heater pads to control the temperature
of individual slides so that the chemical reactions will occur
under optimum conditions
During a run of the instrument, the six step sequence above is
repeated according to the protocol specified for each slide.
l Reagent selection and the time between dispense steps are
part of the protocol for a given slide
l Each slide the BenchMark XT / DISCOVERY XT /
BenchMark LT instrument can hold may have a separate
protocol, or all may have the same protocol
instrument obviously saves a lot of laboratory manpower and
potential for error compared to doing it all by hand

BenchMark XT / DISCOVERY XT / Benchmark LT Service Manual Major System Modules
3.0 Major System Modules

BenchMark XT / DISCOVERY XT / BenchMark LT instrument is
comprised of four major modules:
l The stainer subassembly
l The automated fluidics module (AFM)
l The waste subassembly
l The personal computer

This subassembly is where the chemistry is performed.
l The BenchMark XT and DISCOVERY XT instruments can
hold up to 30 slides
l The BenchMark LT instrument can hold up to 20 slides
l Each of the slide positions has a fixed integrated slide holder
and slide heater pad
l It has a rotating nozzle plate that is rotated by a stepper
motor
¨ The rotary position of the nozzle plate is relative to a
home position obtained from a sensor
¨ The nozzle plate incorporates
¨ A slide barcode reader
¨ A variety of valves and nozzles for dispensing and
removing fluids
l It has a reagent carousel with spaces for 35 reagent
dispensers
¨ The reagent carousel is rotated by a stepper motor
¨ The rotary position of the reagent carousel is relative to
a home position obtained from a sensor
¨ Reagents are dispensed from disposable containers that
snap into the dispenser plate on the lower part of the
reagent carousel
¨ To dispense a reagent, BenchMark XT / DISCOVERY
XT / BenchMark LT instrument rotates the reagent into

position below a plunger which presses down on a

syringe built into the container
¨ The dispensed liquid drops directly from the reagent
container onto a slide below it
l The content of each reagent dispenser in the carousel is
indicated by a barcode on the dispenser
l The tissue on each slide is indicated by a barcode on the
slide
l The barcode reader looks at the barcodes on the slides and
the reagent dispensers
l The barcode reader sends this information to the personal
computer
l The personal computer sends commands to the instrument
to dispense appropriate reagents and fluids onto specific
slides
The stainer subassembly also houses a variety of valves,
nozzles, slide heater pads, motors and sensors and a control
computer that monitors them. All mechanical functions except
for carousel movement are air pressure actuated.
3.2 Automated Fluidics Module (AFM)

This subassembly supplies the stainer subassembly with
pressurized air and seven pressurized liquids.
l Pressure for air and liquids is provided by an air compressor
¨ Separating these functions provides more flexible
installation options than an all-in-one design
3.3 Waste Subassembly

Two waste bottles receive liquids drained from the tub of the
stainer subassembly and the AFM. The tub receives waste
liquids drained from the stainer subassembly.
The system includes an ultrasonic waste sensor which is used
to monitor the fluid level to prevent overflow. There are two
versions of the waste sensor.

· The typical waste sensor has a gray cap. This sensor

detects a Waste Full condition when the carboy contains
approximately 12 liters (approximately 60% full).
· Waste sensors with a green cap are used only for Dual
Color ISH assays. This sensor detects a Waste Full
condition when the carboy contains approximately 2 liters
(approximately 10% full). This is because the Dual Color
ISH assay produces more waste than a typical run, and
the run should not start if the carboy contains 2 liters.
Any run completed without having the waste sensor indicating
full allows the operator to start a new run. The full mark leaves
enough room in the waste carboy for the operator to complete a
worst-case protocol the next run.
If the sensor detects fluid during a run, once that run is
complete the operator must empty the waste carboy before the
program will allow the start of a new run.
3.4 Personal Computer

A personal computer (PC, also referred to as the Host) runs the
BenchMark XT / DISCOVERY XT / BenchMark LT instrument's
control software that
l Tells the control computer in the stainer subassembly what
to do
l Displays status information while the instrument is running
l Tracks reagents
l Provides a variety of quality control, administrative and
hardware diagnostic functions
A single PC can control up to eight instruments, and is
connected to the staining instruments via a communications
cable.
instrument's hardware can be described and understood in
terms of its circuits:
l Electrical (control and power)
l Air
l Liquid

The entire instrument is monitored and controlled by the

microcontroller on the built-in microcontroller PCB, which is in
turn controlled and monitored by the software resident in the
PC. Additional microcontrollers are in the AFM and behind the
instrument control panel.
It is useful to note at this point that once a run of the stainer
subassembly has been initiated, it is capable of completing the
run on its own—even when disconnected from the PC. The
stainer subassembly microcontroller can also perform a variety
of diagnostics without benefit of the PC. Notwithstanding this,
the PC is still a vital and tightly integrated part of the system.
So while the PC performs a variety of non-service related
functions that you do not have to understand, you must
understand its service related functions.

BenchMark XT / DISCOVERY XT / Benchmark LT Service Manual Stainer Subassembly

This section is concerned with the components of the stainer
subassembly and their function. The microcontroller PCB is a
stainer subassembly component, but because of its important
role in coordinating operation of all the instrument’s
components, the microcontroller PCB is given its own major
section.
Reagent
Barcode
Reader
behind
Reagent
Carousel
Reagent
Carousel
Instrument
Control Panel: Slide
Alarm Drawer
Running
Power On
User Button
Figure 8. Stainer Subassembly
The remainder of this section will describe the

l Reagent Carousel
l Nozzle Plate
l Home Sensors
l Slide Tray

l Reagent Dispensers
l Barcode Readers
l Liquid and Air Nozzles
¨ Nozzle Arrangement
¨ Dual Rinse Nozzles
¨ Jet Drain Nozzle
¨ Multispense Nozzles
¨ LCS Nozzles
¨ Air Knife Nozzle
¨ Vortex Mixer Nozzles
l Restrictors and Filters
l Fan and Sensor
l Slide Tray Sensor
l Tub and Overflow Sensor
l Instrument Control Panel
l Power Supply
l Cables and Wiring Harnesses
l Plumbing
4.1 Reagent Carousel and Nozzle Plate

BenchMark XT / DISCOVERY XT / BenchMark LT instrument
uses a rotating carousel to carry reagent dispensers. It also
uses a rotating nozzle plate for dispensing and removing fluids,
and reading slide barcodes.
4.1.1 Reagent Carousel

The carousel is able to rotate either clockwise or
counterclockwise.
l The reagent carousel is rotated by a power transmission
assembly
¨ It is positioned by a stepper motor through a belt drive
and sprockets
A dispenser plate holds the reagent dispensers.
l The microcontroller is able to operate the stepper in either a
low-torque or a high-torque mode

¨ Low-torque mode holds the carousel in a fixed position

when it is stopped
¨ High-torque mode is used for rotation
¨ When testing the carousel, it is important not to leave it
in high-torque mode for more than five minutes at a
time
§ This is to avoid overheating the motor
4.1.2 Nozzle Plate

The nozzle plate is able to rotate either clockwise or
counterclockwise.
l The nozzle plate is rotated by a power transmission
assembly
¨ It is positioned by a stepper motor through a belt drive
and sprockets
The nozzle plate incorporates the fluidic and pneumatic nozzles
used for dispensing and removing fluids.
l The microcontroller is able to operate the stepper in either a
low-torque or a high-torque mode
¨ Low-torque mode holds the nozzle plate in a fixed
position when it is stopped
¨ High-torque mode is used for rotation
¨ When testing the nozzle plate, it is important not to
leave it in high-torque mode for more than five minutes
at a time
§ This is to avoid overheating the motor
4.1.3 Home Sensors

For both the carousel and the nozzle plate, there is a home
position detected by a sensor.
l These home positions provide a reference location from
which the position of each dispenser or nozzle can be known
as the carousel and nozzle plate are rotated
¨ These home positions are also used to precisely align the
dispensers and nozzles with respect to the slides

¨ Each home position is located through use of an optical

sensor and a metal flag
¨ The optical sensor detects the edge of the metal flag
attached to the carousel assembly and the metal flag
attached to the nozzle plate
§ The tab move past the sensor as the carousel or
nozzle plate rotates
4.2 Slide Tray

Each of the slide positions has an integrated slide holder and
slide heater pad. A microprocessor turns the slide heater pad
on and off to maintain the temperature setpoint
4.3 Reagent Dispensers

Reagents are supplied in plastic containers, each with a built-in
syringe and a barcode label. The barcode label identifies the
reagent. When the plunger of the built-in syringe is depressed,
nominally 100 ml of reagent is dispensed.
uses an air cylinder to extend an actuator that depresses the
built-in syringe of the reagent dispenser. The air cylinder has
one valve and one control to extend and retract the actuator.
4.4 Barcode Readers

has two barcode readers.
l One barcode reader is used to read labels affixed to slides
¨ This barcode reader is mounted on the nozzle plate
l Another barcode reader is used to read labels affixed to
reagent dispensers
l The barcodes are read once before the run begins
¨ Thereafter, the home position of the carousel becomes
the reference for the content of each carousel position
l The barcode reader signals the processor to “beep” upon a
successful read and illuminates its green LED

4.5 Liquid and Air Nozzles

Liquid and air nozzles are used to manage liquids on the slides
in the slide tray.
Outer
Vortex Mixers
Slide BC
Reader
Dual
Rinse
Jet Multi-
Drain spense Air Inner Vortex
LCS Knife Mixers
Dispense
Figure 9. Nozzle Plate Assembly
4.5.1 Nozzle Arrangement

All of the liquid nozzles and the air nozzles are located on the
nozzle plate assembly.
l The nozzle plate rotates inside the circle of slides
¨ The nozzle plate has several Noryl blocks attached to
tubing
¨ As the nozzle plate rotates, these blocks dispense and
remove fluids

4.5.2 Dual Rinse Nozzles

A block is drilled with two rows of nozzle holes, a top row and a
bottom row.
l Each row is connected to a valve via tubing
¨ There are actually three valves controlling flow to the
rinse nozzles, providing for a variety of rinsing sequences
l For normal rinsing, the top and bottom nozzles are actuated
alternately in short bursts
¨ Note that the top and bottom nozzle are aimed at slightly
different angles
¨ The initial rinsing pulses push fluid off the slide
¨ The pulses are divided into two rinse sequences
separated by a one second pause
§ During the pause, diffusion of reagents out of the
tissue sample can occur
§ This way, the second rinse effectively removes all
remaining reagents from the slide
Figure 10. Dual Rinse Nozzles

4.5.3 Jet Drain Nozzle

The jet drain is a single row of holes that emit EZ Prep,
Reaction Buffer, or SSC to lower the residual slide volume
during in situ (ISH) probe applications.
There are two possible configurations.
· On the old configuration, SSC (red) and Reaction Buffer
(blue) Jet Drain supply tubes mount to either side of the
nozzle.
· On the new configuration, the SSC (red) tubing is
attached to the trailing side of the Jet Drain nozzle, joined
together with the Reaction Buffer (blue) tube using a Y-
fitting.
The new configuration eliminates the possibility of fluid from the
Dual Rinse action splashing onto the leading Jet Drain tube and
later depositing an errant drop onto a slide.
The old configuration must be upgraded if present.
Figure 11. Jet Drain Nozzle, Old Configuration and New Configuration
(Splash Guard Not Shown)
4.5.4 Multispense Nozzles

The multispense station has four needle-like nozzles. One is
for volume adjust and for the mixing of salt solutions for
adjustments in the stringency. The two additional nozzles are

for dispensing CC1 and CC2. The fourth nozzle is the select
nozzle.
Reagents and antibodies are diluted by the buffer solution
remaining on the slide after rinsing.
l It is important to control this dilution
¨ So, after the rinse station delivers a charge of buffer to a
slide, the volume adjust station rotates to the slide
¨ The action of the rinsing nozzles is quite vigorous, and
varies slightly from one instrument to another
¨ The volume adjustment nozzle compensates for this
variance by sedately adding a calibrated amount of
additional buffer to the slide
CC1 EZ Prep/
Nozzle Select Volume
Adjust Nozzle
CC2 Reaction
Nozzle Buffer Volume
Adjust Nozzle
Figure 12. Volume Adjust and Stringency Adjust Nozzles

4.5.5 LCS Nozzles

Directly after the volume adjust station, LCS is emitted by two
holes at the LCS station.
l Just like a solid coverslip, the LCS prevents evaporation and
forms a suitable environment for the chemistry
l LCS is a light oil that floats over the surface of the
buffer/reagent puddle on the slide
l Unlike a glass coverslip, it can easily be washed away prior
to each new step in the protocol
LCS
Dispense
Nozzles
Bar Code
Blowoff/Air
Knife Nozzles
Figure 13. LCS Dispense Nozzles and Barcode Blowoff/Air Knife

Nozzles
4.5.6 Barcode Blowoff/Air Knife

After LCS is applied, the air knife is rotated over the slide.
l As the air knife is rotated over the slide, air jets on the
bottom of the arm sweep liquid from the barcode label
l Additionally, the air jets separate the puddle over the
specimen from the edge of the barcode label into a puddle
centered over the tissue specimen

l Everything is now in order for mixing and incubating the

reactions necessary to produce a stain.
4.5.7 Vortex Mixer Nozzles

Mixing is performed by air jets called vortex mixers.
l The single inner mixer is located under the air knife
Inner
Mixer
Nozzles
Figure 14. Inner Mixer

Figure 15. Outer Mixer
l The three outer mixers extend to the outer end of the slide
l The inner and outer vortex mixers create a gentle vortex
effect over the liquid puddle on the slide
¨ As the nozzle plate rotates, the vortex mixers swirl the
liquid puddle on the slide clockwise, then
counterclockwise at several stations
¨ This stirring action
¨ Thoroughly mixes the reagents and antibodies
¨ Provides uniform wetting of the specimen during
incubation

4.6 Restrictors and Filters

There are five flow restrictors used in the stainer subassembly.
These are similar in appearance, with barbed ends to fit into the
tubing. Filters in the AFM protect the restrictors.
l Additional restrictors are used in air lines for the
¨ Air knife
¨ Vortex mixer nozzles
4.7 Fan and Sensor

The temperature of the slides is regulated by heating the slides
on the slide tray individually.
l Slide heater pads and a temperature sensor are used for this
purpose
¨ Each slide position has a slide heater pad located
beneath it
¨ The slide heater pad incorporates a temperature
sensor and a heating element
¨ A DC fan mounted on the back of the stainer
subassembly continuously circulates the air
¨ The slide heater pad temperature is reported to the
system microcontroller from a temperature sensor chip
located on each slide heater pad
¨ Slide tray board software regulates temperature by
cycling the slide heater pad element on or off
4.8 Slide Tray Sensor

When the slide tray is closed, it is centered under the nozzle
plate so that fluids can be evenly dispensed onto and removed
from the slides. Once the slide tray is closed, it needs to be
raised to the nozzle plate. The slide tray should remain closed
and in the raised position during normal operation.
l The system can detect when the slide tray has been
unexpectedly opened by monitoring an optical sensor
located near the left rear corner of the base plate
¨ The optical sensor has its own light source

¨ The sensor detects the tray is closed when the slide

tray is close enough to the sensor to reflect the
sensor’s light back to it
4.9 Tub and Overflow Sensor

During normal operation, fluids are spilled from slides into a
black plastic tub beneath the slide tray. The liquid is drained
from the tub through a hole connected to a drain hose.
l Blockage of this drain is detected by an overflow sensor—
two long screws protruding from the bottom of the left rail
¨ When electrically conductive liquid (buffer and reagents)
touches the ends of these probes, the probes notify the
system that the tub is full
l The operator may not want to interrupt tests underway and
can choose not to heed this warning
4.10 Instrument Control Panel

Three status lights are located on the staining unit front panel:
l Alarm—(red) the microcontroller lights the alarm to warn the
operator of an error condition
l Running—(yellow) indicates that BenchMark XT /
DISCOVERY XT / BenchMark LT instrument is processing a
batch of slides or has received commands needed to
perform a test
l Power On—(green) lights when the system is turned on
A user interface button located behind the Ventana logo is a
pushbutton that field service personnel use for various test
procedures (described elsewhere in this manual).
4.11 Power Supply

l A 24 V power supply provides power for the system’s valves,
relays and motors
l The microcontroller PCB contains a 5 volt DC-DC converter
to power the microcontroller electronics
l The 24 VDC power supply is auto sensing so it can be
operated with either a 100, 115, or 230 VAC power source

4.12 Cables and Wiring Harnesses

The system incorporates replaceable wiring, including plugs
and ties (wiring harnesses). For some components, such as
slide heater pads and motors, the cabling is part of the
component, not a separate part number. Schematic diagrams
of the instrument’s electrical system are in Appendix E.
4.13 Plumbing
Schematic diagrams showing the instrument’s pneumatics and
fluidics systems are in Appendix E.

BenchMark XT / DISCOVERY XT / Benchmark LT Service Manual Microcontroller PCB
5.0 Microcontroller PCB

The microcontroller PCB is a microcomputer that monitors and
controls all functions in the system.
l It also communicates with the PC
¨ It receives instructions from the PC
¨ It provides status information to the PC
l The processor uses non-volatile memory
¨ This means that the microcontroller will not “forget” things
even if the power is turned off or the connection between
BenchMark XT / DISCOVERY XT / BenchMark LT
instrument and the personal computer is severed
l In normal operation, the microcontroller receives a program
from the PC
¨ It then operates autonomously
¨ However, it supplies status information to the PC
¨ It can also accept additional instructions if the PC
remains connected, as it usually does
¨ Communication with the PC is via a serial port configured
as RS-422
¨ This arrangement allows multiple DISCOVERY XT /
BenchMark XT instrument's microcontrollers to
communicate with a PC through a single port
The microcontroller PCB is supplemented with circuitry on the
serial output board, which controls the air and liquid valves.
The figure below shows the location of each connector, each
LED, test points and other useful features of the microcontroller
PCB.
The microcontroller PCB’s numerous LEDs (light emitting
diodes) indicate what it is doing at a particular time. These are
very useful in diagnosing system problems. The figure below
shows the location, number and function of each LED and is
referred to frequently throughout the rest of the manual.
CAUTION: Do not plug the power supply into any connector
other than J1 in the upper left corner.

4 24 VOLTS
From 3 J3 TO REAGENT J6 TO NOZZLE
Power 2 D1 MOTOR DRIVER PLATE MOTOR
Supply 1 DRIVER
J1
Input From DISP/ STAINING

Drawer Up D2
ENCL UNIT
Sensor J2 ADDRESS
D3 ADDRESS JU4 JU3
J3 SWITCH
D33 LTRQ D34
Beep Input D4 D35 DIS D36 TP4
from Bar Code SW1
J4
Reader on D37 STEP D38
Good Read D5 L H
D39 CW D40 R39 R40
D6
TP1 TP2 TP3 TP5
J5 L H REAGENT SLIDE
R23 R24
24 D7 GND +5 +24
V D8 VENTANA J20 1 Input from
o J6 D18 D19 MEDICAL D53 2 Slide Door
3
l D9
SYSTEMS, INC
4 In Sensor
t D10
NEXES XT Input from
J7 J21 1
MICROCON- Nozzle
D54 2
O D11 TROLLER 3 Plate Home
u Sensor
D12
t J8 R10 ASSY P/N J22 1 Input from
p 1378901 D55 2 Reagent
D13 (J9- D15 & 3 Home
u D14 D16 Spares-
Sensor
t J9 Not Used)
1
s J23 2 Input from
D15 User
BEEPER 3
D16 D56 4 Switch/
VOLUME
J10 5 Display
Ribbon Cable R15 6
to Serial
Output PCB D20 BCRSEL J24 1 Input from
D57 2 Overflow
D21 RXD D58 3
4 Sensor
J27 D22 TXD
AFS 1
JU1 D51 D52 2
TO PRESSURE U15 J25 To AFS
SENSOR PROG 3
J11 4
JU2 WD +5
J12 J14 RUN 1 To Port
J26 2
Expander
J15 D31 D41 D42 3
4 PCB
Serial Input/ J13 COMP S. HTR B. HTR

J16
Output to HOST
PC SERIAL
J17
Figure 16. Microcontroller PCB LEDs and Connectors

5.1 Serial Port

The microcontroller PCB’s serial port communicates with
the PC.
LED D21 (RXD) and LED D22 (TXD) indicate data respectively
received and transmitted through the microcontroller PCB’s
serial port. These indicators are useful in diagnosing
communications problems.
5.2 Address Switch

A rotary switch is set to one of eight addresses (numbered 0-7).
l This is the address used when communications from the PC
arrive over the RS-422 port
¨ If only one system is connected to the PC, then address 0
(zero) should be used
¨ Each additional staining unit connected to a PC must
have a distinct address setting
5.3 Microcontroller IC
The microcontroller IC is an 8051 compatible device running at
14 mHz, with 128 kb of onboard non-volatile battery backed
RAM.
l It plugs into a 72-pin SIMM socket in the center of the
microcontroller PCB
l The microcontroller IC can control 24 separate outputs, 22 of
which are used
l Serial output data to control valves and other 24-volt devices
is latched into a shift register
l A clock signal is then used to latch the current status and
switch (drive) all devices in the system simultaneously
¨ Only the device or devices whose latched output state
has changed will respond
l Logic level inputs (9 used) are multiplexed on the 8-bit data
bus
l Temperature (serial) data is received through microcontroller
IC I/O ports from each slide temperature sensor

5.4 Serial Output Board

The serial output board controls all of the stainer subassembly
liquid and air valves as well as the cooling fan. The board also
provides a switched 24 VDC power source for the nozzle plate.
Each valve connector has a corresponding LED to indicate
when the valve is on. Outputs are controlled via a serial bus
connected to the microcontroller PCB via a 14-conductor ribbon
cable. Below is a list of connectors.
l Select Rinse Bottom #1 J1

l Select Rinse Top J2
l Select Volume Adjust J3
l Reaction Buffer Rinse Bottom #1 J4
l Reaction Buffer Rinse Top J5
l Reaction Buffer Volume Adjust J6
l CC1 Multispense J7
l EZ Prep J8
l Spare J9
l Select Rinse Bottom #2 J10
l Select Rinse Jet Drain J11
l Select Rinse Top J12
l Reaction Buffer Rinse Bottom #2 J13
l Reaction Buffer Rinse Jet Drain J14
l Spare J15
l CC2 Multispense J16
l Vortex Mix J17
l Coverslip J18
l Dispense Cylinder Air Valve J19
l Drawer Lift Air Valve J20
l 24 V Power Supply Cooling Fan J21
l Fan Exhaust J22
l Spare J23
l 24 V Power Supply J24
l Not used J25

5.5 Motor Controllers

Two stepper motor controllers are implemented on the
microcontroller PCB, one for the nozzle plate, the other for the
reagent carousel.
l These rotate their respective assemblies under software
control
¨ The motors are operated at half-step resolution
¨ The jumper provided for full-step operation of each
controller is never used
l Each controller has four status LEDs, labeled D33 through
D40 which indicate
¨ Motor enabled
¨ Stepping
¨ Torque level
¨ Rotation direction
5.6 Valve, Nozzle Plate, 24 VDC Power, and

Cooling Fan Outputs
All valves, the nozzle plate, 24 VDC power, and the cooling fan
are actuated directly from the 24-volt logic output circuitry.
l Each output has a corresponding LED on the serial output
(I/O) circuit board
l An LED on each valve indicates when the output is
actuated (ON)
5.7 Air Pressure Sensor

The air pressure sensor is located on the chassis by the
microcontroller PCB and plumbed into the air supply with a
tube.
l Analog output from a pressure transducer goes through an
analog-to-digital converter
¨ The output from the converter is presented serially to a
processor I/O port

5.8 Beeper
A sound alarm (beeper) is installed on the processor board.
The beeper is used to
l Indicate successful barcode reading
l Prompt for user actions during titration
l Indicate that the stainer subassembly is being powered up
l Signal inputs during self-test
5.9 Slide Heater Circuit Boards

The slide heater circuit boards receive 24 VDC power from the
24 volt power supply and receive control data from the
microcontroller PCB. A synchronized serial port that is located
on the microcontroller PCB is used to control operation of both
the AFM and the port expander.
The slide heater circuit boards receive slide heater setpoint
data and transmit slide heater pad temperature via the
synchronous serial port. A microprocessor on the slide heater
circuit boards turns the slide heater on and off to maintain the
temperature setpoint. Each of the slide heater pads is
individually controlled and each may have its own setpoint
temperature.
Each of the 30 slide positions has an integrated slide holder
and slide heater pad. Each slide heater pad is connected via a
flex circuit to the slide heater circuit board that is mounted on
the bottom of the heater plate.
5.10 Port Expander Circuit Board

The port expander PC board provides expansion of the main
microcontroller for additional instrument functions. The board
communicates with the main microcontroller via the instrument
I2C serial bus (J1). I2C is a synchronous serial protocol
employing a master clock signal and a master/slave shared
data line. (The same I2C synchronous serial bus is also used
by the main microcontroller to control the serial I/O PC board in
the AFM.) The port expander’s functions include two
asynchronous serial ports for the slide and reagent barcode
readers (J3 and J4), a synchronous serial port (see below) for

heater control, and a second I2C port for communication with

slide heater temperature sensors (both on J5). Additionally, an
output from the port expander board is provided to signal the
main microcontroller PCB when a barcode read occurs (J6). J2
on the board is for factory use only.
Each of the serial port connectors to the barcode readers
includes five volt power to the reader, transmit and receive
data, plus an input from the reader indicating a good read. The
serial transmit and receive signal levels are five volts and
ground. The serial data rate is 9600 bps.
The synchronous serial port (Serial Peripheral Interface or
Microwire standard) for heater control uses a data line, clock
line, and a strobe to send serial data to the four heater driver
boards mounted beneath the slide heaters. The I2C serial bus
to the heater driver boards includes the standard clock and data
signals. The synchronous serial port sends data to the four
heater driver boards for heater on/off control as well as data
used to connect the I2C bus to the temperature sensors, one at
a time.
All port expander board functions are achieved using a
Microchip PIC microcontroller operating at 20 MHz.

BenchMark XT / DISCOVERY XT / Benchmark LT Service Manual Automated Fluidics Module
6.0 Automated Fluidics Module

The automated fluidics module (AFM) supplies pressurized air
and liquids to the stainer subassembly through plastic tubing
with color-coded connectors. In addition, the AFM monitors the
status of each bulk fluid level along with the waste bottle fluid
level.
Balance
Tube
Figure 17. Automated Fluidics Module
The major systems of the AFM include:

l A bottle liner
l A fluidics drawer
l A compressor that is the source of pressurized air
l A pressure relief valve, air filter, moisture trap, and pressure
regulator that controls compressor output
l A solid state relay switch for turning on the compressor
l A vacuum pump, ballast, vacuum relief valve, and vacuum
trap for a controlled vacuum supply

l Eight bulk fluid bottles and capacitive proximity sensors

¨ The bottles have quick disconnect fittings
¨ Two of these bottles hold six liters of Reaction Buffer and
are linked by a balance tube
l Secondary fluid reservoirs with a float sensors for each of
the seven bulk fluids
l Solenoid valves for controlling pneumatics for the transfer of
liquids
l An air cylinder lowers a safety gate to prevent bottles from
being removed during operation
l Tubing, connectors, filters, etc. for a means of fluid transfer
l A 24 VDC power supply for the solenoid valves and vacuum
pump
l A PCB for controlling all I/O communication between the
AFM and the stainer subassembly.
The heart of the unit is the air compressor.

l This supplies air pressure at 40 psi and regulated at 13 psi in
order to
¨ Operate lift cylinders for the slide drawer
¨ Deliver bulk fluids to the stainer subassembly
¨ Provide pressurized air for the vortex mixers, barcode
blowoff/air knife and dispenser air cylinder
instrument cannot operate without its air supply
¨ An air pressure sensor is located by the microcontroller
PCB of the stainer subassembly
¨ The sensor can be monitored via the PC software
l The AFM has its own 24 V power supply
6.1 Pneumatics Systems of the AFM

The AFM pneumatics use vacuum and air pressure.
A schematic diagram of the pneumatics can be found in
Appendix E.

6.1.1 Pressurized Air

l Air enters the compressor through a muffler.
l From the compressor, the air goes first through a length of
tubing that cools the compressed air and allows moisture to
condense
l The air then goes to a filter which cleans the air and collects
the moisture
¨ At the bottom of the moisture collection bottle is an
adjustable pressure relief valve
¨ This valve bleeds air (and with it collected moisture)
when the compressor reaches 40 psi
¨ This controlled leak causes the compressor to have
less vibration, quieter operation, and longer life
l From the filter/pressure relief valve, the air then goes to the
pressure regulator, where it is regulated to the desired
pressure
l From the pressure regulator, the air goes to a cross fitting
l From the cross fitting, the air goes to
¨ The stainer subassembly via a white air line
¨ Two bottlegate air cylinders
¨ A tee fitting, from which the air goes to
¨ The vacuum trap valve
¨ The pneumatic valve assembly manifold, from which
the air goes to the multi-chamber reservoir
6.1.2 Vacuum
The vacuum pump provides vacuum to the vacuum tank.
l One end of the vacuum tank is connected directly to the
vacuum pump.
l The other end of the vacuum tank is connected to a T-fitting.
¨ One branch of the T-fitting is connected to the vacuum
relief valve for maintaining a constant vacuum of - 4.5 psi.
¨ The other branch of the T-fitting is connected to the
normally open port of the vacuum trap valve.
l The common port of the vacuum trap valve is connected to
the vacuum trap (reservoir).

l The vacuum trap is connected to a T-fitting.

¨ One branch of the T-fitting is connected to the manifold of
the pneumatic valve assembly.
¨ The other branch of the T-fitting is connected to the
vacuum assist.
l Each valve of the pneumatic valve assembly is connected to
a corresponding chamber of the multi-chamber reservoir
assembly.
l The pneumatic valves are opened to allow the chambers
to fill.
l When the float sensor in one of the chambers senses that
the chamber is full, it sends a signal to close the appropriate
valve of the pneumatic valve manifold assembly.
6.1.3 Vacuum Assist

Residual pressure in the air lift cylinders can cause them to lift
after the slide drawer is pulled out. The vacuum assist consists
of tubing and fittings that remove residual pressure from slide
drawer air lift cylinders so they remain lowered properly. The
vacuum assist taps into the vacuum line between the
pneumatic valve manifold and the vacuum trap reservoir.
l A T-fitting is located in the tubing between the pneumatic
valve manifold and the top of the vacuum trap.
l The normally open port on the drawer lift valve is then
connected to this T-fitting.
6.1.4 Pneumatic Valve Manifold Assembly

The pressure and vacuum supply discussed above are directed
to their respective ports on this manifold.
l These ports feed channels through the manifold and are
plugged at the opposite end
l Seven solenoid valves, each with two inlet ports, are
mounted on the manifold aligning with passages that
intersect either the pressure channel or the vacuum channel
¨ The pressure inlet port is normally open and the vacuum
is normally closed

l A third port from each valve is directed through the manifold

directly to an individual exit port
¨ This third port is referred to as the common outlet port of
the valve
¨ This third port is open to either the pressure inlet port
or the vacuum inlet port
l Each of the seven outlet ports from the manifold connects to
the top ports of the secondary fluid reservoirs
6.1.5 Compressor
The compressor receives air through a muffler to reduce noise.
l The compressor design is such that it cannot be started
when it is under pressure
¨ Attempting to do so could trip the circuit breaker
l In normal operation, the software will always open the
following two bleed sources at the end of a test function or a
run
¨ Vortex mixers
¨ Barcode Blowoff/Air knife
l The compressor has a finite life
¨ After approximately 8,000 hours, it will need to be
replaced
6.2 Connectors
Air and liquids are transported to the stainer subassembly
through colored tubing.
The colored tubing connects to the AFM via a matched color
coded connector. All the connectors, except for black, have
shutoff valves so the tubing can be removed without leaking.
6.3 Fluidics Systems of the AFM

6.3.1 Multi-Chamber Fluid Reservoir
Each of the seven bulk fluids feeds into a multi-chamber fluid
reservoir through a replaceable 250 micron filter and a check
valve that prevents fluid from flowing back into the bottle.

l Each chamber has an outlet port that leads to a normally

closed valve in the stainer subassembly via a color-coded
tube, a second inline filter, and a panel mount quick
disconnect connector with a shutoff valve
l As described above, each chamber is connected to the
pneumatic valve manifold assembly supplying a source of
pressure or vacuum
l Each chamber contains a float sensor to signal when the
reservoir is full
l When a pneumatic valve is energized, vacuum is applied to
the chamber, and fluid will be drawn into the chamber from
the bulk fluid bottle until the float sensor indicates the
reservoir is full
l The pneumatic valve is normally open to pressure in its de-
energized state and fluid will exit the chamber when a
fluidics valve is opened in the stainer subassembly
l An eighth chamber in the reservoir assembly is used as a
vacuum trap to collect any fluids that may exit the chambers
through the top port when vacuum is applied
l The vacuum trap also has a float sensor to detect when it is
full of fluid and will energize the vacuum trap valve which
pressurizes the trap and drains the collected fluid to waste
¨ NOTE: During normal operation, only a small amount of
fluid will collect in the trap and is automatically drained at
the end of the run
¨ The sensor will interrupt a run if the trap fills with fluid
during the run since this is not a normal occurrence and
would indicate a problem
6.3.2 Automated Fluidics Bottles

Eight plastic reagent bottles are provided with the AFM.
l The bottles plug into a fitting then to a filter on the AFM
¨ If the filter needs to be replaced, unscrew it from the fitting
l The bottles’ fluid level is monitored by capacitive proximity
sensors mounted in the cabinet

¨ The sensors only check the fluid level at the beginning of

a run and will indicate if the level is above or below what
is required for a full run of thirty slides
l The bottle caps have a vent hole to allow air to displace the
fluid as it is transferred to the secondary fluid reservoir
l When the compressor starts, an air cylinder lowers a safety
gate in the cabinet to prevent any of the bottles from being
removed
6.3.3 Waste Collection

The instrument uses a gravity fed waste collection system. All
waste fluid from the slide tub is drained through a center drain
fitting into waste tubing. The fluid waste is then collected into
one of two waste bottles located in the waste cabinet.

BenchMark XT / DISCOVERY XT / Benchmark LT Service Manual Personal Computer
7.0 Personal Computer

instrument is controlled by a specially configured desktop PC
running the Windows operating system.
l The BenchMark XT / DISCOVERY XT / BenchMark LT
instrument's software enables
¨ The customer to print reports and run stains using a
familiar Windows interface
¨ A single PC to control from one to eight instruments
l The system provides automatic backup of all relevant
databases included in the system
¨ This is accomplished through a built-in USB flash drive
¨ A USB flash drive must, therefore, be in place during
any system operation involving changes to the
customer’s data
l The PC software also enables the customer to easily
¨ Program protocols
¨ Run the protocols
¨ Receive reports upon completion of a run
l A variety of information is communicated between the PC
and the stainer subassembly microcontroller
¨ Information transferred from the PC to the subassembly
¨ All software the subassembly microcontroller will run
¨ All steps needed to perform a run
¨ Test commands
¨ Information transferred from the subassembly to the PC
¨ Barcode data
¨ Temperature readings
¨ Air pressure
¨ Run status (carousel positions, etc.)
¨ Alarms (slide tray open, etc.)

7.1 PC Configuration and Accessories

The personal computer is specially configured by Ventana to
operate the BenchMark XT / DISCOVERY XT / BenchMark LT
instrument's system. The latest PC hardware at the time of this
publication is as follows:
l Intel processor
l USB 2.0 ports
l USB flash drive
l USB hardware key
l Ethernet port
l Parallel ports: LPT-1
l Serial ports: COM-1
l Monitor: 17-inch color VGA
l Keyboard
l Mouse
l Printer: EBar II Label Printer
l USB to RS 422/485, 2 port (also known as a MOXA)
l XT Adapter
l Reagent read probe with port adapter
l Power supply for reagent read probe
7.2 Connectors and Cables

Refer to the "BenchMark/DISCOVERY XT Installation Guide"
(PN SP100015) which shows all of the interconnections
required to configure the BenchMark XT / DISCOVERY XT /
BenchMark LT instrument's system.
7.3 Hardware Key

The hardware key plugs into an empty USB port. The key ties
the database information to the computer, assuring validity of
the quality control database.

7.4 USB to Serial Adapter

A serial RS-422 port (COM-2) is used to communicate with up
to eight instruments. The USB to Serial Adapter must be
configured to communicate using RS-422, a multi-drop protocol
suitable for chained operation. An XT Adapter is used to
customize the serial pin configuration and must be installed for
proper communication.
7.5 Reagent Read Probe

The reagent read probe is used to input data from a button
attached to Ventana reagent kits. The button contains memory
that updates the database with
l Kit master lot number
l Individual reagent fill-lot numbers
l Expiration dates
l Number of dispenses allowed per dispenser
This information provides a high level of quality control and
reporting capability.
The reagent-read probe will also write a code to the button that
prevents it from being registered by any other BenchMark XT /
DISCOVERY XT / BenchMark LT instrument's PC. This feature
is a critical part of the database security built into the
BenchMark XT / DISCOVERY XT / BenchMark LT instrument.
7.5.1 Reagent Read Probe Power Supply

The reagent read probe requires external power which is
supplied by a small universal input (100-260 VAC) power
supply. The supply plugs into the 25 pin read probe adapter
connector.

BenchMark XT / DISCOVERY XT / Benchmark LT Service Manual NexES Software
8.0 NexES Software

instrument's PC system software includes a complete set of
functions for monitoring and controlling the hardware. These
functions are used for:
l Making adjustments to various components
l Diagnosing hardware problems
l Monitoring the status and performance of the system
This section of the service manual will describe only the tests
portion of the software.
l Each of the tests is documented
l For information on other software components and functions,
refer to the user manual
The Tests portion of the BenchMark XT / DISCOVERY XT /
BenchMark LT instrument's software is available via the Tests
button of the main screen when the system is “Connected.”
l The system is “Connected” when the green “Connected”
symbol on the screen is lit
l If the stainer subassembly is not “Connected,” the Tests
button is not shown

Figure 18. Software Main Screen
After you select the Tests button on the main screen, you can
select Function Tests, Service Tests, or Service Tests with
Calibration from the Test Task menu shown in the figure below.
Figure 19. Test Task Menu

8.1 Function Tests

Selecting Function Tests allows access to the Download Tests
screen shown below. The tests are listed in alphabetical order.
Figure 20. Download Tests Screen
Select a test, then click the Run button to download the test.
Then press the Start button on the stainer subassembly to run
the test.

8.2 Service Tests

Selecting Service Tests displays the Service Tests screen
shown below.
Figure 21. Service/Test Screen (BASIC I/O CONTROL Tab)
The Service/Test screen is composed of a common area for

control information and five tabbed sub-screens. The common
area has the following functions
l EXIT: this button returns to the program’s main menu
l INSTR SERIAL#: this is the serial number of the instrument
to which the software is currently connected
¨ The number is stored in non-volatile memory on the
microcontroller PCB within the stainer subassembly

¨ If the microcontroller PCB is replaced, the instrument’s

serial number can be written to the new microcontroller
PCB via the “Set Button”
¨ It is important to do this because the system’s
database files contain references to this number, which
is the serial number of the entire stainer subassembly,
not just the microcontroller PCB
8.2.1 Basic I/O Control Tab

The BASIC I/O CONTROL Tab is used to turn selected
functions on or off individually as described below.
l INPUTS: The status of each input monitored by the
microcontroller is shown in this window
l OUTPUTS: Using the selections in this window you can
individually control all the outputs on the microcontroller PCB
¨ Some functions trigger others or have built-in time-outs
¨ For example, if the compressor is turned ON, either the
vortex mixers air knife are turned ON automatically
¨ A “LOCK” function can be used to defeat software
generated time-outs if necessary
§ However, some care is needed when manipulating
these outputs, since slide heater pads and high
motor torque settings can overheat the instrument if
left ON for too long
l NOZZLE PLATE and REAGENT TRAY: Three radio buttons
are a shortcut to controlling the stepper motors used to
rotate the nozzle plate and the reagent carousel
¨ These settings are used in the motor torque inspection
procedure.
l TRIGGER BARCODE READER: These buttons command
the barcode readers to read the (reagent or slide) barcode in
front of the reader
¨ The number read from the barcode is displayed in a pop-
up box on the screen
¨ A new scan is triggered every few seconds until the test is
canceled

¨ This function is used to adjust the barcode readers and to

test the effectiveness of the barcode air knife nozzle
l SLIDE TEMPERATURES
¨ Individual slide temperatures can be viewed from this
screen
8.2.2 Test Functions Tab

The figure below shows the TEST FUNCTIONS tab of the
Service Tests with Calibration screen.
Figure 22. TEST FUNCTIONS Tab
The TEST FUNCTIONS tab

l Provides easy access to various higher level system tests
l Enables changes in the volume adjust timing
l Provides a means to manually prime the system

The Test Functions Tab is used to turn selected functions on or

off individually as described below.
l Test Run: contains an “Execute Test” button
¨ If no test is already running (the “Stop Test” button is
grayed-out), you can click the Execute Test button to
display the Download Tests screen
¨ The tests in the Download Tests screen are useful
when making adjustments and diagnosing system
problems
¨ When a test is selected from the Download Tests screen
(by picking it from the menu and clicking Run) it is
downloaded to the stainer subassembly, but does not
start executing immediately
¨ To execute the test you must press the user button
under the logo on the front panel
§ The test will remain loaded until you click Stop Test
§ Thus, every time the User front panel button is
pressed, the currently loaded test will be repeated
l Has a Volume Adjust button
¨ This button on the Test Functions tab controls the amount
of time (in ms) the adjust valve stays on in the dispense
sequence
¨ You will use this when doing slide volume adjustments
as described in Slide Volume Test and Adjustment
Procedure

8.2.3 Instrument Data Tab

The figure below shows the INSTRUMENT DATA tab.
Figure 23. INSTRUMENT DATA Tab
Statistics are accumulated relating to instrument usage in terms

of hours of operation and number of times that various
components have been cycled on and off. This data is primarily
of interest to factory service personnel.
l Communications data concerns the operation of the
connection between the PC and the microcontroller PCB
¨ During normal operation of these components there may
be communications errors
¨ These are automatically corrected by the hardware
and software

l Like the burn-in information, these statistics are used

primarily in factory quality control and servicing rather than
field service
l Two checksums are displayed on the instrument data tab
¨ These verify the integrity of software downloaded to the
microcontroller
8.2.4 Temperature Chart Tab

The figure below shows the TEMPERATURE CHART tab.
Figure 24. TEMPERATURE CHART Tab
The temperature profiles of any one or all slide temperatures

can be observed during a test function such as temperature
verification. They cannot be observed during a normal run.
The temperatures can be viewed by clicking the View button in
the main menu, then clicking View Sensors.

8.3 Service Tests with Calibration

To get to the Tests button (with calibration) from the main
screen, the security in the NexES software needs to be on. If it
is on, log on as the administrator and enter a special code to
enable the Service Test (Calibration). If it is not on, meaning a
log on is not required to use the NexES software, then the
security needs to be turned on. The following steps explain
how to turn the security on and how to log on as the
administrator in order to activate the Service Tests with
calibration.
A) From the NexES Software Main Screen make a note of the
Host ID number and click on the Setup button on the right
side of the screen.
B) On the next screen click on the Setup Host button.
C) Click on the Security tab.
D) Double click the “No” to change it to a “Yes” then to the right
click save. Notice the Lock at the top right of the screen is
now is now red.
E) To move anywhere in the software you will need to unlock
the lock. To do so click on the lock.
F) A small log in box will pop up as shown below.
G) Under the “Name” box choose Administrator from the drop
down menu.
H) The password is needed to enter Service Tests with
Calibration. The Host ID number noted earlier is needed to
calibrate the password.
I) The calculator program on the PC should be used to
calculate the password.
J) The password is generated by multiplying the following four
numbers in the following order:
month (MM) × day (DD) × year (1YY) × Host ID
NOTE: The year is represented as the last two digits of

the year preceded by a 1. For example, for the year 2012
the number to use is 112; for the year 2013 the number to
use is 113.

Example: October 16, 2012; Host ID 13217

Calculation: 10 × 16 × 112 × 13217 =
Password: 236848640
K) Copy this password from the calculator program and paste it

into the log in box, and click Continue.
L) If the password is correct, the lock turns green and is open.
M) Click on the Home icon.
N) From the Home screen, select the instrument to be tested by
clicking on the picture of the instrument in the Software Main
Screen.
O) From the Instrument Status screen, click the Service icon.
P) When finished, set the Login Passwords Enabled back
to No. This prevents unauthorized access.
8.4 Command Line Options

A command line option enables reassigning the ports for the
stainer subassembly and the reagent registration wand. This is
useful as a temporary fix to keep a system operating if one of
its COM ports fails.
The command line options are accessed by right-clicking the
BenchMark XT / DISCOVERY XT / BenchMark LT instrument's
shortcut on the desktop and selecting Properties from the
menu. In the Shortcut tab is a “Target” field. This gives the
name and location of the “.exe” program. Following this
program, separated by spaces, there can be one of three
optional switch statements. They may be entered in any order
and all are optional.
· S:n – where “S:” specifies the stainer subassembly and
“n” specifies a COM port number from 1 to 9. The default
port, if this switch is absent, is COM-2.
· P:n – where “P:” specifies the reagent probe and “n” is a
port number from 1 to 9. The default port, if this switch is
absent, is COM-1.
· NOBACK – specifies that a USB drive is either not
present or will not be used to make backups.

An error message is generated if a single port, by

assignment or default, is assigned to both the probe and
the stainer subassembly.
The NOBACK option should be used only as a temporary
stopgap permitting the customer to continue operating
while a USB drive is being replaced. This entails hazards
for the customer. If the customer’s hard disk fails there
will be no backup and all data could be lost. Upon
replacement of the drive the NOBACK switch should be
removed and a current backup should be made
immediately.

BenchMark XT / DISCOVERY XT / Benchmark LT Service Manual Voltage Conversion
9.0 Voltage Conversion

The instrument is initially configured for 120 VAC/60 Hz, or 100
VAC/50 or 60 Hz.
The instrument can be converted to 230 VAC/50 Hz by
replacing the domestic plug (PN 1953200 XT Domestic Power
Configuration Cable Assembly) with the international plug (PN
1953100 XT International Power Configuration Cable
Assembly).
NOTE: If this conversion has already been made, this should
be indicated by a “230 VAC” overlay on the serial number label
located on the back panel.

To make the conversion for 230 VAC/50 Hz:

A) Make sure that the instrument’s power cord is unplugged.
B) At the back of the instrument, remove the four screws that
hold the Fuse Panel Cover (PN 1852700) in place near the
bottom of the instrument.
Figure 25. Fuse Panel Cover Removed

C) Remove the “domestic plug” located in the upper right corner

of the exposed fuse panel.
Figure 26. Domestic Plug
D) Install the “international plug” in its place.
Figure 27. International Plug
E) Re-install the Fuse Cover Panel.

F) Install the XT Fuse Overlay Label (PN 1966500) included in
the XT Label Accessory Kit (PN 1981500) on the serial
number label to show the new voltage configuration.
¨ The serial number label is located on the back panel
G) Install the 230 VAC/50 Hz power cord (PN 1854300).

BenchMark XT / DISCOVERY XT / Benchmark LT Service Manual Preventive Maintenance Tests and Adjustments
10.0 Level One Tests and Adjustments

This chapter covers tests and adjustments, some of which
require qualitative measurements. Some of the adjustment
procedures may also require special tools and fixtures.
For specification ranges and test function requirements, refer to
the current revision of the Level One checklist.
During reassembly, discard old patch screws and replace with
new patch screws whenever possible.
Take precautions to avoid ESD. Failure to do so may result in
damage to electronic components such as PCBs.
Prior to removal of subassemblies, power down the
instrument and unplug it from the wall circuit.
A level one is intended to ensure that the instrument‘s
assemblies are operating properly and that the instrument is
within calibration. A level one is required after any service has
been performed on the instrument unless otherwise specified
by either a Service Bulletin or the customer. If the customer
requests a level one not to be performed on the instrument then
the FSE is required to stay and verify the instrument has
completed a successful staining run. The steps for completing
a level one are as follows and should be performed in order:
10.1 Inspect Compressor Muffler

l Inspect muffler filter for dirt and signs of clogging.
l If necessary, perform muffler replacement per Section 11.1.
10.2 Verify Reagent Homing Alignment

This test is used to confirm the proper function of the home
sensors and motors for the reagent carousel.
Execute the test function “Test - Home Reagent Tray XT.”

l Press the user button to home the reagent carousel.
¨ Verify that the reagent carousel dispense hole is centered
in the arch plate pass-through hole after the tray homes.

¨ If necessary, loosen and adjust the reagent carousel

homing flag position and repeat test to verify
alignment.
§ NOTE: Fine motor rotation adjustment may be
needed.
10.3 Jog Reagent Tray

This test is used to confirm the proper function of the motors
and drift for the reagent carousel by stepping around one
position per button push.
l Verify position to position alignment by monitoring carousel
dispense hole centering to arch plate pass-through hole.
¨ Carousel should exhibit smooth and consistent movement
from position to position – if not, inspect drive belt
¨ If drift is observed - perform Motor Test, verify motor
torque voltages and check for mechanical binding.
l To test select “Test – Jog Reagent Tray CW XT” from the
menu, then click the Run button
l The test instructions are sent to the stainer subassembly
l The “Running” status light on the control panel will glow
yellow
The software will then

l Prompt you to press the user button under the Ventana logo
You must then

l PRESS THE USER BUTTON

l Move the reagent carousel to the home position
You must then



l Move the reagent tray forward one position
You must then

l PRESS THE USER BUTTON repeatedly until all positions
have been traversed
10.4 Verify Nozzle Plate Homing Alignment

This test is used to confirm the proper function of the home
sensors and motors for the nozzle plate.
l Place the slide barcode centering tool (PN 1969400) on slide
position 12.
NOTE: The vortex mixer alignment tool (PN 2197000) may
be used instead.
l Execute the test function “Test - Home Nozzle Plate”.
l Press the user button to home the nozzle plate.
¨ The homing sensor mark on the nozzle plate (indicated
with an “H”) should line up with the center line of the
centering tool.
¨ If necessary, loosen and adjust the sensor bracket
position and repeat test to verify alignment.
NOTE: Pressing the user button (even when the
nozzle plate is moved drastically) should bring the two
lines into alignment every time, when the sensor is
properly adjusted.
§ Also, when homing the nozzle plate, verify that the
hard stop post does not hit the rubber bumper.
§ Adjust the stop if necessary and repeat test to verify
alignment.
NOTE: Fine motor rotation adjustment may be
needed.

10.5 Jog Nozzle Plate

This test is used to confirm the proper function of the motors
and drift for the nozzle plate by stepping around one position
per button push.
l Verify position to position alignment by installing the
centering tool first in position 15, then position 20 and last
position 10.
¨ The centering mark “H” on the nozzle plate should line up
with the center line on the centering tool in each of the
three positions.
¨ The nozzle plate should exhibit smooth and consistent
movement from position to position – if not, inspect drive
belt.
¨ In the last position, prior to the nozzle plate being
returned to the previously established home position,
verify the hard stop post does not hit the rubber bumper.
Adjust if necessary.
¨ If drift is observed check belt, verify motor torque voltages
and check for mechanical binding.
To test select “Test – Jog Nozzle Plate CW XT” from the menu,
then click the Run button
l The test instructions are sent to the stainer subassembly
yellow

You must then


l Move the nozzle plate to the home position
You must then


l Move the nozzle plate forward one position
You must then

l PRESS THE USER BUTTON repeatedly until all positions
have been traversed
10.6 Verify Slide Barcode Read Alignment

This test is to verify the alignment and readability of the slide
barcode reader in relation to the slide barcode label.
l Place the slide barcode centering tool (PN 1969400) on slide
position 12.
NOTE: The vortex mixer alignment tool (PN 2197000) may
be used instead.
l Execute the test function “Test – Home Nozzle Plate”.
l Press the user button to home the nozzle plate.
l Activate the slide barcode reader in BASIC I/O CONTROL.
l Verify the following and adjust as needed:
¨ The barcode reader beam hits between letters “C” and “E”.
¨ The beam is parallel to the graduations on the tool.
¨ The beam must scan off the edge of the tool on each side
to be properly centered.
l Remove the centering tool and place a barcoded slide in
position 14.
l Verify read of slide barcode label.
¨ If barcode reader does not read slides, check alignment,
slide label, and barcode reader lens.
CAUTION: Clean the lens with lens paper only.

10.7 Verify Reagent Barcode Read Alignment

This test is to verify the alignment and readability of the reagent
barcode reader in relation to the reagent dispenser barcode
label.
l Execute the test function “Test – Home Reagent Tray XT.”
l Place a barcoded dispenser in front of the reagent barcode
reader.
l Activate the reagent barcode reader in BASIC I/O
CONTROL.
¨ The beam from the reader should hit the middle of the
barcode on the dispenser and is parallel (left to right) to
the barcode label.
¨ Adjust by removing the upper back panel and loosening
the mounting screws.
10.8 Verify Dispense Cylinder to Dispenser

Alignment
The software tests the dispense hammer alignment to the
reagent dispenser. This test dispenses a reagent (position 1)
onto slide 15.
A slide should be placed at slide position 15 and a dispenser

with fluid in it should be placed in reagent position 1.
To test the dispense hammer

l Follow the steps to the Download Tests screen.
l Then select Test – Dispense Reagent XT from the menu,
then click the Run button.
¨ The test instructions are sent to the stainer subassembly.
¨ The “Running” status light on the control panel will
glow yellow

l Turn on the compressor and pressurize the system.
l Lift slide heater drawer.

l Home nozzle plate.

l Home the reagent tray.
l Prompt you to press the user button under the Ventana logo.
You must then

l PRESS THE USER BUTTON.
Next, the software will

l Move the dispense point on the nozzle plate to slide 15.
l Move reagent 1 to slide 15.
l Dispense reagent.
l Move Dual Rinse to slide 13 and wait.
You can repeat the test by pressing the user button.
l Visually verify that the dispense cylinder plunger is centered

in relation to dispenser.
¨ If it is not, loosen dispenser arm set screws and adjust.
10.9 Verify Operation of Barcode Blowoff

This test checks the function of the barcode blowoff to ensure
that liquid is removed from the barcode. This test requires a
slide (with barcode label attached) to be placed on slide
heater 15.
Follow the steps to the Download Tests screen.

l Then select Test-Bar Code Blowoff XT from the menu, then
click the Run button.
glow yellow.

l Lift the slide tray.
l Home the nozzle plate.

You must then


l Move the dual rinse nozzles to slide #15 and rinse the slide.
l Move the multispense nozzle to slide #15 and adjust the
slide volume.
l Move the coverslip nozzle to slide #15 and coverslip the
slide.
l Turn on the barcode blowoff, move the nozzle plate forward
one position, and then turn off the barcode blowoff.
l Move the dual rinse nozzles to slide #13 and wait.
l Visually verify that the dual rinse, multispense, coverslip and

barcode blowoff nozzles are adjusted properly.
¨ Adjust if necessary.
¨ You should hear the air jets as the barcode blowoff
nozzle passes over the slide label.
§ After the blowoff the label should be cleared of
liquid.
10.10 Verify Mixer Height, Alignment, and

Performance
10.10.1 Vortex Mixer Height
This alignment check verifies that the outer mixers are at the
proper height in relation to the slide.
Clear vortex mixers

l Using the output in BASIC I/O CONTROL, turn on
Compressor and Slide Tray Up.
l Disable nozzle plate motor.

l Place the Vortex Mixer Height Gauge (PN 1159800) in slide

position 15.
l Manually rotate the nozzle plate so the vortex mixers pass
through the gauge.
l If mixer protuberance does not pass through gauge:
¨ Adjust mixer height by installing shims, if possible.
¨ Verify height of slide drawer.
¨ If height of slide drawer is correct, replace mixer.
¨ If height of slide drawer is incorrect, adjust slide drawer
height per Section 12.15.
l Remove the gauge to allow the vortex mixers to rotate
before being reset into position to check the height of the
next vortex mixer.
l Repeat for all mixers.
White vortex mixers

l Place the Vortex Mixer Alignment Tool (2197000) in slide
position 15.
through the alignment tool.
l The protuberances on the outer mixers must pass through
the alignment tool without touching it.
l If necessary, loosen the screw on the vortex mixer guide
block, adjust the guide block so both nozzles pass through
the gauge without touching, and then tighten the screw.
l Remove the alignment tool to allow the vortex mixers to
rotate before being reset into position to check the height of
the next vortex mixer.
Black vortex mixers



position 15.
l Adjust vortex mixer outer nozzle height using the adjustment
screw. Turn the adjustment screw clockwise or counter
clockwise to raise or lower the outer nozzle, such that both
metal orifice fittings pass through the tool without touching.
10.10.2 Vortex Mixer Alignment

This alignment check verifies that the mixers are centered in
relation to the slides.
Clear vortex mixers

l Visually check mixers are centered between heater bases.
NOTE: There is no alignment tool for clear vortex mixers.
l If necessary, loosen the screws on the vortex mixer and
adjust so the mixer is centered, and then tighten the screws.
White vortex mixers

l Run test function “Test – Jog Nozzle Plate CW XT” to raise
the slide tray and fix the nozzle plate to the same indexing
positions used during staining runs.
l Press the User button to index the vortex mixers to an
accessible position for vortex mixer centering.
l Adjust mixer centering alignment using the red vortex mixer
centering tool (PN 2173500).
l Press the User button to jog the nozzle plate around until the
vortex mixer is at position 15.

l After the nozzle plate comes to a complete rest, place

centering tool on position 15.
l Ensure the mixer lightly contacts the pins on the centering
tool.
l If necessary, loosen the screws on the mixer and adjust the
mixer position, and tighten the screws.
l Lift the centering tool out of position.
CAUTION: Be sure to remove centering tool prior to
indexing or damage to instrument may occur.
l Index nozzle plate one position and place centering tool on
position 15 to verify alignment.
l Exit the test function.
Black vortex mixers

l Run test function “Test – Jog Nozzle Plate CW XT” to raise
the slide tray and fix the nozzle plate to the same indexing
positions used during staining runs.
l Press the User button to index the vortex mixers to an
accessible position for vortex mixer centering.
l Adjust mixer centering alignment using the green Vortex
Mixer Centering Tool (PN 06626238001).
l Press the User button to jog the nozzle plate around until the
vortex mixer is at position 15.
l After the nozzle plate comes to a complete rest, place
centering tool on position 15.
l Ensure the mixer lightly contacts the pins on the centering
tool.
l If necessary, loosen the mounting screws on the mixer and
adjust the mixer position, and tighten the screws.
l Lift the centering tool out of position.
CAUTION: Be sure to remove centering tool prior to

indexing or damage to instrument may occur.
l Index nozzle plate one position and place centering tool on
position 15 to verify alignment.

l Exit the test function.
10.10.3 Vortex Mixer Performance

This test validates the side to side alignment of the mixers in
relation to the slide.
The vortex mixers are air jets directed at the surface of the slide
The mixers are located on the nozzle plate.
By adding a drop of hematoxylin to the slide (after the barcode
blowoff passes over it) you can observe the swirling action
produced by the vortex mixers.
Place a slide at position #15.
l Select “Test-Vortex Mix XT” from the menu, then click the
Run button.
l The test instructions are sent to the stainer subassembly.
yellow.

l Turn on the vortex mixers.

l Move the dual rinse nozzles to slide #15 and rinse the slide.
l Move the multispense nozzle to slide #15 and adjust the
slide volume.
l Move the coverslip nozzle to slide #15 and coverslip the
slide.
l Turn on the barcode blowoff, move the nozzle plate forward
one position, and then turn off the barcode blowoff.
l Move each vortex mixer nozzle to slide #15 and dwell for six
seconds.

l Visually inspect the slide as the mixers stop to mix.

l Check for side to side alignment of the inner and outer
mixers and for even mixing of the hematoxylin.
¨ Some reasons for poor performance are:
¨ Improper flow to the vortex mixer nozzles.
¨ Instrument not level.
¨ Nozzle plate homing is off.
¨ Mixer nozzles are improperly aligned.
¨ Mixer nozzles are plugged.
¨ Restrictors plugged.
10.11 Verify Waste Sensor Performance

Test the waste sensor per Section 13.20.
10.12 Verify Instrument Level

To ensure that the instrument is properly leveled:
l Level the instrument using the Level, 30 Min. Bubble
(1467100) on the nozzle plate while in the home position.
l Ensure the bubble is entirely within the circle. Use the
Caster, Center Leveling (1972900) “Leveling Foot” to adjust.
10.13 High System Pressure

To validate that 40 psi is being supplied to the four slide drawer
lift cylinders
l Turn on the compressor using the output in BASIC I/O
CONTROL. Allow compressor to warm up prior to testing
(30 min. if from a cold start).
NOTE: Pressure depends on operating temperature, which
depends on how long the instrument has been running.
l For BLACK or WHITE Vortex Mixers: Ensure the outputs
for Vortex Mixers, Barcode Blowoff, and Slide Tray Up are
set to OFF in the Basic I/O Control Tab of the Service Tests
Screen.

l For CLEAR Vortex Mixers: Ensure the outputs for Barcode

Blowoff, and Slide Tray Up are set to OFF and Vortex Mixers
set to ON in the Basic I/O Control Tab of the Service Tests
Screen.
l Connect a pressure gauge into the high pressure quick
disconnect fitting mounted in the AFM.
CONTROL.
¨ If the pressure falls outside of this range adjust by
unlocking (lifting) pressure relief valve cap and
rotating.
¨ After adjustment is complete, lock (push down)
pressure relief valve cap and recheck high pressure.
Repeat if necessary.
10.14 Low System Pressure

To validate that 13 psi is being supplied to the staining
subassembly and bottle gate air cylinders.
CONTROL. Allow compressor to warm up prior to testing
(30 min. if from a cold start).
NOTE: Pressure depends on operating temperature, which
depends on how long the instrument has been running.
l For BLACK or WHITE Vortex Mixers: Ensure the outputs
for Vortex Mixers, Barcode Blowoff, and Slide Tray Up are
set to OFF in the Basic I/O Control Tab of the Service Tests
Screen.
l For CLEAR Vortex Mixers: Ensure the outputs for Barcode
Blowoff, and Slide Tray Up are set to OFF and Vortex Mixers
set to ON in the Basic I/O Control Tab of the Service Tests
Screen.
l Connect a pressure gauge into the low pressure quick
disconnect fitting mounted in the AFM.
¨ If the pressure falls outside of this range, adjust by
loosening lock nut on regulator knob stem and rotating
regulator knob.

¨ After adjustment is complete, tighten lock nut on

regulator knob stem and recheck low pressure again.
Repeat if necessary.
l Set Cal Span as follows:
¨ When low system pressure is at desired level, click the
Cal Span button in the Service Tests with Calibration
screen to set system pressure in the software.
l Set Cal Zero as follows:
¨ Ensure all outputs are set to OFF in the Basic I/O Control
Tab of the Service Tests with Calibration Screen.
¨ When the pressure gague is reading zero, click the Cal
Zero button in the Service Tests with Calibration screen to
set system pressure in the software.
10.15 Vacuum
To verify correct vacuum is present at the vacuum trap
reservoir.
l Turn on the vacuum pump using the output in BASIC I/O
CONTROL.
l Disconnect tubing from vacuum trap reservoir to vacuum
trap check valve.
l Plug in pressure gauge to top of vacuum trap reservoir.
l Wait until pressure gauge stabilizes.
l If necessary, adjust vacuum trap relief valve:
¨ Loosen lock nut on vacuum relief valve.
¨ Turn cap of vacuum relief valve until desired vacuum is
achieved.
¨ Tighten lock nut on vacuum relief valve.
10.16 Mixer Flow Rates

l Home the nozzle plate to ensure the mixers are above the
correct slide positions.
l Using the Basic I/O Control tab, under the Outputs list, turn
ON “Compressor” and “Mixers” ONLY. [Ensure that only the
compressor and vortex mixers are ON].

l Using a Flow Meter, hold the end of the tubing over the
protuberance of the vortex mixer to be read.
l Measure the flows from the inner and outer mixer nozzles.
l If needed, adjust the variable restrictor for the mixers such
that they are within range.
l Once the restrictor is set, record the measured reading from
each mixer nozzle.
10.17 Fluid Volumes

Five consecutive volumes (trials) for each test must be
collected based on instructions below. Each trial must be
between the min-max specified for each test on the Level 1
sheet. If any adjustments are made to bring the fluid volumes
into specification, test must be repeated until five consecutive
trials are collected which fall within the specified range.
10.18 Test-Cell Conditioner #1 XT

The software tests the CC1 dispense needle. This test
dispenses a known amount of CC1 to test the flow through that
fluid path. The nozzle plate does not move and the slide
drawer does not lift for this test. CC1 volumes are obtained by
capturing the liquid in a weigh boat directly from the
multispense nozzle.
l Turn the nozzle plate by hand so that the nozzles are at the
front of the instrument and are accessible.
l Execute "Test – Cell Conditioner #1 XT"
l Tare an appropriately sized weigh boat on the scale.
l Place weigh boat beneath the CC1 dispense nozzle
l Press the user button.
l Weigh the collected fluid
l If the volumes are not within specification, check the
following:
¨ Low volume results may indicate a defective valve,
clogged nozzle or kinked tubing.
¨ High volume results from a defective valve, restrictor,
nozzle, or air pressure being too high.

10.19 Test-Cell Conditioner #2 XT

The software tests the CC2 dispense needle. This test
dispenses a known amount of CC2 to test the flow through that
fluid path. The nozzle plate does not move and the slide
drawer does not lift for this test. CC2 volumes are obtained by
capturing the liquid in a weigh boat directly from the
multispense nozzle.
l Execute "Test – Cell Conditioner #2 XT"
l Place weigh boat beneath the CC2 dispense nozzle
following:
¨ High volume results from a defective valve, restrictor,
10.20 Test-Coverslip XT
The software tests the LCS nozzle. This test dispenses a
known amount of LCS to test the flow through that fluid path.
The nozzle plate does not move and the slide drawer does not
lift for this test. LCS volume is obtained by capturing the liquid
in a weigh boat directly from the LCS nozzle.
l Execute “Test – Coverslip XT”
l Place weigh boat beneath the LCS dispense nozzle


following:
¨ Low volumes may indicate a defective LCS valve or a
clogged nozzle or tubing.
¨ High volumes may result from a defective LCS valve,
restrictor, nozzle, or air pressure too high.
10.21 Test-Rinse Mix 1x SSC XT

The software tests the SSC Rinse mixing. These tests are
used to check the SSC stringency dilution on the instrument.
2X SSC is diluted to 1X SSC by adding EZ Prep. The nozzle
plate does not move and the slide drawer does not lift for this
test. Rinse mix volume is obtained by capturing the liquid in a
weigh boat directly from the multispense nozzle.
l Turn the nozzle plate by hand so that the multispense nozzle
is at the front of the instrument and is accessible.
l Execute “Test – Rinse Mix 1x SSC XT”
l Place weigh boat beneath the multispense nozzle
following:
¨ High volume may result from a defective valve, restrictor,
10.22 Test-Rinsing (EZ Prep) XT

The software tests the fluid volume being dispensed from the
Dual Rinse nozzle. This test checks the rinse function for EZ
Prep rinse bulk fluid. The nozzle plate does not move and the
slide drawer does not lift for this test. Rinse volume is obtained
by capturing the rinse liquid in a weigh boat directly from the
nozzles.

l Execute “Test – Rinsing (EZ Prep) XT”
l Place weigh boat beneath the dual rinse nozzle
following:
¨ Low volume results may indicate a defective rinse valve
or a clogged nozzle or kinked tubing.
¨ High volume results may result from a defective rinse
valve, restrictor, nozzle, or air pressure being too high.
10.23 Test-Rinsing (Option) XT (Only needed

for SISH)
Dual Rinse nozzle. This test checks the rinse function for
Option rinse bulk fluid. The nozzle plate does not move and the
slide drawer does not lift for this test. Rinse volume is obtained
by capturing the rinse liquid in a weigh boat directly from the
nozzles.
l Execute “Test – Rinsing (Option) XT”
following:

10.24 Test-Rinsing (RB) XT

Dual Rinse nozzle. This test checks the rinse function for
Reaction Buffer rinse bulk fluid. The nozzle plate does not
move and the slide drawer does not lift for this test. Rinse
volume is obtained by capturing the rinse liquid in a weigh boat
directly from the nozzles.
l Execute “Test – Rinsing (RB) XT”
following:
10.25 Test-Rinsing (SSC) XT

Dual Rinse nozzle. This test checks the rinse function for SSC
rinse bulk fluid. The nozzle plate does not move and the slide
drawer does not lift for this test. Rinse volume is obtained by
capturing the rinse liquid in a weigh boat directly from the
nozzles.
l Execute “Test – Rinsing (SSC) XT”


following:
10.26 Test-Volume Adj (EzPrep) XT

The software tests the Volume Adjust for EzPrep. This test
dispenses a known amount from the Volume Adjust to test the
flow throughout that fluid path. The nozzle plate does not move
and the slide drawer does not lift for this test. EzPrep volume
adjust volumes are obtained by capturing the liquid in a weigh
boat directly from the multispense nozzle.
l Execute “Test – Volume Adj (EzPrep) XT”
following:
¨ High volume results may result from a defective valve,
restrictor, nozzle, or air pressure being too high.
10.27 Test-Slide Vol IHC (RB) XT

The software tests the residual slide volume for IHC. This test
is used to check the Dual Rinse alignment and the Volume
Adjust timing. Slide Volume is the amount of buffer liquid that
should remain on the slide after rinse and volume adjust. Rinse
should leave a little less than the required volume. Then the
volume adjust function adds a controlled amount of buffer to
precisely set the total volume. The highest and lowest volumes

from these measurements will determine whether or not

adjustment is required. Slide volumes are obtained by
collecting residual slide volume fluid with a tared laboratory
tissue and weighing it.
l Place a clean, dry slide (with a Ventana barcode) in position
#15 of the slide tray.
l Ensure that the slide is centered side-to-side and positioned
against the outer slide posts.
l Execute “Test – Slide Vol IHC (RB) XT”
¨ The software will turn on the compressor to pressurize the
system. The slide drawer will lift and the nozzle plate will
move to the home position.
l Press the user button
¨ During the test, the nozzle plate will rotate so that the
Dual Rinse nozzle will move to slide position 15 to rinse
the slide then the nozzle plate will rotate so that the
multispense nozzle is moved to slide position 15 adjust
the slide volume.
l Before taking any measurements, execute the test several
times to observe the flows from the dual rinse nozzle.
l Check to see that no holes are plugged and that the liquid
streams do not overshoot the edges of the slide.
l Use a laboratory tissue to remove the liquid, being careful to
remove only that liquid in the puddle on the slide (exclude
any liquid on the barcode label).
l Weigh the tared laboratory tissue to obtain the weight.
¨ If the ranges are not in specification, check the dual rinse
nozzle for clogs and/or adjust dual rinse nozzle position.
10.28 Test-Slide Vol IHC (SSC) XT

The software tests the residual slide volume for IHC. This test
is used to check the Dual Rinse alignment and the Volume
Adjust timing. Slide Volume is the amount of buffer liquid that
should remain on the slide after rinse and volume adjust. Rinse
should leave a little less than the required volume. Then the
volume adjust function adds a controlled amount of buffer to
precisely set the total volume. The highest and lowest volumes

from these measurements will determine whether or not

adjustment is required. Slide volumes are obtained by
collecting residual slide volume fluid with a tared laboratory
tissue and weighing it.
l Execute “Test – Slide Vol IHC (SSC) XT”
the slide then the nozzle plate will rotate so that the
multispense nozzle is moved to slide position 15 to adjust
the slide volume.
times to observe the flows from the dual rinse nozzle.
¨ If the ranges are not in specification, check the dual rinse
nozzle for clogs and/or adjust dual rinse nozzle position.
10.29 Test-Slide Vol ISH (Opt) XT (Only needed

for SISH)
The software tests the residual slide volume for SISH. This test
is used to check the Jet Drain functionality and alignment.
Slide volumes are obtained by collecting residual slide volume
fluid with a tared laboratory tissue and weighing it.


l Execute “Test – Slide Vol ISH (Opt) XT”
the slide then the nozzle plate will rotate so that the Jet
Drain is moved to slide position 15 to jet drain the slide.
times to observe the flows from the Jet drain nozzle.
¨ If the ranges are not in specification, check the jet drain
nozzle for clogs and/or adjust jet drain position.
10.30 Test-Slide Vol ISH (RB) XT

The software tests the residual slide volume for ISH. This test
l Execute “Test – Slide Vol ISH (RB) XT”


10.31 Test-Slide Vol ISH (SSC) XT

The software tests the residual slide volume for ISH. This test
l Execute “Test – Slide Vol ISH (SSC) XT”



11.0 Preventive Maintenance Tests and

Adjustments
This chapter covers preventive maintenance (PM) tests and
adjustments, some of which require qualitative measurements.
Some of the adjustment procedures may also require special
tools and fixtures.
For specification ranges and test function requirements, refer to
the current revision of the Preventive Maintenance checklist.
PM is intended to ensure that the instrument‘s assemblies are
operating properly and that the instrument is within calibration.
The steps for completing a PM are as follows and should be
performed in order:
11.1 Replace Compressor Muffler

l Unscrew the muffler from the fitting. Do not remove the
fitting from the compressor.
l Apply approximately 3 1/2 wraps of Teflon tape to the
threads of the new muffler.
l Screw the new muffler into the fitting. Hand-tighten only.
11.2 Check Moisture Trap

l Visually inspect the moisture trap for excessive fluid, leaks or
cracks. Replace as needed.
11.3 Replace All In-Line Filters Between Fluid

Reservoirs and Nozzles
Replace each of the in-line filters connected to the color-coded
tubing connected to the bottom of the fluidics reservoir
assembly, which is routed through the Igus chain.
11.4 Inspect Reservoir Chambers

Inspect individual reservoir chambers and associated fittings,
filters and check valves for evidence of cracks, leaks,
contamination and debris. Repair or replace as necessary.

11.5 Inspect Bottle Filters

Inspect bottle filters for evidence of cracks, leaks,
contamination and debris. Repair or replace as necessary.
11.6 Inspect Motor Gear Pulleys, Tighten

Pulley Set Screws
l Visually inspect the pulleys for damage or wear.
l Tighten the set screws to ensure they are secure.
11.7 Inspect Reagent Belt

l Visually inspect the belt for damage or wear. Replace as
needed.
l Check the belt for proper tension. Adjust as needed.
11.8 Inspect Nozzle Plate Belt

l Visually inspect the belt for damage or wear. Replace as
needed.
l Check the belt for proper tension. Adjust as needed.
11.9 Inspect Tubing to Nozzle Plate Assembly

l Visually inspect the tubing for damage or wear, clogging,
loose connections, bulges, or pinches.
l Inspect the tubing at tie-down locations to ensure tubing is
not constricted or damaged by cable ties.
l Verify tubing in the center shaft is not binding, knotting, or
tangling due to insufficient lubrication.
l Replace damaged components as needed.
11.10 Inspect and Clean Tub Drain

l Visually inspect the tub for excessive amounts of residue,
leaks, or cracks.
l Visually inspect the waste tubing for damage and clogs.
l Visually inspect the drain for clogs.

l Clean or replace components as needed.
11.11 Inspect Underside of Slide Drawer and

Heater PCBs for Fluid Leaks
Visually inspect components for signs of abnormal leakage.
11.12 Verify Operation of Tub Overflow Sensor

l Slide out the slide drawer completely and locate the two long
screws on left side.
l Put the shaft of a screwdriver in contact with both screws on
the sensor and monitor the Tub Overflow input in BASIC I/O
CONTROL.
¨ The input should change from “Not Overflowed” to
“Overflowed.
11.13 Verify Operation of Bulk Bottle Sensors

l Verify operation of bottle sensors as follows:
¨ Ensure that all bulk bottles are filled above sensor level.
¨ Monitor the appropriate input in BASIC I/O CONTROL to
verify bulk is “Full”.
¨ Remove bulk and input should change to “Empty”.
¨ Repeat for all bulk bottles.
11.14 Verify Waste Sensor Performance

Test the waste sensor per Section 13.20.
11.15 Verify Operation of Vacuum Trap Check

Valve
l With vacuum pump on, install a pressure gauge on opposite
end of check valve.
l Pressure gauge reading should be 0 psi.

11.16 Verify Reagent Homing Alignment

Perform the steps in Section 10.2
11.17 Jog Reagent Tray

11.18 Verify Nozzle Plate Homing Alignment

11.19 Jog Nozzle Plate

11.20 Verify Slide Barcode Read Alignment

11.21 Verify Reagent Barcode Read Alignment

11.22 Verify Operation of Fans

l In the Outputs list in the BASIC I/O CONTROL tab, turn on
the FAN.
l In the Outputs list in the BASIC I/O CONTROL tab, turn on
the COOLING FAN.
l Using laboratory tissue paper, ensure both fans are blowing
air out of the instrument.
11.23 Verify Dispense Cylinder to Dispenser

Alignment
11.24 Verify Operation of Barcode Blowoff


11.25 Verify Mixer Height, Alignment, and

Performance
11.26 Verify All Technical Bulletins Have Been

Completed
Complete all Technical Bulletins or Service Bulletins as needed.
11.27 Verify Instrument Level

11.28 High Pressure System Leak Rate

To control the instruments functions during this procedure, use
the output in BASIC I/O CONTROL.
Two hemostats are required for this procedure. For old
configurations, use a hemostat and a needle-nose vise grip or
large hemostat. See the steps below for details.
l Determine if the instrument is the old or new configuration,
based on the two figures below.
¨ For the old configuration, the clamp points are as shown.
¨ For the new configuration, install the test fixtures inline as
shown. The clamp points are in the test fixtures. Test
fixtures are color coded to match the instrument tubing.
l Make sure that the slide drawer is in the down position.
l Plug the pressure meter into the high pressure test port.
l Turn on the compressor and let the pressure rise to 40 psi.
l Clamp off the tubing connected to input of the regulator,
using a hemostat.
l Clamp off the high pressure tubing exiting the compressor,
using a needle-nose vise grip or a large hemostat.
l Immediately turn off the instrument power switch.
l Wait several seconds to allow pressure reading to stabilize.
l Note the initial pressure reading.
l Wait one minute.

l Read the pressure again.

l The pressure should not drop more than 0.4 psi in one
minute.
l Remove the hemostats and/or vise grips.
l Remove test fixtures if installed.
Figure 28. Old Configuration, Hose Barb Fittings

Figure 29. New Configuration, Push Lock Fittings
11.29 Low Pressure System Leak Rate

To control the instruments functions during this procedure, use
the output in BASIC I/O CONTROL.
One hemostat is required for this procedure.
l Determine if the instrument is the old or new configuration,
based on the two figures in Section 11.28.
¨ For the old configuration, the clamp point is as shown.
¨ For the new configuration, install the test fixture inline as
shown. The clamp point is in the test fixture. Test fixture
is color coded to match the instrument tubing.
l Make sure that the barcode blowoff and vortex mixers are
turned off.
l Plug the pressure meter into the low pressure test port:

¨ Old configuration: Use low pressure test port on

instrument chassis.
¨ New configuration: Use test port on test fixture.
l Turn on the compressor and let the pressure rise to 13 psi.
l Clamp off the low pressure tubing connected to the output of
the regulator, or at the test fixture, using a hemostat.
l Immediately turn off the instrument power switch.
l Wait several seconds to allow pressure reading to stabilize.
l Note the initial pressure reading.
l Wait one minute.
l Read the pressure again.
l The pressure should not drop more than 0.4 psi in one
minute.
l Remove the hemostat.
l Remove test fixture if installed.
11.30 Disassemble, Clean, and Calibrate

Vacuum Relief Valve, Record Vacuum
1. Loosen the lock nut, disassemble the cap, spring and ball
and clean all surfaces (including the inside of the body)
before reassembly.
2. Remove the cap from the valve body.
NOTE: Take care to maintain control of the ball and spring
or the ball can be lost.
3. Remove the lock nut from the cap.
4. Remove old Teflon tape if present.
5. Clean inside and outside of all parts with a lint-free
laboratory tissue and a cotton swab, both moistened with
water.
6. Wrap the cap of the relief valve with 2-3 turns of Teflon
tape.
l Care should be taken to wrap the Teflon tape in
clockwise direction.
l Ensure the tape does not block the hole where it could
interfere with proper spring operation.

7. Assemble the lock nut of the relief valve onto the cap.
8. Assemble the spring inside the housing/body. Care should
be taken to align the spring inside the groove.
9. Assemble the ball on top of the spring.
10. Assemble the cap on the housing/body. Care should be
taken to align the ball with the hole inside the cap.
11. After application of tape, reinstall cap and adjust vacuum to
specification.
12. Set vacuum per Section 10.15
Lock nut
Ball
Cap
Spring Body
Figure 30. Vacuum Relief Valve, Disassembled
Figure 31. Cap with Teflon Tape and Lock Nut
Figure 32. Vacuum Trap Relief Valve, Reassembled

11.31 Test-Rinse Mix 0.1x SSC XT

2X SSC is diluted to 0.1X SSC by adding EZ Prep. The nozzle
l Execute “Test – Rinse Mix 0.1x SSC XT”
following:
11.32 Test-Rinse Mix 0.5x SSC XT

2X SSC is diluted to 0.5X SSC by adding EZ Prep. The nozzle
l Execute “Test – Rinse Mix 0.5x SSC XT”


following:


2X SSC is diluted to 2X SSC by adding EZ Prep. The nozzle
l Execute “Test – Rinse Mix 2x SSC XT”
following:
11.35 Run Temperature Verification Slides

The software tests functionality of the individual slide heaters.
The purpose of this test is to check the heater calibration and
functionality at high temperatures using the Temperature
Verifier Slides. Each slide has two temperature sensitive

strips, one indicating 93°C and the other indicating 99°C, which
change from white to black when the indicated temperature has
been reached.
l Place Temperature Verifier Slides on all slide positions.
l Execute “Test – Temp Verify XT”
¨ The software will then ramp up all slide heaters to 95°C
for 16 minutes and then disable them for 4 minutes to
cool. It takes approximately 20 minutes to complete this
operation.
l Evaluate all slides upon completion of the Temp Verify run.
¨ The strip on each slide indicating 93°C should have
turned black while the strip indicating 99°C should have
remained unchanged.

12.0 Additional Tests and Adjustments

12.1 Motor Test
The purpose of this test is to verify that the reagent carousel
and nozzle plate stepper motors switch between three states.
The three states are:
l Disabled
l Low-torque
l High-torque
Use the Service/Tests, BASIC I/O CONTROL tab to set these

states and manually rotate the reagent carousel or nozzle plate
by hand using the following instructions:
l Set DISABLED.
¨ The reagent carousel or nozzle plate should rotate freely
when turned by hand
¨ If the reagent carousel or nozzle plate does not rotate
freely the stepper motor, bearing and belt may have to be
replaced.
¨ Also inspect drive system for mechanical interference.
l Set LOW-TORQUE.
¨ The reagent carousel or nozzle plate should rotate, but
with some effort required
¨ This setting is for holding the reagent carousel or nozzle
plate in a fixed position
l Set HIGH-TORQUE.
¨ The reagent carousel or nozzle plate should strongly
resist manual rotation, although with enough force
deployed it will rotate
If the Motor does not switch to DISABLED, LOW-TORQUE or

HIGH-TORQUE check the motor, motor drivers, motor torques
and the microcontroller PCB.

12.2 Motor Torque Voltages

The purpose of this test is to verify and correct the motor torque
voltages for the following conditions:
l Disabled
l Low-torque
l High-torque
Slide motor high torque voltage 0.45 ± 0.01 VDC

Slide motor low torque voltage 0.22 ± 0.01 VDC
Reagent motor high torque voltage 0.45 ± 0.01 VDC
Reagent motor low torque voltage 0.22 ± 0.01 VDC
1. Ensure that the motors are disconnected from the

microcontroller board.
2. Connect the ‘negative’ (or ‘common’) test lead of the

meter to the microcontroller ‘GND’ terminal (TP2).
NOTE: Adjust high torque first, then low torque.
3. Using the Service Test with Calibration screen, set the

Slide torque voltage at TP4 as follows:
Slide Motor Disabled:

“DIS” LED (D36) On
‘’LTRQ” LED (D34) On
Slide Motor High Torque:

“DIS” LED (D36) Off
‘’LTRQ” LED (D34) Off
If needed, adjust Pot R40 according to chart above.
Slide Motor Low Torque:


4. Using the Service Test with Calibration screen, set the

Reagent torque voltage at TP1 as follows:
Reagent Motor Disabled:

“DIS” LED (D35) On
Reagent Motor High Torque:

‘’LTRQ” LED (D33) Off
Reagent Motor Low Torque:

12.3 Continuous Tray Check Tests

The purpose of these tests is to verify correct operation of the
stepper motors. These tests should be allowed to run five times
or more for best results.
The stepper motor is stepped 40 times for one index

Minor reagent carousel misalignment error >5 steps <40 steps
Major reagent carousel misalignment error >40 steps
Minor nozzle plate misalignment error >8 steps <40 steps
Major nozzle plate misalignment error >40 steps
12.3.1 Continuous Reagent Carousel

The stepper motor rotates 40 steps for one index. A reagent
carousel minor misalignment will result if the stepper motor is
off by more than 5 steps. A reagent carousel major

misalignment will result if the stepper motor is off by more than

40 steps, which is one index.
l Execute the test function “Test - Cont Reag Chk XT - 2 Dir”
l Allow the test to run five times or more.
l In the Service Tests with Calibration screen, on the Tray
Check Data tab, click the Get Data button. Click the button
as needed to refresh the data in the histogram.
l Using the histogram data, for reagent data add 5 steps to get
a true representation of the data.
l Optimally, the results should be as close to zero as possible.
Results should be consistent.
l Replace the stepper motor, belt, or entire motor drive
assembly as needed.
12.3.2 Continuous Nozzle Plate

The stepper motor rotates 40 steps for one index. A nozzle
plate minor misalignment will result if the stepper motor is off by
more than 8 steps. A nozzle plate major misalignment will
result if the stepper motor is off by more than 40 steps, which is
one index.
l Execute the test function “Test - Cont Slide Chk XT - 2 Dir”
l Allow the test to run five times or more.
l In the Service Tests with Calibration screen, on the Tray
Check Data tab, click the Get Data button. Click the button
as needed to refresh the data in the histogram.
l Using the histogram data, for nozzle plate data subtract 5
steps to get a true representation of the data.
l Optimally, the results should be as close to zero as possible.
Results should be consistent.
l Replace the stepper motor, belt, or entire motor drive
assembly as needed.
12.4 Draining the Fluidics System

The software empties the fluidics system. This test will drain
the fluidics system.

l Disconnect the bulk fluid bottles and connect the tubing

harness.
¨ Connect the tubing harness connectors to the
corresponding bulk fluid connectors.
¨ The tubing harness connectors are labeled “1”
through “8.”
¨ Tubing harness connector #2 is a separate piece that
draws air, NOT FLUID.
§ Beginning from the left, the bulk fluid connectors are
#1 through #8.
Connector
Bulk Fluid
#2 (draws air)
Connector #1
Figure 33. Connecting the Tubing Harness

l Then select Test – Drain System XT from the menu, then
glow yellow.

l Lift the slide heater drawer.


l Move the nozzles to the back of the instrument to empty the
fluid into the tub.
l Empty the fluidics system.
l Move Dual Rinse to slide 1.
12.5 Empty Vacuum Trap

The software empties the vacuum trap. This test will empty the
vacuum trap, and is used if the instrument reports that the
vacuum trap is full.
l Then select Test – Empty Vacuum Trap XT from the menu,
then click the Run button.
glow yellow.

l Empty the vacuum trap.
12.6 Priming the Fluidics System

This test fills the tubing with liquid from the buffer bottles in the
AFM and stainer subassembly, and removes any air from the
lines, any time the fluidics system is serviced or after the
instrument has remained unused for an extended period.
l If any air is observed in the fluid lines.
¨ Test-Prime XT needs to be run only once to completely
remove all air from the system.
l Verify all bulk bottles are full with fluid.
l Then select “Test – Prime XT”, then click the Run button.
glow yellow.


l Move the nozzles to the back of the instrument.
l Refill the reservoirs.
l Turn each fluid valve to prime the lines.
l Refill the reservoir with the bulk fluids again.
l Finish priming the fluid paths to remove air from the lines.
12.7 Reservoir Fill

The software refills each of the bulk fluid reservoirs. Each
reservoir is filled separately with a button push in between.
l Then select Test – Reservoir Fill XT, then click the Run
button.
glow yellow.

You must then


l Fill the EZ Prep reservoir.
You must then



l Fill the LCS reservoir.
You must then


l Fill the Reaction Buffer reservoir.
You must then


l Fill the CC1 reservoir.
You must then


l Fill the CC2 reservoir.
You must then


l Fill the Optional reservoir.
You must then


12.8 Slide Drawer Test

The software tests movement of the slide drawer. This test is
used to confirm the function of the drawer sensors and lift air
cylinders.
l Then select Test – Slide Drawer XT from the menu, then
glow yellow.

You must then


l Lift the Slide Heater Drawer once the drawer is pushed in all
the way.
You must then


l Lower the Slide Heater Drawer.
12.9 Jet Drain Test

The software tests the Jet Drain nozzle. This test will turn on
the Jet Drain valve for a specific fluid.

The nozzle plate does not move and the slide drawer does not
lift for this test.
l Then select Test – Jet Drain (RB) XT or Test – Jet Drain
(SSC) XT from the menu, then click the Run button.
glow yellow.

You must then


l Dispense fluid from the Jet Drain and wait.
You can repeat the test by pressing the user button
12.10 Purge Tests

The software flushes new fluid through the fluidics system.
These tests are used to replace an existing bulk fluid on the
system with a new bulk fluid. Each bulk fluid position has its
own purge test, and there is also a purge test for all bulks.
l First remove the existing bulk fluid bottle from the system
and insert the new bulk fluid.
l Run the appropriate purge test.
l Then select Test – Purge All XT (or other appropriate purge
test) from the menu, then click the Run button.


glow yellow.

l Lift slide heater drawer.
l Move the nozzles to the back of the instrument to empty the
existing bulk fluid into the tub.
l Refill the reservoir with the new bulk fluid.
l Drain the fluid again to rinse the lines with the new bulk fluid.
l Refill the reservoir with the new bulk fluid again.
l Prime that fluid path to remove the air from the lines.
12.11 Select Tests

The software purges the selected fluid out of the Rinse nozzles.
This test is used when testing slide volumes of different fluids to
ensure the correct fluid has be purged into the Rinse nozzles
l Then select Test – Select EZ Prep XT (or other appropriate
Select test) from the menu, then click the Run button.
glow yellow.

l Lift the slide heater drawer.
l Move the nozzles to the back of the instrument.
l Refill the reservoirs.
l Purge the selected fluid into the Rinse nozzles.
l Move nozzle plate back to position 1.

12.12 Beeper Volume

The volume of the beeper can be adjusted using trim-pot R-15.
l Turn on the beeper from the test screen.
l Adjust the volume.
l Turn the beeper off.
12.13 Fuses
Remove the power cord before changing the fuse.
The fuses for the stainer subassembly and AFM are located on
the power block at the back of the staining unit.
l Use a screwdriver to pry the power block open from the top.
¨ The red fuse holder can then be pried out.
¨ Two fuses are needed.
¨ The holder accepts both 3AG style and European
(5x20 mm) style fuses.
§ For 100 or 115 volt systems use 6.3 amp fast-acting
fuses.
§ For 230 volt systems use 6.3 amp fast-acting fuses.
Troubleshooting Blown Fuses

If the main AC fuse on the stainer subassembly has blown,
install a new fuse and turn on the stainer subassembly. If the
fuse blows, replace the 24 VDC power supply.
12.14 Power Supplies, +24 Volt and +5 Volt

Two LEDs D1 (24 volts) and D52 (5 volts) indicate that power is
available to the microcontroller PCB. J1 receives +24 VDC
power. The +5 VDC power is generated on the microcontroller
PCB with a DC-DC converter.
Power supply voltages can be measured on the microcontroller
PCB using a digital voltmeter.
CAUTION: The stainer subassembly and the AFM must be

powered down before disconnecting or reconnecting ANY
connector or damage to the electronics will occur. When

powering down, wait a minimum of ten full seconds before

disconnecting or reconnecting any electrical plugs or
connectors.
l With test point TP-2 (Gnd) as negative, measure to TP-3

(+5 volt) and TP-5 (+24 volt).
¨ The voltages should be in the ranges specified below
Test Point Voltage
Range
TP-5 (+24 volts) 23.6 to
24.4
TP-3 (+5 volts3) 4.9 to 5.1
If the required voltages are not present:

If the 24 volt power is available, but the 5 volt power is not:
l Check that no external device is shorting the 5 V power by
unplugging inputs one at a time
l Watch for D52 to illuminate (indicating 5 VDC restored)
l One at a time, disconnect
¨ J2 (dispense)
¨ J3 (barcode beep)
¨ J4 (spare-usually unused)
¨ J20 (slide door)
¨ J25 (nozzle plate temperature)
¨ J26 (AFM)
l If unplugging one of these restores power, replace the
defective sensor.
l If the above does not work, replace the microcontroller PCB.
If 24 volt power is not available

l Verify AC power
l Check fuses
l Check J1 and associated wiring for corrosion, shorts, broken
or frayed wires

l Verify the connections on the power entry terminal block are

secure, and tighten nine center screws on terminal block
l Replace any defective components
l Replace the 24 volt power supply
12.15 Slide Tray Height and Parallelism

This process ensures the slide tray is at the proper height and
position after replacing or removing a slide tray.
NOTE: It is important to understand there are two versions of

slide trays; some versions of slide trays contains a clamp ring.
Trays with clamp rings will be approximately ¼ inch higher than
those without the clamp ring.
IMPORTANT NOTE: IT IS IMPORTANT TO ADJUST THE

POSTS TO THE CORRECT STARTING HEIGHT BEFORE
RAISING THE TRAY FOR THE FIRST TIME OR DAMAGE
COULD RESULT TO SLIDE TRAY OR NOZZLE PLATE.
l Level the instrument using the Level, 30 Min. Bubble

(1467100) on the nozzle plate while in the home position.
Ensure the bubble is entirely within the circle. Use the
Caster, Center Leveling (1972900) “Leveling Foot” to adjust.
l Prior to raising the drawer the first time, apply a thin layer of
grease (2496300) to each of the 3 kinematic mounts (as
shown below). Raise each post (as shown below). For trays
WITHOUT a clamp ring, the post should be raised so that
the nut is flush with the base and the post is 14-15 threads
above the nut. For trays WITH the clamp ring, the post
should be raised so that the nut is flush with the base and
the post is 6-7 threads above the nut.

Figure 34. Kinematic Mounts
Figure 35. Posts
12.16 Slide Tray Centering

This process ensures the slide tray is properly centered after
replacing or removing a slide tray.
l Place vortex mixer alignment tool (PN 2197000) in slide
position #20. With the drawer in the up position, turn on the

slide barcode reader test function in the service test I/O

screen.
l Ensure that the tool is positioned flat against the outside
slide posts on the heater base. Rotate nozzle plate until
barcode reader beam is on and parallel to the graduations of
the slide.
l Note beam position relative to the nearest graduation on the
slide.
l Move the tool to position 11 and repeat steps 2 and 3.
l Move the tool to position 3 and repeat steps 2 and 3.
l Determine the mean position on the tool for all three
recorded beam positions, and move the tool back to
position 20.
l Loosen the four socket head cap screws on the front left lift
cylinder arm just enough to allow planer movement of the
cylinder and drawer positioning ball (minimize vertical
movement and sag). See Figure below.
Figure 36. Lift Cylinder Arm
l Adjust arm position to align barcode reader to the mean

graduation position on slide.
l Re-tighten socket head cap screws on air cylinder arm.

l Move the tool to position 11 and repeat steps 7-9 for the left
rear lift cylinder arm.
l Double check centering by moving the tool to slide position
28 for Benchmark XT and DISCOVERY XT instruments or
position 1 for a Benchmark LT instrument and recording
beam position. Beam position should be identical to beam
position for slide position 11 and 20. If not, repeat step 10.
12.17 Bottle Inlet Check Valve Test

This test verifies that the check valve closes with pressure with
no leakage.
l Remove bulk bottles from the AFM.
l With compressor on, install a female quick disconnect fitting
at the EZ Prep input and check for leakage.
¨ There should not be any fluid leakage from the fitting.
¨ Repeat for 2x SSC, Reaction Buffer, CC1, CC2 and
Option.
l Install a male quick disconnect fitting at the input to the
coverslip.
¨ There should not be any fluid leakage as well.
12.18 Reagent Carousel and Nozzle Plate Belt

Inspection
To check reagent and nozzle plate belts for proper installation
and for wear and tear.
l With motors disabled, rotate reagent carousel then nozzle
plate.
l Inspect for belt teeth to pulley alignment and for signs of
wear.
12.19 Nozzle Plate Tubing Inspection

This inspection verifies that all tubing is lying flat on the nozzle
plate and routed to the left, thus eliminating the possibility of
tubing catching on the underside of the arch plate or wearing on
the flex cable.

l Inspect tubing on nozzle plate to verify that tubing is lying flat

as possible on nozzle plate.
l With the nozzle plate in the Home position, verify all tubing is
routed to the left as shown below.
¨ Adjust if necessary.
Figure 37. Proper Routing of Tubing
12.20 Cooling and Exhaust Fan Test

This process verifies functionality and proper air flow direction
for the cooling (power supply) and exhaust (reaction area) fans.
l In output of BASIC I/O CONTROL ensure that “Fan” and
“Cooling Fan” are on.
¨ If not turn them on.
l With fans turned on, verify function and flow by putting hand
in front of fan.
¨ Flow direction should be out and away from rear of
instrument.
12.21 Adjustment of the Slide Tray Up Sensor

This process verifies adjustment of the Slide Tray Up sensor.

l Ensure the slide tray is fully up and seated before adjusting.

l Adjust the UP sensor so that the output reads “SLIDE TRAY
UP”. The sensor shall be approximately 1/8” (or 3 mm) from
the lift plate and approximately parallel to the plate.
12.22 Adjustment of the Slide Tray In Sensor

This process verifies adjustment of the Slide Tray In sensor.
l The slide drawer must be down and the drawer must be all
the way in. With the drawer fully closed, move the slide
drawer forward on the rails so the drawer is still closed but
the lift plate is all the way forward towards the front of the
instrument.
l Pull the sensor all the way out so the sensor does not
recognize the drawer. Then slowly adjust the sensor until the
output just reads “IN”. The sensor must be approximately
parallel to the edge of the plate.
12.23 Slide Heater Test

The software tests independent heater performance. This test
is used to confirm the function of the slide heaters at 40°C,
turning the heaters on sequentially. This test can also be used
to resolve slide heater errors such as 12-63: Run stopped due
to heater(s) abnormally hot.
l Select "Test – Slide Heaters XT" from the menu, then click
the Run button.
glow yellow.
¨ The software will heat each slide heater to 40°C,
turning on each heater sequentially.
l Click on the TEMPERATURE CHART tab

l Click on the START button.
l Allow the test run for a minimum of 450 seconds and a
maximum of 500 seconds.
l Expand the view for each of the slide heaters and verify that:

¨ Each slide position is ramping up individually

¨ Each slide position ramps up to 40 degrees and levels off
l Ensure that slide position #1 begins at 0 seconds and that all
slide positions colors are represented on the chart. If any
slide position colors do not appear, make sure to zoom in to
determine if multiple slide positions are overlapping.
l To expand any portion of the graph, click and hold (with the
mouse) on the upper left and drag to the lower right of that
portion you wish to expand.
l To return to the original view of the graph, click and hold
(with the mouse) on the lower right and drag to the upper
left.
l Once the problematic slide position(s) has been identified,
replace the associated Heater Driver PCB.
NOTE: In the figures below, slide positions are ramped up

individually and reach and hold a setpoint of 40 C.
Figure 38. Temperature Chart showing properly functioning slide

positions

Figure 39. Temperature Chart showing slide positions 8 and 9 are

problematic
Figure 40. Detail of slide positions 8 and 9

13.0 Assembly Removal / Installation

This chapter describes procedures to remove the major
subassemblies to gain service access to various components.
Reassembly is typically the exact reverse of the removal steps.
During reassembly, discard old patch screws and replace with
new patch screws whenever possible.
Take precautions to avoid ESD. Failure to do so may result in
damage to electronic components such as PCBs.
Prior to removal of subassemblies, power down the
instrument and unplug it from the wall circuit.
13.1 AFM Drawer

A) Power down the instrument and unplug it from the wall
circuit.
B) Remove the fluidic drawer cover (1942600).
C) Drain and purge the fluidics reservoir and depressurize the
system.
D) Extend the drawer until it latches.
E) Disconnect the cables and tubing that are routed through the
Igus chain.
F) Lift the drawer glide extension lock levers and pull the
drawer out enough to gain access to the Igus chain screws.
G) Remove the screws that attach the Igus chain to the drawer.
H) Pull the drawer out completely, disengaging the inner drawer
rails from the outer ones.
NOTE: When replacing screws in slide drawer rail,
apply threadlocker to threads (PN 1161700 or equivalent).
13.2 Bottle Fittings

Mating quick disconnect fittings are attached to the bulk bottles
and to the bulk bottle liner. The quick disconnects are a 1/8
NPT Thread. To replace a fitting, unthread the old one and
thread in a new one, noting depth and orientation.

13.3 Compressor
l Power down the instrument and unplug it from the wall
circuit.
l Remove the painted covers to gain access.
l The compressor is mounted to a bracket and the bracket is
mounted to the instrument frame.
l Remove the compressor from the bracket.
l Disconnect the cable and ground wire.
l When re-installing the compressor:
l Use threadlocking compound on the mounting screws to
eliminate the possibility of their vibrating loose.
l Route high pressure tubing using cable ties (PN 1114704) to
secure tubing to frame as shown in Figure 41. Cut off
excess length of cable ties.
l Install cable tie pad (PN 1201300) on compressor mount and
use cable tie (PN 1114700) to secure compressor wires as
shown in Figure 42.
Figure 41. Cable Ties

Figure 42. Cable Tie Pad
13.4 Drive Belt Replacement

The procedure for replacing belts is different for the carousel
and nozzle plate. This section outlines the steps needed to
replace belts, but due to the amount of disassembly required,
this should not be undertaken except by Ventana trained
personnel.
13.4.1 Reagent Carousel Belt Replacement

Follow the steps below to replace the reagent carousel belt.
circuit.
B) Remove the reagent carousel drive assembly.
C) The drive belt, motor and carousel drive sprocket will now be
clearly visible.
D) Remove the spring near the motor, using needle nose pliers.
E) Unhook the spring from the post that holds it.
¨ This spring tensions the belt by letting the motor move
back and forth
F) Remove the motor’s three screws.
¨ The belt can now be replaced
¨ Note the guide posts between which the belt passes
G) First fit the belt around the carousel drive sprocket, then
between the guide posts.

H) Fit the belt around the motor’s drive sprocket.

I) Pinch a loop of the belt to hold tension around the sprocket
while remounting the motor.
J) Pay attention to the direction that the motor wiring exits from
the motor.
K) Mount the motor so that the wiring points toward the rear of
the instrument.
L) Test for free movement of the belt and sprockets.
¨ The belt should not bind against the guide posts
M) Replace the spring and test for free movement once again.
N) Re-assemble the unit by the reversing the order of
disassembly.
¨ Remount the assembly to the bottom of the cover (five
screws)
¨ Reconnect the stepper motor (J18)
¨ Remount the reagent drive carousel (with part number
stamp facing down)
O) Retest homing and barcode reading.
13.4.2 Nozzle Plate Belt Replacement

Replacement of the nozzle plate belt requires removal of
several components for access. Follow the procedure below
circuit.
B) Remove the upper chassis.
C) Remove the screw at the center of the mixer cover.
D) Remove the six screws that hold the mixer plate on.
¨ Leave the tubing connected
¨ Disconnect the wiring from the quick disconnect
¨ Remove the plate
E) Remove the four screws from the nozzle plate.
¨ Before removing the carousel, remove the rinse mix
needles, jet drain, and slide oiler
¨ Remove the nozzle plate

¨ At this point, the motor, carousel drive sprocket and

related parts are exposed
F) Disconnect the motor from J19 on the microcontroller PCB.
¨ Turn the module on its side
¨ Loosen the four screws that hold the motor in place on
the bottom of the chassis
¨ Move the motor forward to release tension on the belt,
then remove the old belt
¨ Since the workspace is cramped, take special care to
thread the belt properly around the guides
¨ Also verify that the belt is properly engaged with the
motor sprocket before tightening the motor mounting
screws
G) When reassembling the unit, pay special attention to proper
orientation of the carousel drive sprocket relative to the
carousel.
13.5 In-line 250-micron Bottle Filter

The In-line bulk bottle fitting is a 1/8 NPT thread on the entry
end and ¼” HB on the exit end. To replace it, disconnect the
tubing, unthread the filter, (with sealant applied to the threads)
thread in the new filter, and reconnect the tube.
13.6 In-line 65-micron and 25-micron Filters

The 65-micron filters are installed in-line for EZ Prep, LCS,
SSC, Reaction Buffer, and Option. The 25-micron filters are
installed in-line for CC1 and CC2.
The In-line filters are 1/8” HB. To replace one, disconnect the
tubing and reconnect the tubing, noting the flow direction.
13.7 Microcontroller PCB, 24V Power Supply,

and Associated Electronics Boards
To remove the Microcontroller PCB and associated electronics
boards:

A) If the Microcontroller PCB is being replaced, run the test

software and record the volume adjust valve timing in
milliseconds.
B) Power down the instrument and unplug it from the wall
circuit.
C) Remove the front stain module cover.
D) Remove the left rear stain module cover.
¨ This will expose the quarter-turn fastener on the painted
electrical cover.
E) Unscrew the quarter-turn fastener and remove the cover.
¨ At this point, most of the boards are accessible.
F) To access the 24V power supply and the remainder of the
boards, remove the keypad mount panel by removing the
two flat head mounting screws underneath the panel.
¨ This will fully expose the PCB mounting plate and all
boards mounted to it.
G) Unplug all connections and remove the four M5 SHCS
holding the PCB mounting plate.
H) Remove the desired board or power supply by removing its
appropriate mounting SHCS.
13.7.1 Microcontroller PCB with Programmed

Microcontroller IC
A) Install the Programmed Microcontroller IC into the SIMM
socket on the Microcontroller PCB.
B) Set the Address Switch to match the setting on the board
that was replaced.
C) Start up the PC and the stainer subassembly.
D) Verify a “CONNECT” light on the PC screen.
E) Inspect LEDs:
· Power Supplies: D1 (24 Volts) and D52 (5 Volts) should
be lit.
· D19 (Heartbeat) on the MPU board should be blinking.
· D21 (RXD) and D22 (TXD) on the MPU board should be
blinking.

· Microcontroller LEDs D33 and D34 (LTRQ); D35 and D36

(DIS); D39 and D40 (CW) should be lit.
· D37 and D38 (STEP) should be extinguished.
F) If any of the LEDs are not correct, recheck all connectors.
13.7.2 Microcontroller IC
The staining module processor is mounted in the 72 pin SIMM
(single inline memory module) socket located on the
Microcontroller PC board (U15).
To install the Microcontroller IC:
A) Turn off the instrument power switch.
B) Perform the steps that follow while wearing a static wrist
strap connected to the chassis.
C) The processor SIMM socket has metal locking clips located
at the base of the socket at each end.
D) Push the bottom clip down and the top clip up so that the
processor board may be rotated out of the socket.
E) The new processor must be inserted at about a 45 degree
angle into the socket.
F) Push the processor board so that the edge fingers are
inserted into the connector pins of the socket.
G) Then rotate the board up until it is perpendicular to the
microcontroller board and the locking clips snap into place.
H) Reapply power and reenter the instrument serial number and
volume adjust setting (see Section 13.7.1).
13.7.3 Programming the Microcontroller IC

In order to program a new microcontroller IC, the NexFact
software is needed. This section covers the downloading of the
operating code, changing of the instrument personality, and
inputting of the serial number. BenchMark XT IHC, ISH,
IHC/ISH, and DISCOVERY XT all share the same operating
code. When servicing any of these instrument configurations,
the BenchMarkXTStainer code must be downloaded.
Personalities include IHC, ISH, IHC/ISH, and Discovery. The
default personality will always be IHC. For example, if the
instrument being serviced is a BenchMark XT IHC, the “assign

personality” section need not be completed, as the personality

defaulted to IHC when the operating code was downloaded.
For any other configuration of BenchMark, the “assign
personality” section must be completed. For example, when
servicing a DISCOVERY XT instrument, the BenchMark XT
operating code must be downloaded, and the personality
changed to Discovery.
13.7.3.1 Downloading Operating Code

To download operating code:
A) Turn the instrument off.
B) Turn off any additional instruments that are connected to the
system.
C) Install the new microcontroller IC in the XT microcontroller
PCB.
D) On the microcontroller PCB, remove the jumper from RUN
(JU2) and place it on PROG (JU1).
E) Ensure the instrument is connected to COM2.
F) Turn the instrument on.
G) Copy the NexFact program from a USB drive to the
Windows desktop.
H) Run the NexFact software (NexES Remote Factory System
Factory Install).
I) Enter generated password (refer to Section 8.3 for for an
example of calculating the password).
J) Select <instrument type> (for Discovery XT, choose
Benchmark XT)
K) Press the following buttons in this order:
l Wake UP
l Clear Remote Memory
l Download Program
l Download Application Program
L) Wait for the download to complete.
M) Turn instrument OFF
N) Move jumper from PROG (JU1) to RUN (JU2)
O) Turn instrument ON. It should beep once.

P) Delete the NexFact software from the desktop
Figure 43. NexFact Main Screen
Q) Choose BenchMark XTStainer as the instrument type.

R) There is a row of buttons down the left side; press each one
in succession and observe the messages in the black text
window for success or failure.
S) First press Wake Up Remote, followed by Clear Remote
Memory, Download Loader Program, Download Application
Program, then Exit.
T) Power down the XT instrument.
U) Remove the jumper from PROG (JU1) and place it on
RUN (JU2).
V) Power up the XT instrument.
W)You may now power up any additional modules that were
turned off previously.
X) Run the NexES Host software.
Y) Delete the NexFact program from the Windows desktop and
empty the Recycle bin.

Z) If the instrument being serviced is an IHC, the “assign

personality” section need not be completed, as the
personality defaulted to IHC; otherwise, continue.
13.7.3.2 Assigning Instrument Personality

To assign instrument personality:
A) Enable the passwords in the NexES software.
B) Click on Setup.
· Enter the password if necessary.
· Click on Setup Host.
· Click on the Security tab at the top.
o If Enabled is set to “No,” double click on “No”.
o Enabled should now say “Yes”.
C) Click on Save and then Close.
D) Click on Setup.
E) Click on Setup Staining Modules.
F) Under Type of Instrument, select the appropriate personality
for the instrument being serviced.
· A code will be generated onscreen that must be
communicated to the regional support contact.
o The regional support contact will issue a return
code, and once you enter the code, the instrument
will change to the personality selected.
G) Verify the correct personality in the main screen.
13.7.3.3 Inputting the Serial Number

To input the instrument serial number:
A) Click on Tests.
· Enter the password if necessary.
B) Click on Service Tests with Calibration.
C) Click on Set.
D) Input the instrument serial number.
· A code will be generated onscreen that must be
communicated to the regional support contact.

o The regional support contact will issue a return

code.
E) Enter the return code.
F) Click on Authorize.
G) Verify that the serial number is correct.
13.8 Nozzle Plate

circuit.
B) Remove the slide drawer.
C) On the nozzle plate disconnect the following.
¨ Unplug the red (2xSSC) tube from the side of the
manifold.
¨ Unplug the blue (Reaction Buffer) tube from the side of
the manifold.
¨ Disconnect the connector from the rear of the PC board.
¨ Unplug the yellow (LCS) tube from the fitting.
¨ Unplug the orange (CC2) tube from the top front of the
CC2 liquid valve.
¨ Unplug the green (CC1) tube from the top front of the
CC1 liquid valve.
¨ Unplug the clear (EZ Prep) tube from the top front of the
EZ Prep liquid valve.
¨ Unplug the white (Air) tube from the side of the manifold.
D) Remove the nozzle plate stepper motor (see Section 13.19).
E) Remove the four #3 hex screws securing the nozzle plate
pulley to the nozzle plate bearing.
F) Remove the three #4 hex screws securing the nozzle plate
bearing to the center support.
G) Supporting the bottom center of the nozzle plate, lift the plate
up slightly and turn the nozzle plate bearing tabs clockwise
to disengage the nozzle plate assembly from the center
support.
H) After disengaging, slowly lower the nozzle plate, being
careful of the cable and tubes.

I) Remove the cable and tubes from the center of the plate
bearing.
J) Remove the nozzle plate pulley.
K) Lift and remove the nozzle plate assembly.
L) To remove the nozzle plate power/communications cable,
cut the tie wraps holding the cable to the inner wall of the
arm post in the center of the instrument.
M) Unplug the power/communications cable from the valve
connector PCB assembly on the nozzle plate.
N) Unscrew the two M2 SHCS holding the slip cable PCB
assembly at the top of the arm post.
O) Pull the PCB and the power/communications cable up until
the PCB clears the top of the arm post.
P) Disconnect the ribbon cable at the top of the instrument and
remove it.
Q) Disconnect the power/communications cable.
R) Set the PCB aside and feed the large connector at the
nozzle plate side of the cable through the bottom of arm post
using your fingers, from underneath the nozzle plate,
through the hole in the middle of the nozzle plate.
S) Once the connector is started, the cable can be pulled
straight from the top of the instrument.
13.9 Nozzle Plate Stepper Motor

circuit.
B) Remove the wire ties securing the wires to the motor base
and unplug the connector.
C) Remove the two #4 hex screws located next to the motor.
D) Remove the tensioning springs.
E) Remove the belt from the motor sprocket.
F) Remove the stepper motor.
13.10 Power Inlet Module

circuit.

B) Remove lower back panel (1933500) from the instrument.

C) Disconnect the cables (reference schematic 1908200).
D) Remove the mounting screws.
E) Remove the power inlet module.
13.11 Reagent Barcode Reader

To remove the reagent barcode reader:
B) Remove the upper back panel.
C) Unplug the barcode cable from J4 of the Port Expander
PCB.
D) Use a 3mm hex driver to remove the two mounting screws
that hold the reagent barcode reader to the rear back panel.
NOTE: Ensure the current revision of the laser warning label is
affixed to the right of the reagent barcode reader slot.
13.12 Slide Barcode Reader

To remove the reagent barcode reader:
B) Remove the upper back panel.
C) Unplug the barcode cable from J19 of the Valve Connector
PCB.
D) Use a 3mm hex driver to remove the two mounting screws
that hold the reagent barcode reader to the rear back panel.
NOTE: Ensure the current revision of the laser warning label is
affixed to the right of the reagent barcode reader slot.
13.13 Reagent Stepper Motor

circuit.
B) Remove the wire ties securing the wires to the motor base
and support and unplug the connector.
C) Remove the three # 4 hex screws securing the motor
bracket to the upper support.

¨ While loosening the screws remove the two tensioning

springs
¨ Also, support the motor when removing the last screw
D) Remove the belt from the motor sprocket.
E) Remove the motor assembly.
13.14 Reservoir Float Switches

circuit.
B) Remove the fluidic drawer cover.
C) Depressurize the reservoir assembly.
D) Slide the fluidics drawer out to make the reservoir
accessible.
E) Disconnect the tubing and float switch cables from the
affected side.
F) Remove the reservoir cover screws.
G) Use a pin pusher to remove the connector from the float
switch.
H) Unthread the float switch from the reservoir cover.
NOTE: When reassembling the Fluidics Reservoir Assembly,
please observe torque specifications and figures below.
Torque
PN Part Description Specs Places Tool PN Tool Description
Assy, Float Sensor,
1151300 AFM 10 in-lbs 8 1775200 Assy; Tool; Float Sensor Wrench
Check Valve, 1/4 HB x
1856900 1/8 NPT 8-10 in-lbs 7 1982400 Tool, Wrench, Check Valve 304-314
Screw, Metric, SHCS,
1796332 M4 x 25 10 in-lbs 20 NA 3 mm Hex bit
1164701 Fitting, 10-32 Plug 2.5 in-lbs 1 1561000 Tool, Plastic Fitting Socket, 1/4"
10-32 Fitting; Swivel
1914402 Elbow; 1/8 HB 2.5 in-lbs 8 1560900 Tool, Plastic Fitting Socket, 5/16"
1164300 Fitting, 10-32 x 1/8 HB 2.5 in-lbs 8 1561000 Tool, Plastic Fitting Socket, 1/4"
Fitting, 10-32 x 3/32
1164502 HB 90 Deg, Nylon 2-3.5 in-lbs 1 1561000 Tool, Plastic Fitting Socket, 1/4"

Figure 44. Float Sensor
Figure 45. Check Valve

Figure 46. Torque pattern for screws
Figure 47. Swivel Elbows
Figure 48. 90° Fittings

Figure 49. 90° Fittings Can Be Oriented to Within 30° of Direction

Shown
13.15 Roof Substructure Tubes and Cable

The roof substructure tubes and cables provide fluid, air, and
communications between the nozzle plate and the rest of the
instrument.
There are three cables in the roof substructure that provide
power and communications between the nozzle plate and
electronics panel:
· 1967800: Valve Connector to Slip Cable PCB Cable
Assembly
· 1959600: 18-Inch Flat Flex Cable (i.e., Slip Cable)
· 1967900: Slip Cable PCB to Electronics Chassis Cable
Assembly
13.15.1 Tubes
Follow the steps below to replace one or more tubes.

A) Remove the front cover and top cover.

B) Drain/purge all fluids and depressurize the system.
C) Cut tie wraps securing the tubing to roof substructure.
D) Remove reagent carousel tabbed cover, by removing the
three screws holding it together.
E) Remove the reagent carousel access plate by unscrewing
the screws at the top of the reagent carousel post, and the
two screws clamping the sides of the access plate to the
reagent carousel lower plate.
F) Remove both drip shield parts by loosening their mounting
screws a few turns and sliding the shields out the front of the
instrument.
G) Remove tube to be replaced from fitting which joins the two
sections of the tube on the roof structure (leave fitting in end
of 60” tube which goes through the opening in the back
panel).
NOTE: If a quick disconnect fitting is present on any of
these seven tubes, cut the tubing at each end of the quick
disconnect fitting and replace it with a pass-through fitting.
Use a pass-through fitting that matches the tube diameter.
H) Obtain/Use a fitting which matches the diameter/size of the
tube to be replaced (this fitting will be used temporarily to
thread the new tube through the center post and down to the
nozzle plate).
I) Connect one side of the fitting to the tube to be replaced
which is extending through the top of the center post and out
the back of the acrylic ring.
J) Cut desired length of tube and connect one end to other side
of fitting.
K) Lightly coat new tube with medical grade silicone oil (be
careful not to allow tube to get dirty).
L) Connect end of new tube to fitting which is still connected to
the 60” length of tube coming from the opening in the back
panel.
M) Disconnect other end of tube from its respective valve
manifold (this is tube being replaced which is running down
the center post).

N) Once the tube is disconnected from the manifold, gently pull

the tube so that the new tube is threaded down the center
post and the temporary fitting can be reached.
O) Remove the old tube and temporary fitting and connect end
of new tube to the fitting on the manifold. (The old tube can
be discarded and the fitting can be reused).
P) Repeat for other tubes to be replaced.
Q) Ensure all tubing is routed to the left when the nozzle plate is
in the Home position as shown below. This is important to
avoid wear of tubing and flex cable.
Figure 50. Proper Routing of Tubing
13.15.2 Valve Connector to Slip Cable PCB Cable Assembly

Follow the steps below to replace the Valve Connector to Slip
Cable PCB cable assembly.
outlet.
B) Remove the front cover and top cover.
C) Drain/purge all fluids and depressurize the system.
D) Disconnect all bulk fluid connections on top of roof and cut
tie wraps securing the tubing.

E) Remove reagent carousel tabbed cover, by removing the

three screws holding it together.
F) Remove the reagent carousel access plate by unscrewing
the screws at the top of the reagent carousel post, and the
two screws clamping the sides of the access plate to the
reagent carousel lower plate.
G) Remove both drip shield parts by loosening their mounting
screws a few turns and sliding the shields out the front of the
instrument.
H) Pull slide drawer out completely.
I) Reach under nozzle plate to remove all fluid tubing from the
center post.
J) Cut the two tie wraps holding the cable to inner wall of the
arm post in the center of the instrument; one at the top of the
center post and one just below the reagent belt/pulley.
(See figure below.)
Figure 51. Location of Tie Wraps
K) Remove the valve connector PCB assembly from the nozzle

plate by removing the two screws securing it.
L) Unplug the power/communications cable from the valve
connector PCB assembly.
M) Unscrew the two screws holding the slip cable PCB
assembly at the top of the center post.

N) Pull the slip cable PCB and the power/communications cable

up until the PCB clears the top of the center post.
O) Disconnect the ribbon cable from the slip cable PCB and set
aside it.
P) Disconnect the power/communications cable from the slip
cable PCB; set the PCB aside.
Q) Feed the large connector at the nozzle plate side of the
cable through the bottom opening of the center post and
down through the hole in the center of the nozzle plate.
R) Begin to feed the small connector of the
power/communications cable down the center post.
S) The cable can be pulled straight down the center post from
underneath the nozzle plate, through the hole in the middle
of the nozzle plate and discarded.
T) Feed the small connector of the new power/communications
cable from underneath the nozzle plate through the hole in
the center of the nozzle plate and through the center post.
U) Continue to feed the cable through the center post until the
small connector clears the top of the center post.
V) Secure the cable (loosely) to the inner wall of the center post
with tie wraps in two places; one at the top of the center post
and one just below the reagent belt/pulley. DO NOT tighten
tie wraps. (See figure above.)
W)Feed all fluid tubing back up the center post from under the
nozzle plate; medical grade silicone oil can be used to lightly
coat tubes before feeding through the center post.
X) Route fluid tubing from center post through cutout in post
and through cutout in acrylic ring on the roof substructure.
(The white air tube is routed out the top of the center post
and over the top of the acrylic ring).
Y) Match tubes by color and secure by reattaching to the
fittings.
Z) Ensure that all fluid tubing is routed towards the left with the
nozzle plate in home position.
AA) Straighten all tubing and use cable tie (PN 1114704) to
secure tubing by creating large, loose loop around tubing
and through metal mounts on roof substructure.

BB) Connect small connector of the power/communications

cable down to the slip cable PCB
CC) Reconnect ribbon cable to slip cable PCB
DD) Reconnect the slip cable PCB to the acrylic ring and
adjust the power/communications cable so that it is not
extending past the top of the center post.
EE) Tighten the two cable ties securing
power/communications cable to the center post and trim
excess.
FF) Feed the large connector of the power/communications
cable through the center of the nozzle plate and up through
the opening of the center post at the nozzle plate.
GG) Reconnect the large connector to the valve connector
PCB and reattach the valve connector PCB to the nozzle
plate.
HH) Rotate the nozzle plate to ensure that all tubing and
cables move freely with no occlusion.
II) Replace all covers and panels
JJ) Plug instrument into wall outlet and turn power on
KK) Run prime test several times to remove air from fluid
tubing.
13.15.3 Slip Cable

Follow the steps below to replace the slip cable.
outlet.
B) Remove the top cover
C) Unplug power/communication cable from slip cable PCB.
D) Unplug Slip Cable from slip cable PCB.
E) Remove screws holding outer ribbon cable clamp onto
acrylic ring
F) Rotate nozzle plate so that screws for ribbon spring clamp
can be reached through slit in acrylic ring.
G) Remove ribbon spring clamp.
H) Remove Slip Cable and discard
I) Replace Slip Cable using figures below

ITEM QTY PART DESCRIPTION

1 2 SCREW, METRIC, SOCKET FLAT HEAD, M3 x 8, PREFERRED
2 4 SCREW, METRIC, SHCS, M2 X 5, PREFERRED
3 2 WASHER, FLAT, M2
4 1 CLAMP, OUTER, RIBBON CABLE
5 2 ASSEMBLY, SLIP CABLE PCB
6 1 CABLE; FLAT FLEX; 18"
7 1 SPRING CLAMP, RIBBON
Figure 52. Flex Cable Installation (Slip Cable)

Figure 53. Flex Cable Routing
Figure 54. Flex Cable Installed
J) Reattach all clamps and power/communication cable to slip

cable PCB
K) Ensure that slip cable moves freely and does not excessively
rub on tubing.
L) Replace top cover
M) Plug instrument into wall outlet and turn power on.

13.16 Lift Cylinder

A) Remove each Air Cylinder Mounting Bracket complete with
Air Cylinder assembly.
B) Remove old Air Cylinders from air cylinder mounting
brackets.
C) Thread the 1/8 NPT restrictors (2199200) into the top ports
of the new air cylinders (2199100) using Teflon tape to help
create a seal between the threads. Ensure Teflon tape does
not block or impede restrictor orifice.
D) Tighten until the top of the restrictor is about 0.1” from the
top of the air cylinder
E) Install the 1/8” NPT 1/8” HB fitting (1186400) into the lower
port using Teflon tape.
· Do not over tighten as fitting may rub on air cylinder
shaft internally.
· Be sure to align fitting to mate with air supply tube in the
proper orientation.
F) Install new air cylinder assemblies into the air cylinder
mounting brackets reusing the large clamping washers, used
between air cylinder mounting nut and air cylinder mounting
bracket, from the old air cylinder assemblies.
G) Slide Self-Centering Ball Thrust Washer (2181700) on to air
cylinder shaft. Then slide on new lift washer (2205200) from
upgrade kit. Be sure round edges or unmarked washer
surface is facing toward the ball thrust washer.
H) With lift washers in place, thread two 1/4-28 jam nuts
(1290812) onto threaded end of air cylinder rod all the way
up to the top.
I) Back nuts off 1/2 turn then tighten jam nuts against each
other to 30 in-lbs. DO NOT USE LOCTITE.
J) Reattach each Air Cylinder Mounting Bracket and Air
Cylinder assembly with its four mounting screws.
K) Reconnect air supply tubing to each air cylinder fitting.

Restrictor
Verify that tubing

does not contact
slide drawer front
cover
Mounting Air Cylinder

screws (qty: 4) Mounting Bracket
Figure 55. Lift Cylinder
Self-Centering Ball
Thrust Washer
(2181700)
Lift Washer
(2205200)
Figure 56. Lift Cylinder and Washers

13.17 Slide Drawer

A) Turn instrument power off and unplug power cord to
instrument.
B) Remove front cover, left and right rear covers, reagent
carousel cover, reagent carousel access plate, condensation
shield and both drip shields (removing shim and jet drain
cover).
C) Pull out the slide drawer and drain as much fluid as possible
from the tub.
D) From underneath the slide tray, disconnect power cable and
loosen screws on data cable and remove.
E) Remove shoulder screw from the Igus chain mount on the
underside of the slide tray.
NOTE: Ensure the pivoting end link of the Igus chain is
affixed to the slide tray and the non-pivoting end link is
affixed to the chassis.
F) Disconnect waste tubing from Igus chain to the tub ensuring
that no fluid leaks onto the floor or the instrument.
G) Remove slide tray from instrument.
H) Install a new slide tray into slide drawer.
I) Connect Igus chain using new shoulder screw and 242
Loctite (or equivalent).
J) Connect power and data cables and tighten screws on data
cable connector.
K) Connect waste tubing from Igus chain to the fitting on slide
tray.
L) The following tests must be performed whenever a slide tray
is replaced:
· Slide Tray Height and Parallelism per Section 12.15
· Slide Tray Centering per Section 12.16
· Adjustment of the Slide Tray Up Sensor per Section 12.21
·
· Adjustment of the Slide Tray In Sensor per Section 0
· Verify Slide Barcode Read Alignment per Section 10.6

· Vortex Mixer Height per Section 10.10.1

· Using the output in BASIC I/O CONTROL, turn on
position 15.
l Adjust vortex mixer outer nozzle height using the adjustment
screw. Turn the adjustment screw clockwise or counter
clockwise to raise or lower the outer nozzle, such that both
metal orifice fittings pass through the tool without touching.
· Vortex Mixer Alignment per Section 

· Verify Nozzle Plate Homing Alignment per Section 10.4
· Verify Instrument Level per Section 10.12
13.18 Slide Heater Assembly

A) Turn instrument power off and unplug power cord to
instrument.
B) Remove three screws from the heater assembly using
a 3 mm hex wrench.
CAUTION: Keep screws and washers from falling onto the
slide heater PCB, which is located below the slide holder.
C) Unplug the heater assembly from the slide heater PCB.
D) Discard the heater assembly including O-ring, hex screws,
and washers.
E) Using alcohol wipes, clean the mounting surface, the
underside of the new heater assembly, and the new O-ring.

F) Install the O-ring in the groove on the underside of the

heater assembly. Be careful not to roll or twist the O-ring
when installing it. The O-ring should lay flat in the groove.
G) Verify that the mounting surface is clean and dry.
H) Plug the heater assembly connector into the slide heater
PCB.
I) Ensure the O-ring is still in the groove.
J) Hold the heater assembly in place and finger-tighten three
new hex screws and washers. Using a calibrated torque
driver, tighten the screws to 12 in-lbs.
13.19 Slide Heater PCB

When replacing a failed Slide Heater PCB, it is recommended
that all slide heater assemblies in that quadrant (including the
H-seal O-rings) be discarded to avoid another PCB failure.
Older configurations do not include a canopy between the slide
tray and PCB. When upgrading to the new configuration with
the canopy, the entire quadrant should be completely replaced.
A) Power down the instrument and unplug it from the wall.
B) Pull the slide drawer all the way out.
C) Remove all the slide heater assemblies from the quadrant
containing the affected PCB (see Section 13.18).
K) Invert the slide drawer to access the components underneath.
L) Remove the PCB Cover using a 2.5 mm hex driver to
remove and retain six M3 SHCS.
NOTE: During replacement, finger-tighten the hex screws to
avoid cross-threading, and then tighten to 5 in-lbs using a
calibrated torque driver.
M) Unplug all power and communication cables from the PCB.
N) Remove the 5 mm hex standoffs using a 5 mm socket driver
or 5 mm wrench.
O) Remove the PCB. Discard spacers and damaged PCB.
NOTE: The following additional steps are only required for

performing an upgrade. If no upgrade is required, replacement

is the reverse process of the steps above. For an upgrade, the

entire quadrant must be completely replaced with new parts.
P) Install socket set screws and tighten approximately 12 turns

to a height of 1/2 inch (~13 mm) using a 1.5 mm hex tool.
Do not over-tighten or the plastic tub may be damaged.
Q) Slide the sealing washers over the socket set screws.
R) Install the canopy and nylon spacers over the set screws.
S) Replace the PCB, cover, and heater assemblies according
to the removal steps above.
PCB Cover
PCB
Canopy
Figure 57. Inverted View of PCB Cover, PCB, and Canopy
13.20 Waste Sensor

There are two types of waste sensors. The typical configuration
has a gray cap and detects approximately 60% full. The other
configuration has a green cap and detects approximately 10%
full, because Dual Color ISH assays produce more waste.
Always replace with the same type, unless intentionally
changing types.
Replace the waste sensor:

A) Power down and unplug the instrument from AC power.
B) Remove waste carboy(s) from waste cabinet, allowing
residual waste to drain into carboy before withdrawing
completely. Have absorbent material on-hand to clean up
any spills.

C) Remove the four screws that hold the rear inside panel of
the waste cabinet to the instrument chassis.
D) Guide panel away from rear of instrument, working it past
the adjacent side-panel screws. Tip panel top forward while
easing the waste tubing through the black rubber grommet.
E) Disconnect sensor wire at the quick disconnect and remove
from grommet. Keep the tubing connected to the old cap to
prevent the panel from falling free.
F) Slide connector of the new waste sensor cable through the
grommet alongside the waste tubing.
G) Connect the new sensor cable to either of the pre-existing
instrument-side female connectors available.
H) Gently pull on waste tubing as the rear panel is maneuvered
back into position, ensuring the panel rests flat against the
chassis frame, and that the tubing is not curled or kinked
behind it.
I) Reinstall the four screws.
J) Disconnect the tubing (x3) from the old waste cap.
K) Install the three tubes just removed from the old waste cap
onto the new waste cap. The large yellow hose connects to
the large fitting while the two small remaining tubes connect
to either of the remaining small fittings.
L) Discard old waste cap assembly.
M) Restore power connection to instrument and turn instrument
on and wait for instrument beep.

ATTACH
TUBING TO
NEW CAP
Figure 58. Waste Sensor Removal
GREEN LIGHT ON TOP OF

NEW WASTE SENSOR
Figure 59. Green Light On Waste Sensor
Test the waste sensor:

A) The cap should be positioned so that no surface is within 13
in. (33 cm) or else the sensor may be detecting that surface.
B) From front of the instrument, observe the light on top of the
new sensor cap. The gray cap should be tested by moving

your hand approximately 8 in. (20 cm) below the sensor. The
green cap should be tested by moving your hand
approximately 12 in. (30 cm) below the sensor.
l If a green light is observed, test the sensor by moving
your hand under the bottom of the sensor tube. The
sensor light should change from green to amber,
indicating a functioning sensor.
l If an amber light is observed, verify that something is
close to the bottom of the sensor tube. Also verify that
the sensor is dry and there is no fluid film (bubbles) in
the tube. If necessary, clear the tube by tapping lightly
on the lip of the carboy or remove fluid from the face of
the sensor by wiping.
l If no light appears, either power is not on or the
connection has not been made properly.
C) Using the NexES software, in the input section of the service
test screen, observe the status of the waste sensor. The
gray cap should be tested by moving your hand
approximately 8 in. (20 cm) below the sensor. The green cap
should be tested by moving your hand approximately 12 in.
(30 cm) below the sensor.
l If the status is EMPTY, test the sensor by moving your
hand under the bottom of the sensor tube. The status
should change from EMPTY to FULL.
l If the status is FULL, verify that something is close to
the bottom of the sensor tube. Also verify that the
sensor is dry and there is no fluid film (bubbles) in the
tube. If necessary, clear the tube by tapping lightly on
the lip of the carboy or remove fluid from the face of
the sensor by wiping.
D) Install sensor cap on one of the 20 liter carboys.
E) A green light should be observed if:
l Grey cap: carboy is less than 60% full (~12 liters)
l Green cap: carboy is less than 10% full (~2 liters)
F) Clean up any waste that may have spilled onto the floor.
G) Install extra carboy in waste cabinet.

13.21 Dispense Cylinder

outlet.
B) Rotate dispense arm to front of instrument.
C) Remove housing and dispense cylinder from dispense arm
by removing the three screws.
CAUTION: Do not let weight of cylinder pull tubing from the
dispense arm. If tubing is pulled out, it is difficult to route back
inside the instrument.
D) Disconnect white tubing from air cylinder fitting.
E) Extend shaft of air cylinder and insert Allen wrench into hole
on side of shaft to secure the shaft in the extended position.
F) Unscrew plunger from end of shaft. Some difficultly may be
encountered because the plunger is attached with 242
Loctite (or equivalent). Retain the plunger for reinstallation.
G) Remove Allen wrench from shaft and discard old air cylinder.
H) Insert new air cylinder into housing.
I) Extend shaft of new air cylinder and insert Allen wrench into
hole on side of shaft to secure the shaft in the extended
position.
J) Clean threads of plunger and apply a small drop of 242
Loctite (or equivalent) roughly three to four threads from tip
of plunger. If properly applied, threads on plunger will be
visible through Loctite.
K) Loosely thread plunger onto new shaft of new air cylinder.
L) Tighten plunger onto shaft of new air cylinder and wipe away
any excess Loctite.
M) Remove top cover on instrument.
N) Reinstall white tubing on air cylinder fitting
O) Orient air cylinder such that air cylinder fitting is pointed
towards center of instrument.
P) Locate and pull dispense air cylinder tubing to remove slack
in tubing as needed. Do not pull tubing tight.
Q) Install housing over dispense cylinder and reattach housing
to arm with three screws.

R) Reinstall top cover on instrument.
13.22 Bottle Sensors

The removal and installation procedure is essentially the same
for all bottle sensors, with the exception that the new
configuration sensors require a bracket.
All sensors should be of the same configuration as listed below.
Old and new configuration sensors should not be used
together.
The Smart Level sensors are hybrid sensors that check for
changes in capacitance and conductivity, for all fluids except
LCS. Smart Level sensors are not used for LCS because LCS
is an oil and is not conductive. The new LCS sensor is a
capacitive sensor, but it is specialized for high sensitivity.
Requires
PN Part Description Position
Bracket
New 100847500 Assy; Bottle Sensor; LCS LCS Bottle Yes
Configuration 100847400 Assy; Bottle Sensor; Smart Level All Others Yes
Old 1970200 Bottle Sensor ASSY XT All Others No
Configuration 1970300 ASSY; BOTTLE SENSOR; SSC; XT SSC Bottle No
CAUTION: For the new configuration sensors, do not

attempt to adjust the sensor.
The following procedure is used to upgrade to the new

configuration.
circuit.
B) Assemble the sensor to the bracket using the M3 screws,
if necessary.

Figure 60. Bottle Sensor and Bracket (New Configuration)
C) Unscrew two M3 socket head screws that mount the old

bottle sensor to the bottle liner.
Figure 61. Bottle Sensor Removal (Old Configuration Shown)
D) Perform the following steps to gain access to the Serial I/O

PCB inside the AFM:
1. Remove the Back Lower Panel of the AFM.
2. Remove the Fluidics Drawer Cover from the front of
the instrument by turning the quarter-turn screws.
Retain the screws and springs.
3. Slide the Fluidics Drawer forward.
E) Unplug the sensor from the Serial I/O PCB and pull the cable
down through the routing path to remove it from the
instrument. Cut cable ties as needed to remove this cable.

Figure 62. Bottle Sensor Connection
F) Route the new sensor cable through the same path as the
sensor that removed, securing with new cable ties as
needed.
G) Mount the new bottle sensor to the liner using two M3 socket
head screws.
Figure 63. Bottle Sensor Assembly (New Configuration Shown)
H) Plug the new sensor connector into the same input as the
sensor that was removed.
I) Old sensor can be discarded.
CAUTION: For the new configuration sensors, do not

attempt to adjust the sensor.

13.23 Volume Adjust Block

A) Power down the instrument and unplug it from the wall.
B) Remove front cover.
C) Remove reagent carousel cover.
D) Remove reagent carousel access plate.
E) Remove drip shield with dispense hole.
F) Remove evaporation shield.
G) Unplug all tubing from rear of volume adjust block.
H) Remove the volume adjust block from the nozzle plate.
(Move nozzle back and forth while lifting up.)

14.0 Common Problems and Solutions

This section provides detailed instructions to solve common
problems.
14.1 Stainer Subassembly Power-on LED on

Front Panel is OFF
The front panel LED lights when 24 VDC power is available to
the microcontroller PCB. This requires:
l AC power
l 24 VDC power supply and wiring to J1 on the microcontroller
PCB
l Intact wiring between J23 on the microcontroller PCB and
the front panel display board
A) Check AC power cable and fuses.
B) Check 24 VDC LED (D1).
¨ Is this or any other LED on microcontroller PCB
illuminated?
C) If no microcontroller PCB LEDs are illuminated, check the
wiring between J1 and power supply.
D) If D1 is not illuminated but any other microcontroller PCB
LED is illuminated, replace the microcontroller PCB.
E) If wiring (step C) is intact, replace the power supply.
F) Check wiring from J23 for corrosion, shorts, and frayed
wires.
¨ Replace if necessary
G) Replace the front panel display board.
14.2 Valve Associated Function Is Inoperable

Valves can malfunction due to electrical control problems or
because the valve is clogged or mechanically defective.
A) Actuate the valve from the TESTS, BASIC I/O CONTROL
menu.
¨ Does the valve turn?

¨
If so, the valve is probably defective or clogged and
should be replaced
B) Does the Serial I/O PCB LED corresponding to the valve
output illuminate?
¨ If not, actuate the output for an adjacent valve to verify
that the Serial I/O PCB is operating
¨ If this does not work either, suspect a defective
microcontroller PCB
¨ Try plugging the inoperative valve’s electrical connector
into the working output adjacent to it, then trigger the
working output
NOTE: Do not plug or unplug any valve with the valve
turned on as this can cause damage to the PCB Driver IC.
¨ If the valve still does not operate, then the valve is
defective
14.3 Reagent Carousel or Nozzle Plate Will

Not Move
Reagent carousel or nozzle plate movement requires:
l AC power
l 24 VDC power and wiring to J1 of the microcontroller PCB
l 24 VDC power and wiring to J3 of each motor drive module
l Functional microcontroller PCB
l Intact wiring between J3 of the microcontroller daughter PCB
and J1 of the reagent motor driver module
l Intact wiring between J6 of the microcontroller daughter PCB
and J1 of the nozzle plate motor driver module
l Intact wiring between J2 of the reagent motor driver module
and the reagent carousel motor
l Intact wiring between J2 of the nozzle plate motor driver
module and the nozzle plate motor
l Functional motors
l Intact drive belts
WARNING: Do not unplug or plug J1 on either motor driver

module or the motor wiring connectors (J101/P101, J102/P102)

while AC power is ON. Failure to turn off power before working

with these plugs will damage the microcontroller!
A) Verify 24 VDC power indicated by D1. If D1 is not lit, refer to
Section 12.14.
B) Using the TEST FUNCTIONS screen in the software, try
moving the other motor.
¨ If neither motor can be moved, first recheck the wiring
from the power supply to J1
¨ Then replace the microcontroller PCB
If one motor moves, but the other will not:
A) Turn off the AC power switch
B) Temporarily swap microcontroller daughter board connectors
for reagent (J3) and nozzle plate (J6) motor drivers.
¨ The daughter board is in the corner of the board opposite
the 24 volt power connector J1
C) Turn AC power back on.
D) Try both motors again.
¨ If swapping the cables on the microcontroller PCB’s does
not enable the previously dead motor, power off and swap
the cables back to the original positions, then before
reapplying power:
¨ Swap the motor cables going to the J2 connectors of
the motor drivers
¨ Turn AC power back on
¨ If the previously dead motor now works replace the
motor driver module for that motor
¨ If the motor still does not work check the wiring to the
motor
§ If the wiring is intact, replace the motor
NOTE: If any of the above connectors have been swapped, do

not forget to return them to their proper assignments while AC
power is OFF.

14.4 Compressor Not Coming On

The compressor is turned on by a solid state relay. To function,
the compressor needs:
l AC Power
l A good AFM Serial I/O board
l A working compressor
If the compressor will not come on:
l Make sure the power switch is on
l Make sure that the circuit breaker next to the power switch is
pushed in
l Inspect AC wiring within the AFM
l Replace the compressor, the starting capacitor, and/or the
compressor relay
14.5 Homing Input Not Working

The homing sensors used for the reagent and nozzle plate are
electrically identical. Proper function requires:
l Working sensors
l Intact wiring between the sensors and their respective jacks
on the microcontroller PCB (J21 Nozzle Plate, J22 Reagent)
l A functioning microcontroller PCB
A) Use an opaque object such as cardboard to trip the sensor.
¨ Check the LED on the side of the sensor and the
microcontroller PCB LED (D54 Nozzle Plate, D55
Reagent)
¨ If either LED does not change state, check the
connectors (J21 Nozzle Plate, J22 Reagent) for
corrosion and broken, shorted or frayed wires
B) Plug the INPUT TEST plug into the connector (J21 Nozzle
Plate, J22 Reagent)
¨ If LED (D54 Nozzle Plate or D55 Reagent) does not come
on, replace the microcontroller PCB
¨ Check the INPUTS section of BASIC I/O CONTROL
¨ If testing slide home, the SLIDE HOME input should
indicate “ON HOME”

¨ If testing reagent home, the REAGENT HOME input

should indicate “NOT ON HOME”
¨ If the input is incorrect but other inputs are functioning,
replace the microcontroller PCB
C) Replace the sensor.
D) Refer to Sections 10.2 and 10.4 for reagent homing and
nozzle plate homing.
14.6 Slide Tray In Sensor Not Working

For the optical Slide Tray In sensor to work properly:
l The slide tray must be in the down position.
l With the drawer pulled out, ensure the tray lift plate is
positioned at the front of the drawer.
l Carefully close the drawer.
l The sensor must be parallel to the tray lift plate.
l The sensor should be backed off and then adjusted toward
the tray until the software indicates "IN."
l The face of the sensor must be 1/8” (or 3 mm) from the tray
lift plate.
l Further requirements are:
¨ A functional microcontroller
¨ Intact wiring associated with J20
¨ A functional optical sensor
If the sensor will not illuminate the LED (D53):
A) Check the plug at J20 (next to D53) for corrosion and
replace corroded components.
B) Plug the INPUT TEST plug into J20.
¨ If D53 does not illuminate, replace the microcontroller
PCB.
¨ If the SLIDE TRAY IN does not indicate “IN,” but other
inputs are functioning, replace the microcontroller
PCB.
C) Test the sensor with a reflective object such as a piece of
white paper.

¨ The sensor should detect the reflective object to a

maximum range of about 0.375”.
¨ If D53 does not illuminate and the cable appears to be
intact, replace the sensor.
14.7 Slide Tray Up Sensor Not Working

For the optical Slide Tray Up sensor to work properly:
l The slide tray must be in the Up position.
l The sensor must be parallel to the tray lift plate.
l The sensor should be backed off and then adjusted toward
the tray until the software indicates "UP."
l The face of the sensor must be 1/8” (or 3 mm) from the tray
lift plate.
l Further requirements are:
¨ A functional microcontroller
¨ Intact wiring from the sensor to J2
¨ A functional optical sensor
If the sensor will not illuminate the LED (D2):
A) Check the plug at J2 (next to D2) for corrosion and replace
corroded components.
B) Plug the INPUT TEST plug into J2.
¨ If D2 does not illuminate, replace the microcontroller PCB
¨ If the SLIDE TRAY UP does not indicate “UP,” but
other inputs are functioning, replace the microcontroller
PCB.
C) Test the sensor with a reflective object such as a piece of
white paper.
¨ The sensor should detect the reflective object to a
maximum range of about 0.375”.
¨ If D2 does not illuminate and the cable appears to be
intact, replace the sensor.

14.8 Overflow Sensor Not Working

The overflow sensor requires intact wiring and a working
microcontroller PCB.
If the sensor will not illuminate the LED (D57) when tested:
A) Check the wiring between J-24 and the sensor pins.
¨ Check for broken, frayed or shorted wires
B) Disconnect the plug at J-24.
¨ Inspect the pins for corrosion
¨ If corrosion is found, replace the corroded components
C) Plug the INPUT TEST plug into J-24
¨ If D57 does not light, replace the microcontroller PCB
14.9 No Beep on Power-up

The “beep” on power-up indicates that the microcontroller PCB
has power and that its software is running. If there is no beep,
either there is no power or the microcontroller PCB is defective.
A) Check fuses
B) Check 24 VDC power LED (D1).
¨ If this is not illuminated, there is no power. Refer to
Section 12.14
C) Failing all of the above, replace the microcontroller PCB.
14.10 Barcode Reading Problems

Barcode reading requirements:
l Functional barcode reader
l Alignment of barcode reader
l Clean barcode reader lens

l Correct homing of the carousel
l Intact wiring between the barcode readers and the port
expander PCB
l Intact wiring between the port expander PCB and J4
(barcode beep input)

l Correct operation of the port expander PCB

l Intact wiring between the microcontroller PCB and the port
expander PCB
l Communications between microcontroller PCB and PC
To isolate barcode reading problems, use TESTS, BASIC I/O

CONTROL screen in conjunction with the tests below.
A) Clean the barcode reader lens.
B) Trigger a scan.
¨ Is the scanner projecting a red beam? If not:
¨ Check the scanner wiring
§ Replace defective components
¨ Replace the barcode reader
C) If the scanner is projecting a beam, check the barcode
reader alignment per Section 10.6 or 10.7.
D) Verify proper homing of the reagent carousel or nozzle plate
per Section 10.2 or 10.4.
14.11 No “Connected” Light

This refers to the “CONNECTED” indicator on the main screen
of the PC program, which establishes that the stainer
subassembly microcontroller PCB software is communicating
with the PC software.
A) Check the address switch on the microcontroller PCB.
¨ Verify that the address is correct and does not conflict
with any other instrument connected to the PC
B) Check the serial cable between the PC and the instrument.
¨ Verify the XT Adapter is plugged in to the USB to RS 422
adapter (MOXA)
¨ Verify that the correct serial port is being used (MOXA
port 1, set to COM2)
C) Perform the serial port diagnostics.
¨ This determines whether the problem is at the PC or the
stainer subassembly

¨If the problem is at the PC, stop here

D) Make sure that the instrument is receiving power and is
turned on.
E) Observe LEDs on the microcontroller PCB.
¨ If any LED is illuminated, the instrument is powered up
¨ If NO lights are on, the instrument is not receiving AC
power
¨ Check power and fuses
F) Cycle the power to the instrument OFF then ON.
¨ If there is no “beep,” refer to Section 14.9
G) Observe the “heartbeat” LED (D19) on the microcontroller
PCB.
¨ This should be blinking at a rate of about once per second
¨ If there is no heartbeat but there is power (LED D1 is lit),
try the Remote Code Download procedure from SETUP
menu of the NexES software.
¨ If this fails, replace the microcontroller PCB
H) Observe the receive (RXD-D21) and transmit (TXD-D22)
LEDs on the microcontroller PCB.
¨ These should both be blinking approximately once per
second
¨ If the RXD light is not blinking, the microcontroller is
not receiving data from the PC
¨ Check the address and cabling again per steps A)
and B), above
¨ The PC serial port may also be defective
I) If the RXD light is blinking but the TXD light is not, and
everything else checks out, the microcontroller PCB is
defective.
14.12 Drive Belt Slipping

If the reagent carousel or nozzle plate drive belt is slipping, the
belt must be tightened or replaced.

14.12.1 Nozzle Plate Belt

A) Remove the reagent carousel cover.
B) Loosen the two clamping screws that hold the housing,
dispense motor adjust plate enough so that the drive belt re-
tensions itself when pressed on from the side.
¨ This will allow the springs in the assembly to tension the
belt to the proper load automatically
C) Retighten the screws, using care not to twist or move the
plate while tightening.
NOTE: The best method is to tighten each screw gradually,
switching back and forth between the two until the correct
tightening torque is reached.
14.12.2 Reagent Carousel Belt

A) Remove the reagent carousel cover.
B) Loosen the three clamping screws, from the top of the
reagent carousel top plate, that hold the housing, dispense
motor adjust plate (make sure these screws are loose)
enough so that the drive belt re-tensions itself when pressed
on from the side.
¨ This will allow the springs in the assembly to tension the
belt to the proper load automatically
C) Retighten the screws, using care not to twist or move the
plate while tightening.
NOTE: The best method is to tighten each screw gradually,
switching back and forth between the two until the correct
tightening torque is reached.
14.13 Port Expander PCB Fuse Check

Slide tray communication errors can result from a non-
functional fuse on the Port Expander PCB.
A) Ensure power to the instrument is turned off.
B) To gain access to the Port Expander PCB, remove fluidics
drawer cover and keypad mount panel.
C) Use a multimeter set to Ohms.
D) Measure the resistance across the fuse (see figure below).

E) Verify resistance is <0.3 ±0.2 Ohms.

F) If resistance is >1.0 Ohms, replace the Port Expander PCB.
Figure 64. Port Expander PCB Fuse Check
14.14 Serial Output PCB Failure

Ferrites should be in place on the following cable assemblies to
prevent Serial Output PCB failure.
1939000 – Microcontroller to Serial Out Cable Assembly:

A) Add ferrite pairs, 1554400 and attach with clips 1293904
onto the ribbon cable.
B) The ferrites are wrapped with silicone tape to protect the
insulation on the ribbon cable. Slide the ferrites as close to
the Serial output PCB as possible.
C) Once the location has been determined, clean the area with
alcohol and allow to dry.
D) Remove the protection liner off the double sided tape and
press the ferrite into position. Hold pressure for
approximately 30 seconds to secure the ferrite.

Figure 65. Ferrite on Microcontroller to Serial Out Cable
1938900 – Microcontroller to Host Communications

Connector Cable Assembly:
A) Add ferrite pairs, 1554400 and attach with clips 1293904
onto the ribbon cable.
B) The ferrites are wrapped with silicone tape to protect the
insulation on the ribbon cable. Slide the ferrites as close to
the host connectors as possible.
C) Once the location has been determined, clean the area with
D) Remove the protection liner off the double sided tape and

Figure 66. Ferrite on Microcontroller to Host Communications

Connector Cable
Motor and Homing Cables:

A) Add ferrite, 1293905 onto the bundle of cables that run from
the top of the electronics panel, 1908900 to the Reagent and
Slide motors and homing sensors.
B) Locate the ferrite on the top of the electronics panel cover.
C) Slide the ferrites into the middle of the horizontal area of the
cover. The instrument cover panel will clear the ferrite.
D) Once the location has been determined, clean the area with
E) Remove the protection liner off the double sided tape and

Figure 67. Ferrite on Motor and Homing Cables
14.15 Vortex Mixer Flow Rate Issues

This process addresses problems with flow rates on the inner
and outer vortex mixers. This is essential for even staining on
tissue specimens.
A) Perform high and low pressure leak rate tests per Sections
11.28 and 11.29.
B) Repair any leaks found.
C) Clean the holes on the inner and outer vortex mixers using
a 0.020” pin gauge.
D) Turn on the compressor and inner and outer vortex mixer
valves in the BASIC I/O CONTROL tab.
E) Make sure that the barcode blowoff is turned off.
F) Adjust the flow by rotating the stem of the valve on the outer
mixer nozzle's single variable restrictor.
G) Adjust the flow by rotating the stem of the valve on the inner
mixer nozzle's single variable restrictor.
H) Ensure flow rates fall within the ranges specified in Level
One checklist.

15.0 Error Messages

The error messages displayed by the system software fall into
two broad categories, hardware related messages and software
related messages.
A complete list of error messages and explanations is included
as Appendix E: Error Codes.
Some of these messages are normal to the operation of the
instrument, simply showing that an event has occurred, i.e.,
“Fluid in tub exceeded maximum level.” Others indicate a
potential service problem, such as “Pressure exceeded
absolute maximum limit.”
Hardware messages typically indicate that a hardware function
did not perform as expected or that the user has done
something unexpected, such as opening the slide door during a
run.
Software related messages typically indicate communications
errors, errors in the files and control problems relating to
capturing reagent data or downloading instructions or software
to the microcontroller.
NOTE: The instrument must be powered up and connected
when running tests; otherwise, false error messages may be
displayed.
15.1 Misalignment of Nozzle Plate or Reagent

Carousel
The following messages occur as the result of misalignment.
Error Error Message

Class #
12 53 Nozzle plate check at end of run indicated minor misalignment
12 54 Nozzle plate check at end of run indicated major misalignment
12 55 Reagent tray check at end of run indicated minor misalignment
12 56 Reagent tray check at end of run indicated major misalignment
l Check the gear screws. Tighten as needed.

l Check the belt for proper tension or damage. Replace as

needed.
l Check the gears for damage or loose fasteners. Replace
parts or assemblies as needed.
l Check the torque voltage on the microcontroller PCB. Refer
to Section 12.2 for more information.
These errors are detected by the software.

Slide misalignment means that the nozzle plate did not rotate
properly and therefore the slides, nozzles, and dispense points
were not lined up. The slides stained on such a run are invalid.
Reagent carousel misalignment means that the reagent
carousel did not rotate properly at some point and the
dispenses were incorrect. The slides stained on such a run are
invalid.
Causes
The drive belt may be damaged. Use Test – Jog Reagent Tray
or Test – Jog Nozzle Plate to check the functionality of the
drive. The test selected will home the reagent carousel or
nozzle plate and then take one position steps each time the
user button is pushed. Check that the reagent carousel or the
nozzle plate moves to the next position and lines up correctly.
If it does not, this may indicate a bad drive belt.
If the reagent carousel or nozzle plate fails to find home, this
may indicate a bad sensor.
For reagent carousel misalignments in particular, check for
sticky residue on the bottom of the reagent carousel. A leaky
dispenser can gum up this surface and cause the reagent
carousel to stick.
15.2 Recharge Error Messages

The following messages occur as the result of failure to
recharge fluids. Take the following corrective action:
l Check the O-ring seal for the bottle
l Confirm the operation of the vacuum pump
l Check the bottle’s check valve and replace it if necessary

l Check the operation of the three-way valve
Error Error Message

Class #
12 43 Reaction buffer reservoir failed to recharge itself in time.
12 44 SSC reservoir failed to recharge itself in time.
12 45 EZ Prep reservoir failed to recharge itself in time.
12 46 Cell conditioner #2 reservoir failed to recharge itself in time.
12 47 Cell conditioner #1 reservoir failed to recharge itself in time.
12 48 LCS reservoir failed to recharge itself in time.
12 49 Optional reservoir failed to recharge itself in time.
15.3 Priming Error Messages

The following messages occur as the result of failure to prime.
Take the following corrective action:
l Check the O-ring seal for the bottle
l Confirm the operation of the vacuum pump
l Check the bottle’s check valve and replace it if necessary
l Check the operation of the three-way valve
Error Error Message

Class #
12 35 Reaction buffer reservoir failed to prime.
12 36 SSC reservoir failed to prime.
12 37 EZ Prep reservoir failed to prime.
12 38 Cell conditioner #2 reservoir failed to prime.
12 39 Cell conditioner #1 reservoir failed to prime.
12 40 LCS reservoir failed to prime.
12 41 Optional reservoir failed to prime.
15.4 Vacuum Trap Error Messages

The following messages occur as the result of vacuum trap
errors. Take the following corrective action:
l Purge the vacuum trap
l Select Purge Vacuum Trap from the Test Functions screen

l Check for proper operation of the float switch in the reservoir

that overfilled
l Check for proper operation of the three-way valve for the
reservoir that overfilled
Error Error Message

Class #
12 42 Vacuum trap is full of fluid
15.5 Slide Heating Error Messages

Class 12 error messages will occur as the result of slide heating
errors.
Error messages 130-139 will indicate too-low temperatures for
slide heaters 21-30, respectively.
Error messages 160-179 will indicate too-low temperatures for
Error messages 140-149 will indicate too-high temperatures for
Error messages 180-199 will indicate too-high temperatures for
Error messages 150-159 will indicate a bad or disconnected
temperature sensor for slide heaters 21-30, respectively.
Error messages 200-219 will indicate a bad or disconnected
temperature sensor for slide heaters 1-20, respectively.
15.5.1 Temperature Too High or Too Low

This type of error means that at some point during the run, the
heater did not reach its designated temperature in the time
allowed. It can also mean that the temperature drifted from the
set point.
Causes
High temperature errors are usually caused by procedure flaws,
such as trying to control a low temperature while other slides
are maintaining a high temperature.
Low temperature errors indicate that the heater did not reach
the set temperature in time. This can be caused by low

coverslip on the slide, adding large aqueous volumes to the

slide, or by a faulty heater. If possible, check the temperature
chart of the run to look for the part of the run that is problematic.
In general, to check for failing heaters, run Test – Temp Verify
XT. Place temperature verifier slides on all heaters. The 93° C
bar will turn black and the 99° C bar will not if the heater is
working properly.
15.6 Hardware Error Messages: (Normal

Status Reports)
Messages in this section are normal status reports and do not
necessarily indicate failure of any hardware component. Some
can, however, affect the success or failure of the run.
Error Error Message

Class #
12 19 Fluid in tub exceeded maximum level.
12 10 Power failed during run.
12 3 Slide access door was opened during the run.
12 0 Stainer subassembly program ran to completion
12 251 Open slide tray, perform titration/manual application,
close slide tray and press button when complete.
15.7 Hardware Error Messages: (Possible

Hardware Failure)
Fatal errors are those that prevent resumption of the run once
they occur. All errors not marked “(FATAL)” can be signed off
by the operator so that the run can be resumed.
Error Error Message

Class #
12 15 Pressure exceeded the absolute maximum limit
(FATAL).
12 6 Pressure is too high.
12 5 Pressure is too low.

Error Error Message

Class #
12 61 Pressurizing time was exceeded (FATAL).
12 8 Purging failed to complete within required time
(FATAL).
12 7 Reagent tray failed to find home position or tray is
missing (FATAL except in titration).
12 1 Slide heat is too high.
12 18 Slide heat is too low.
12 16 Nozzle plate failed to find home position (FATAL).
12 17 Reagent carousel failed to find home position
(FATAL). Slide tray failed to find home position during
run (FATAL).
12 9 Time limit for existing exception expired (FATAL).
15.8 User Initiated Messages

The following messages occur as the result of a user action.
Error Error Message

Class #
12 23 User aborted run before normal completion.
15.9 Backup Problems

The messages, below, concern difficulties with system backups
from the hard drive to the zip drive.
Error Error Message

Class #
11 3 NexES Host Software Requires A Backup Disk To
Run
11 4 XT Host could not backup the datafiles.
15.10 Run Related Error Messages

The following messages indicate that the system is unable to
find slides or reagent dispensers, either: a) because they are

not installed, b) the barcodes cannot be read, or c) the operator

has entered incorrect information into the system.
Error Error Message

Class #
6 23 No slides found to run.
11 4 XT Host could not backup the datafiles.
14 5 Slide Barcode Count Mismatch, check View Slides for
those found.
15.11 Reagent Database and Encryption

Messages
The error messages in this section deal mainly with database
functions handled by the PC software. Most of the problems in
this section derive from defective or duplicate buttons, improper
use of reagent containers and labels, out-of-date reagents, or
the hardware key.
Error # Error # Message

1 11 Hardware key missing from back of host
computer.
2 3 Seal has already been burned by another NexES
Host XXXXX.
2 4 Seal has already been burned by this NexES
system.
2 4 The touch memory has been changed after reading
its contents.
BenchMark XT / DISCOVERY XT BenchMark XT /

will not run from unencrypted DISCOVERY XT data files
datafiles. are not formatted correctly for
this version of software.
Check hardware key.

BenchMark XT / DISCOVERY XT The software reads all of its

system datafiles will not decrypt. data files on startup to make
sure they are present and
BenchMark XT / DISCOVERY XT valid. If one of these
group datafiles will not decrypt. messages is encountered:
Make sure the hardware key
is installed and that the key
BenchMark XT / DISCOVERY XT
belongs to this computer.
datafiles are missing.
Assuming the key is present,
restore the data from the
current backup.
Product [nnn] was already stored in The product [nnn] associated
database; call Ventana. with this touch memory has
already been read in.
This is likely to be a duplicate
button.
Dispenser with Product Code #[nnn], Dispenser past expiration so
Serial #[nnn] has expired and can the run cannot continue.
not be used in this run. Replace dispenser with
newer one.
15.12 Communications Between PC and

Modules
Checking Communications: All of the error conditions, below,
derive at least partly from communications problems between
the PC software and the stainer subassembly microcontroller
PCB.
To “Check communications,” do the following:
A) If the green “Connected” light on the PC screen is not lit,
check to see if the module is turned on. If power is on,
check the PC-to-module communication cable. Check to
see that the cable is in the correct COM port.
B) Check address switch or switches: Click Setup on the main
screen. Go into Setup Stainer subassembly to find the
address. Check the switch address in the module on the
NPU board.

C) If there are multiple stainer subassemblies, check the

address switch on each and every module. Ensure that no
two modules share the same address number.
D) If there is only one stainer subassembly, its address should
be zero.
Communications problems are most commonly caused by
loose or missing cables or a missing XT Adapter. Barcode
reader problems may also cause messages in this group.
Error Error # Message

Class
3 1 Communica-tion failure attempting to upgrade
software, Retry
3 3 The new staining module software was not loaded
correctly, Retry
3 4 Instrument Not Communicat-ing, Run Terminated
11 2 NexES Com Port conflict, returning to defaults

16.0 Appendix A: Assembly Drawings
Figure 68. Compressor Unit Assembly

Figure 69. Compressor Unit Assembly, Schematic

Figure 70. Compressor Unit Assembly, BOM

Figure 71. Compressor with Connector

Figure 72. Compressor with Connector, Schematic

Figure 73. Compressor with Connector, BOM
Figure 74. Electrical/PCB, Fan Assembly

Figure 75. Electrical/PCB, Fan Assembly (View 1)



Figure 81. Electrical/PCB, Fan Assembly, BOM

Figure 82. Fluidics Drawer Assembly (View 1)



Figure 86. Fluidics Drawer Assembly, BOM

Figure 87. Fluidics Reservoir Assembly (Exploded)

Figure 88. Fluidics Reservoir Assembly
Figure 89. Fluidics Reservoir Assembly, BOM

Figure 90. Left Front Drawer Lift Assembly (View 1)
Figure 91. Left Front Drawer Lift Assembly (View 2)

Figure 92. Left Front Drawer Lift Assembly, BOM
Figure 93. Left Rear Drawer Lift Assembly (View 2)

Figure 94. Left Rear Drawer Lift Assembly (View 1)
Figure 95. Left Rear Drawer Lift Assembly, BOM

Figure 96. Right Front Drawer Lift Assembly
Figure 97. Right Front Drawer Lift Assembly, BOM

Figure 98. Right Rear Drawer Lift Assembly
Figure 99. Right Rear Drawer Lift Assembly, BOM

Figure 100. Motor Rotation Assembly
Figure 101. Motor Rotation Assembly BOM

Figure 102. Nozzle Plate Assembly (View 1)



Figure 106. Nozzle Plate Assembly, Schematic

Figure 107. Nozzle Plate Assembly, BOM (Part 1)

Figure 108. Nozzle Plate Assembly, BOM (Part 2)

Figure 109. Nozzle Plate Power Transmission Assembly
Figure 110. Nozzle Plate Power Transmission Assembly, BOM

Figure 111. Motor Rotation Nozzle Plate Assembly
Figure 112. Motor Rotation Nozzle Plate Assembly BOM

Figure 113. Power Entry Assembly

Figure 114. Power Entry Assembly, BOM

Figure 115. Reagent Carousel Assembly (View 1)


Figure 118. Reagent Carousel Assembly, BOM

Figure 119. Reagent Carousel Power Transmission Assembly

Figure 120. Reagent Carousel Power Transmission Assembly,

BOM

Figure 121. Roof Substructure Assembly
Figure 122. Roof Substructure Assembly, BOM

Figure 123. XT Slide Tray Assembly (View 1)




Figure 128. XT Slide Tray Assembly, BOM

Figure 129. LT Slide Tray Assembly (View 1)




Figure 134. LT Slide Tray Assembly, BOM

Figure 135. XT Stainer (View 1)






Figure 145. XT Stainer, BOM

Figure 146. XT Bottle Liner Assembly (View 1)



Figure 151. XT Bottle Liner Assembly, BOM

Figure 152. XT Complete Assembly (View 1)





Figure 157. XT Complete Assembly, BOM

BenchMark XT / DISCOVERY XT / Benchmark LT Service Manual Appendix B: Wiring Diagrams
17.0 Appendix B: Wiring Diagrams
Figure 158. Wiring Diagram #1908200, Sheet 1




BenchMark XT / DISCOVERY XT / Benchmark LT Service Manual Appendix C: Fluidics and Pneumatics Diagrams
18.0 Appendix C: Fluidics and

Pneumatics Diagrams
Figure 162. Nozzle Plate Diagram

Figure 163. Pneumatic Components Schematic #1935100

Figure 164. XT Bottle Liner Schematic (Part 1)

NOTE: Refer to Figure 151.

Figure 165. XT Bottle Liner Schematic (Part 2)

NOTE: Refer to Figure 151.

BenchMark XT / DISCOVERY XT / Benchmark LT Service Manual Appendix D: Technical Bulletins
19.0 Appendix D: Technical Bulletins

Revision E of this service manual includes updates based on
information taken from the following technical bulletins.
TB-06112003 Igus Chain Installation

TB-06242003 Quick disconnects in roof substructure
TB-06262003 Slide Drawer Rail Screws
TB-08142003 Vacuum Assist to Lower Air Lift Cylinders
TB-09042003 Nylon Patch Screws
TB-10172003 Electro Static Discharge
TB-0000001 Procedure to verify drawer
height/parallelism/centering, nozzle plate
homing, instrument leveling, vortex mixer
height/side to side alignment/performance
TB-0000003 “Slide Tray Open During Run” Errors
TB-0000009 Fluid and Air Tubing to Nozzle Plate
TB-0000017 Power Entry Terminal Block
TB-0000021 XT Dispense Cylinder
TB-0000025 XT/LT Air Cylinder Configuration
TB-0000037 Instrument Waste Sensor
TB-0000038 Laser Safety Notice
TB-0000039 Volume Adjust Block
TB-0000046 Vacuum Relief Valve
TB-0000052 High Pressure Tubing Routing
TB-0000068 Replacement Bar Code Reader Assemblies
TB-0000089 Replacement of the Serial Output PCB
1387700 with assemblies that use Micrel ICs
require the addition of ferrites to cable
assemblies to reduce noise spikes in the
instrument. Ferrites can be used with PCBs that
are assembled with Allegro ICs.
TB-0000091 Update damaged/leaking slide heaters with
corrected slide heaters and new H-seals
TB-0000111 Fluidics Reservoir Assembly Torque
Specification Updates

BenchMark XT / DISCOVERY XT / Benchmark LT Service Manual Appendix D: Technical Bulletins
TB-0000123 Addition of hold-down to XT/LT Discovery

compressor wires
TB-0000138 Slide Heater Delamination
TB-0000177 Jet Drain Tubing Upgrade
TB-0000206 18 L Waste Sensor Assembly
TB-0000227 Bottle Sensor Replacement
TB-0000253 Error: 12-63: Run stopped due to heater(s)
abnormally hot. If this situation persists, call for
service.
TB-0000267 Second Stage – Slide Tray Improvements
TB-0000291 Installation of black Injection Molded Vortex
Mixers
TB-0000299 Port Expander PCB Fuse Continuity Check

BenchMark XT / DISCOVERY XT / Benchmark LT Service Manual Appendix E: Error Codes
20.0 Appendix E: Error Codes

The following list of error codes and corresponding information
has been edited to remove many that are not relevant to XT/LT
instruments; however, some of these may not apply to XT/LT.
Error Error
Error Message Message type Description What To Do
Class Code
1 2 The Date/Time HASP The Time and Replace HASP key
was out of range Hardware Key Date in the
and could not be Errors HASP key are
stored, Reenter. not within 24
hours of each
other when the
software starts
up.
1 4 Error encountered HASP Software can’t Reseat the HASP key. If that
reading hardware Hardware Key start because does not work, reinstall the
key. Errors the data from HASP drivers and try again.
the HASP key If that does not work, it could
can’t be read be a bad parallel port.
during startup. Replace the Lava card if it
has one, or replace the PC if
the parallel port is on-board.
1 6 Error encountered HASP Unable to Reseat the HASP key. If that
reading hardware Hardware Key update the does not work, reinstall the
key. Errors database HASP drivers and try again.
version within If that does not work, it could
the HASP key. be a bad parallel port.
Replace the Lava card if it
has one, or replace the PC if
the parallel port is on-board.
1 8 Error in setting HASP Unable to Ensure the user has the
System Time from Hardware Key update the OS proper permissions to
Hasp Key. Errors Time and Date modify the system time.
from the HASP
key.
1 9 Time in the HASP Unable to detect If this happens on startup of
hardware key is Hardware Key clock movement the software, replace the
not advancing! Errors from the HASP hasp key. If it happens
Contact Ventana key. during run time, shut down
for a replacement. the software and restart the
run.
1 11 Error encountered HASP Unable to Reinstall the HASP drivers.
readinghardware Hardware Key retrieve If that does not clear it up,
key. Errors thedatabase replace the HASP key
version from
thedatabase
version field
inthe HASP Key.
1 12 Error encountered HASP Unable to Reseat the HASP key. If that
reading Hardware Key retrieve the does not work, reinstall the
hardware key. Errors database HASP drivers and try again.

Error Error
Class Code
version from the If that does not work, it could
database be a bad HASP key or a bad
version field in parallel port. Replace as
the HASP Key. needed.
2 1 Bad Touch Product Unable to verify that the wand works
Memory Button Registration retrieve data with another button. If it
from the touch works properly, then replace
memory button. the button. If not, replace the
wand
2 2 Data Retrieval Product Error when verify that the wand works
Error Registration retrieving data with another button. If it
from the touch works properly, then replace
memory button. the button. If not, replace the
wand
2 3 Seal has already Product The touch They burned the button
been burned by Registration memory button already to a different host.
another NexES has been User error. If they didn't,
Host %d. (%d registered by then send them a new
being a Host ID another Host button.
value) system.
2 4 Seal was burned Product The touch The buttons will give you a
by this NexES Registration memory button 10 day window to re-register
system too long has been if it needs to be re-
ago. registered for registered. Send them a new
more than 10 button if prudent.
days and user is
attempting to
reregister it.
2 4 Seal has already Button on Buttoned packages may not
been burned by package was be registered more than
this NexES registered once. Customer should
system. already on this purchase more product from
host computer. Ventana.
2 4 The touch memory The operator Ensure that the operator
has been changed has switched keeps the probe on the
after reading its buttons during button until the current
contents. the process. operation is completed.
(Each button
has a unique
number and the
software
detected that
this changed.)
2 5 The touch memory Product The touch Send a new button
has been changed Registration memory button
after reading its has been
contents. changed after
the contents
have been read,
but not burned.
3 1 Communication Communication The remote Try the download again. If it
failure attempting with the code form was still fails, contact Ventana.
to upgrade Instrument closed before

Error Error
Class Code
software, Retry. the download
was completed.
3 3 The new staining Communication The remote Try the download again, if it
instrument with the code checksum still fails, contact Ventana.
software was not Instrument does not match
loaded correctly, the checksum
Retry. returned from
the staining
instrument,
preventing
switching to the
current version
of remote
software.
3 4 Instrument Not Communication Run is Check the communications
Communicating, with the terminated between the host and the
Run Terminated. Instrument because the instrument by running test
host is unable to functions. If it has no
communicate connection, check the
with the MOXA for the proper
instrument settings. If still no
before connection, replace the
downloading run MOXA
information.
3 7 Invalid or Missing Communication The User Make sure the instrument is
Serial Number! with the Maintenance turned on and connected to
Please, turn on the Instrument Log is opened the computer. If the problem
staining module to and no serial persists contact Ventana.
acquire its Serial numbers have
Number. been obtained
from the
connected
instrument.
3 8 Button wand could Communication System is Check the cable between
not be detected. with the unable to the Probe and the PC. If the
You will not be Instrument communicate problem persists contact
able to register with the product Ventana.
products. Please registration
check the probe through
connections! the serial port.
3 9 Button wand Communication An invalid touch Reinstall VSS
software is wrong with the memory DLL is
version. You will Instrument detected.
not be able to
register products.
Please notify
Ventana.
3 10 Invalid Host Communication Software detects Sign off and continue. If the
Command with the and logs an problem persists, it could be
Instrument error if a host a communicaitions issue.
message Check the MOXA settings
command is not and test and verify
acknowledged instrument connectivity

Error Error
Class Code
by the remote
software.
3 11 Invalid Format of Communication Software detects Retry the action. Check the
Host Command with the and logs an serial cable and MOXA
Instrument error if a host adapter and test
message communicaitons between
command is not the host and instrument.
formatted
correctly for the
remote software.
3 12 Failed to open Communication Communication MOXA is most likely not
com port %d (%d with the port could not be configured propery.
represents port Instrument opened for Reconfigure and test
number). Error communications connectivity
number %d (%d to the remote
represents error) device.
3 13 Failed to setup Communication Unable to Check communications path
buffer sizes. Error with the initialize the
number %d (%d Instrument communications
represents error) parameters for a
communications
device.
3 14 Failed to Set Com Communication Unable to Check communications path
States. Error with the configure a
number %d (%d Instrument communications
represents error) device according
to the
specifications in
a device control
block.
3 15 Failed to Set Com Communication Unable to set Check communications path
Timeouts. Error with the the time-out
number %d (%d Instrument parameters for
represents error) all read and
write operations
on a specified
communications
device.
3 16 Failed to Set RTS. Communication Unable to set Check communications path
Error number %d with the the Request to
(%d represents Instrument Send signal.
error)
3 17 Failed to Set DTR. Communication Unable to set Check communications path
Error number %d with the the Data
(%d represents Instrument Terminal Ready
error) signal.
3 18 Message timed Communication Command on Check communications
out. Address: with the instrument did path. Power loss on the
%0:d Host Instrument not return within instrument while the host
Command: %1:s ( the set time limit software is running can
%2:d ) cause this.
milliseconds:
%3:d'

Error Error
Class Code
3 19 Unknown Tagged Communication Tag values sent Code error. Contact Ventana
Value. Identifier: with the from Host PC
%0:d [ %1:d ] Instrument not defined on
Instrument
Remote Code
4 2 %0:s is not a valid Serial Numbers An invalid serial Reset the serial number
Staining number for the
Instrument serial staining
number. (%0:s instrument is
represents version detected.
number) Call
Ventana technical
support before
starting another
run on this
Staining
Instrument
5 2 Slide number is Software Slide count Verify slide count. Clean off
invalid, Please Re- Application entered did not bar codes if needed. Retry.
enter reflect number of
slides read on
the instrument
5 3 One or more of the Software You have not Complete the actions in the
checklist questions Application checked off the list, then check the boxes
have not been required boxes
checked. on the pre-run
checklist.
5 6 The Starting Date Software An invalid start Enter a valid start date.
is invalid! Application date is entered
for the Product
Usage Report.
5 7 The Ending Date Software An invalid Enter a valid ending date.
is invalid! Application ending date is
entered for the
Product Usage
Report.
5 8 The Ending Date Software The ending date Reenter dates.
precedes Starting Application entered for the
Date! Product Usage
Report is earlier
than the start
date.
5 10 At least one Software No instruments Make sure at least one
Staining Application are connected to instrument is connected to
Instrument must the host. the host.
be connected.
5 17 You must select at Software No product was Select a product.
least one product! Application selected on the
Product Usage
form.
5 18 Product usage is Software No records are Enter a valid date range.
unavailable for Application found for the
specified dates. date range

Error Error
Class Code
selected for the
Product Usage
Report.
5 26 Bulk: %s has Software The bulk product Enter a unique bulk name.
already been Application you are logging
registered (%s has already
represents Bulk been registered.
Name)
5 41 Block: %s has Software The control Enter a unique control block.
already been Application tissue you are
registered (%s logging has
represents Block already been
Number) registered.
5 58 Antibody: %s has Software The antibody Enter a unique antibody.
already been Application you are logging
registered has already
been registered.
5 58 Enter a valid Software The antibody Enter the antibody name
Antibody Name Application name is left
blank when
logging fillable
antibodies.
5 58 Enter a valid name Software The Enter the manufacturer
of an Antibody Application manufacturer name.
Manufacturer. name is left
blank when
logging fillable
antibodies.
5 64 The following AFM Software The listed bulk Fill the bottles or if you are
bottles are not full: Application fluid bottles on sure you have enough for
[list]. Proceed the instrument the run, click Yes to
Anyway? are not full when proceed.
you start a run.
5 65 Waste level is too Software The waste Empty the container.
high. Please Application space available
empty it. is insufficient for
the run.
5 79 This series Software The starting Enter a different starting
overlaps a series Application point for a series point.
that has already of cut control
been received. slides overlaps
the starting point
of another
series.
5 81 The following Software The bulk fluid Fill the listed bottles or click
Automated Application bottles are not 'Yes' to proceed.
Fluidics Instrument full when starting
bottles are not full: a test function.
[list]. Proceed
Anyway?
5 82 Case: %s has Software The case you Enter a unique case.
already been Application are logging has
registered for %s already been

Error Error
Class Code
(%s represents registered.
Case Number)
Waste level is too
high.
5 86 Invalid Date Software Date range is Enter a valid date range.
Range! Dates Application invald
must be between
January 1, 1997
and the current
date. The start
date must not be
after the end date.
5 88 Waste level is too Software The waste bottle Empty the waste container.
high. Please Application is full when a
empty it. test function is
started.
5 102 The Archive Software Archive process Make sure no staining runs
Procedure has Application failed to are in progress then repeat
failed. complete. the archive process. If the
problem persists, Contact
Ventana.
5 108 The Response Software An unauthorized Get a valid Authorization
code you entered Application remote response code and retry
was invalid. message NAK is
received from
the remote
software while
attempting to
change the
staining
instrument
personality.
Authorization
Code was
invalid
5 108 Staining module is Software An unauthorized Put the instrument into
in an invalid state. Application remote response Sleep mode and retry.
message NAK is Reboot the Host PC and
received from Instrumement. Contact
the remote Ventana if the problem
software while persists
attempting to
change the
staining
instrument
personality.
5 111 The Archive Software The archive Perform archive process
Procedure Application process was again.
canceled. canceled by the
User.
5 117 The Starting Date Software An invalid start Enter a valid start date.
is invalid! Application date is entered
for the Bulk

Error Error
Class Code
Usage Report.
5 118 The Ending Date Software An invalid Enter a valid ending date.
is invalid! Application ending date is
entered for the
Bulk Usage
Report.
5 119 The Ending Date Software The ending date Enter valid dates.
precedes Starting Application specified for the
Date! Bulk Usage
Report is earlier
than starting
date.
6 1 Rule operand: Run This should not This could indicate database
XXXXXX only Compilation normally occur. corruption or an internal
valid in a recipe software error.
step.
6 2 Rule operand Run This should not This could indicate database
argument: XXXXX Compilation normally occur. corruption or an internal
missing from software error.
Argument
database.
6 3 Rule operand: Run This should not This could indicate database
XXXX missing Compilation normally occur. corruption or an internal
from Argument software error.
database.
6 4 Rule operator: %s Run This should not This could indicate database
missing from Compilation normally occur. corruption or an internal
Argument software error.
database.
6 5 Rule action: XXXX Run This should not This could indicate database
missing from Compilation normally occur. corruption or an internal
Argument software error.
database.
6 6 Rule action Run This should not This could indicate database
argument: %s Compilation normally occur. corruption or an internal
missing from software error.
Argument
database.
6 7 Rule block: %s Run This should not This could indicate database
has no rules. Compilation normally occur. corruption or an internal
software error.
6 8 Rule block name Run This should not This could indicate database
cannot be blank. Compilation normally occur. corruption or an internal
software error.
6 9 Argument: %0:s of Run The Arguments This could indicate database
type: %1:s missing Compilation database table corruption or an internal
from argument does not contain software error. Run VDBI
database. (%0: the argument and Database Maintenance.
represents the record for the Reinstall VSS if the error
macro) defined macro persists.
step.
6 10 Invalid program Run An invalid macro This could indicate database
step: %s (%s Compilation step is identified corruption or an internal

Error Error
Class Code
represents the during the run software error.Run VDBI
macro step name) compilation and Database Maintenance.
process. Reinstall VSS if the error
persists.
6 11 Macro step: %s Run The required This could indicate database
not in macro Compilation macro step is corruption or an internal
function database. not included in software error.Run VDBI
(%s represents the the MacroFunc and Database Maintenance.
macro function database table. Reinstall VSS if the error
name) persists.
6 12 Error processing Run An invalid sub This could indicate database
sub macro: %s Compilation macro step is corruption or an internal
(%s represents the detected during software error.Run VDBI
sub macro name) the run and Database Maintenance.
compilation Reinstall VSS if the error
process. persists.
6 13 Error in system Run This should not This could indicate database
rule block: %s' Compilation normally occur. corruption or an internal
software error.
6 14 System run- Run The system is Put the system into Ready
generating object Compilation not in the correct mode and retry
not ready to start state to start a
now. run
6 15 Blank system or Run System Block This could indicate database
test block name. Compilation Name is blank. corruption or an internal
This should not software error.
happen normally
6 16 Macro function: Run An invalid macro This could indicate database
%s is not valid in a Compilation function is corruption or an internal
macro. (%s detected. software error.Run VDBI
represents the and Database Maintenance.
macro function Reinstall VSS if the error
name) persists.
6 17 Could not locate Run An argument This could indicate database
macro step Compilation record does not corruption or an internal
argument: %s in exist for the software error.Run VDBI
the ARGUMENT required macro and Database Maintenance.
database. (%s step. Reinstall VSS if the error
represents the persists.
macro step
argument)
6 18 Could not locate Run A macro function This could indicate database
macro step: %s in Compilation record does not corruption or an internal
the MACRFUNC exist for the software error.Run VDBI
database. (%s required macro and Database Maintenance.
represents the step. Reinstall VSS if the error
macro step name) persists.
6 19 Sub macro: %s is Run A macro step This could indicate database
missing from Compilation record does not corruption or an internal
macro step exist for the software error.Run VDBI
database. (%s required sub and Database Maintenance.
represents the sub macro step. Reinstall VSS if the error
macro step name) persists.

Error Error
Class Code
6 20 Sub macro name Run This should not This could indicate database
cannot be blank. Compilation normally occur. corruption or an internal
software error.
6 21 Invalid incubation Run The defined Reprogram protocol(s) to
time: %s (%s Compilation incubation time use valid incubation times.
represents the does not exist in
incubation time) the Arguments
database.
6 23 No slides found to There were no This should not normally
run. barcodes found occur. If it does it could
to perform the indicate an internal software
run on. error or an error in the
Barcodes database.
6 25 Protocol for slide Run The slide Make sure a protocol is
position # %d Compilation barcode record defined for the bar code on
unassigned. (%d does not have a that slide.
represents the protocol
barcode position) associated to
the barcode.
6 26 Protocol for slide Run A recipe is not Reprogram the reported
position # %d has Compilation associated to protocol.
no recipe the protocol
assigned. (%d associated to
represents the the barcode.
barcode position)
6 31 Reagent missing Run The reagent Ensure that the dispenser
in Argument Compilation needed for the has been registered into the
database, product staining run is NexES software.
code: %d. (%d not in the
represents the Argument
reagent product database.
code)
6 32 %0:s dispenser # Run The reagent Ensure that the dispenser
%1:d missing from Compilation data needed for has been registered into the
Dispenser a reagent NexES software.
database. (%0:s dispenser
represents the loaded on the
reagent name and reagent carousel
%1:d represents is not in the
the reagent serial Dispense
number) database.
6 33 Recipe %s Run There are no This may occur if a software
missing. (%s Compilation recipes supplement had been
represents the associated with installed which delivered
protocol recipe) the protocol to new recipes for which
be executed for protocols were created.
the staining run.
6 40 Recipe %s has Run The recipe steps This could indicate database
nonconsecutive Compilation are not in corruption or an internal
steps in it. (%s sequential order software error. Reinstall
represents the when loading VSS and retry.
recipe name) recipe steps
during the run

Error Error
Class Code
compilation
process.
6 41 Recipe %0:s has Run The recipe step This could indicate database
an invalid recipe Compilation is determined to corruption or an internal
step # %1:d. (%0:s be invalid during software error. Reinstall
represents the the run VSS and retry.
recipe name and compilation
%1:d represents process.
the step number)
6 42 Recipe %s has no Run The recipe used This could indicate database
steps. (%s Compilation during the run corruption or an internal
represents the compilation software error. Reinstall
recipe name) process has no VSS and retry.
recipe steps
associated with
it.
6 43 Recipe step %s is Run Recipe step This could indicate database
missing in the Compilation error corruption or an internal
Function file. software error. Reinstall
VSS and retry.
6 46 Protocol step Run Protocol missing Resave protocols and restart
missing for Compilation step - should not the run
required recipe occur
step %0:s, in
protocol #%1:d.
6 47 Protocols in run Run Protocols cannot Contact Ventana
are incompatible Compilation syncronize
with each other.
6 48 Protocol #%d has Run Internal error Check protocol options and
a blank reagent Compilation compiling resave
name. staining run
6 50 Unbalanced Run Incompatible Check protocols and slides
manual application Compilation timing with to make them compatible.
or titration Titration slides
protocols. and Non-
Titration slides
6 51 Macro step %0:s Run The macro step This could indicate database
has an invalid Compilation function is corruption or an internal
macro function outside a valid software error. Reinstall
number: %1:d range (0 to 162). VSS and retry.
(%0:s represents
the macro step
name and %1:d
represents the
macro step
function number)
6 52 Macro step %s Run The MacrFunc This could indicate database
has no match in Compilation database table corruption or an internal
the macro function does not contain software error. Reinstall
database. (%s the a record that VSS and retry.
represents the matches the
macro step name) macro step.
6 55 Missing argument Run When compiling This could indicate database

Error Error
Class Code
for Function %s. Compilation macros for a corruption or an internal
(%s represents the staining run, the software error. Reinstall
macro function) macro function VSS and retry.
does not have
an associated
argument in the
Argument
database table.
6 56 Macro %s is Run Compiling sub This could indicate database
missing in the Compilation macros for a corruption or an internal
Macros file. (%s staining run and software error. Reinstall
represents the sub the sub macro is VSS and retry.
macro name) not included in
the Macros
database table.
6 58 Maximum staining Run The run contains A limited number of steps
run size exceeded. Compilation too many steps can be downloaded to an
for the staining instrument in a run. Report
module to the message to Ventana,
perform. including the protocols in the
run.
6 59 Function : %0:s Run An invalid This could indicate database
contains function # Compilation function is corruption or an internal
%1:d, which is identified in the software error. Reinstall
invalid in a recipe staining VSS and retry.
sync step. (%0:s procedure sync
represents the step.
function name and
%1:d represents
the macro step
function number)
6 62 Could not locate Run When computing This could indicate database
argument: %0:s of Compilation the constructor corruption or an internal
type: %1:s in the steps, an software error. Reinstall
argument argument is VSS and retry.
database. (%0:s missing from the
represents the database.
macro step
argument and
%1:s represents
the argument type)
6 63 Could not locate Run When computing This could indicate database
macro function: Compilation the constructor corruption or an internal
%s in the macro steps, a macro software error. Reinstall
function database. function is VSS and retry.
(%s represents the missing from the
macro step name) MacrFunc
database table.
6 65 Recipe step: %0:s Run Computing This could indicate database
contains function # Compilation macro steps for corruption or an internal
%1:d which is an active case software error.
invalid in a recipe slide and an
step. (%0:s invalid macro

Error Error
Class Code
represents the function is
recipe step name identified in a
and %1:d staining
represents the procedure step
macro step
function number)
6 66 Dispenser %0:s, # Run A reagent Locate the dispenser
%1:d missing from Compilation dispenser reported by this error and
tray. (%0:s needed for the place it on the reagent
represents the staining run is carousel.
reagent dispenser not on the
and %1:d reagent
represents the carousel.
serial number)
6 67 Not enough of Run The reagent on Place another dispenser of
reagent %s to Compilation the carousel the reported reagent on the
perform run. (%s does not have reagent carousel.
represents the enough tests
reagent) remaining to
stain the slides
that are loaded
on the
instrument
6 68 Reagent %s Run A reagent Put the missing reagent on
missing from tray. Compilation needed for the the carousel and restart the
(%s represents the staining run is run.
reagent) not on the
reagent
carousel.
6 69 Dispensers %0:s, Run Reagents Make sure the dispensers
# %1:d and %2:s, Compilation required to be in noted in the error message
# %3:d must be a specific order are beside each other.
beside each other. are not loaded Restart the run.
(%0:s represents on the reagent
the reagent name, carousel in the
%1:d represents proper order.
the reagent serial
number, %2:s
represents the
reagent name, and
%3:d represents
the reagent serial
number)
6 70 Errors in recipe Run error creating This could indicate database
constructor rule Compilation rule block corruption or an internal
block : %s software error. Contact
Ventana
6 71 Errors in recipe Run Error creating This could indicate database
sync rule block : Compilation recpe corruption or an internal
%s syncronization software error. Contact
rules Ventana
6 72 Macro 0 Run Instrument not in Put the instrument in Ready
generating object Compilation Ready mode mode and retry.

Error Error
Class Code
not ready to start
now.
6 74 Blank instrument Run The macro 0 is Ensure that the instrument
name Compilation being compiled name is assigned and is
and the staining nonblank. Restart the run.
instrument does
not have a
defined
instrument
name.
6 75 Duplicate %0:s # Run Qualifying Remove the reagent with the
%1:d dispensers Compilation reagents for a duplicate product code and
on tray. (%0:s staining run and serial number and restart the
represents the more than one run.
reagent name and reagent on the
%1:d represents reagent carousel
the product code) have the same
product code
and serial
number.
6 76 Error loading Run Tempurature Could be database
temperature Compilation groups could not corruption. Reinstal the
arguments. be obtained from software and try again.
Arguments table
6 77 Error loading Run Incubation Could be database
incubation Compilation groups could not corruption. Reinstal the
arguments. be obtained from software and try again.
Arguments table
6 78 %0:s, Serial # Run Loading reagent Load a reagent that is
%1:d has expired Compilation data to compile registered on the current
and can not be a staining run host.
used in this run. and the reagent
(%0:s represents has expired.
the reagent name
and %1:d
represents the
reagent serial
number)
6 78 %0:s, Serial # Run Loading reagent Load a reagent that is
%1:d is owned by Compilation data to compile registered on the current
host %2:d and can a staining run host.
not be used in this and the reagent
run. (%0:s is owned by
represents the another host
reagent name, system.
%1:d represents
the reagent serial
number, and %2:d
represents the
reagent owner)
6 78 Dispenser with Run Loading reagent Load a reagent that is
Product Code Compilation data to compile registered on the current
%0:d, Serial # a staining run host.

Error Error
Class Code
%1:d is owned by and the reagent
host %2:d and not is owned by
found in Products another host
Table (%0:d system and not
represents the in the dispense
reagent product database.
code, %1:d
represents the
reagent serial
number, and %2:d
represents the
reagent owner)
6 78 %0:s, Serial # Run Loading reagent Load a valid reagent.
%1:d has been Compilation data to compile
Deactivated and a staining run
can not be used in and the reagent
this run. (%0:s has been
represents the deactivated.
reagent name and
%1:d represents
the reagent serial
number)
%1:d has no Compilation data to compile
reagent in it and a staining run
can not be used in and the reagent
this run. (%0:s has no tests
represents the remaining.
reagent name and
%1:d represents
the reagent serial
number)
%1:d is not Compilation data to compile
enabled for this a staining run
instrument type and the reagent
and can not be has no argument
used in this run. record in the
(%0:s represents argument
the reagent name database.
and %1:d
represents the
reagent serial
number)
6 78 Dispenser with Run Loading reagent Load a valid reagent.
Product Code Compilation data to compile
%0:d, Serial # a staining run
%1:d has been and the reagent
Deactivated and has been
not found in deactivated and
Products Table not in the
(%0:d represents dispense
the reagent database.
product code and

Error Error
Class Code
%1:d represents
the reagent serial
number)
%1:d has expired and the reagent
and not found in has expired and
Products Table is not in the
product code and
%1:d represents
the reagent serial
number)
%1:d has no and the reagent
reagent in it and has no tests
not found in remaining and is
Products Table not in the
product code and
%1:d represents
the reagent serial
number)
%1:d is not and the reagent
enabled for this has no argument
instrument type record in the
and not found in argument
Products Table database and is
(%0:d represents not in the
the reagent dispense
product code and database.
%1:d represents
the reagent serial
number)
6 78 Dispenser x, Serial Run A reagent on the Replace it with a valid
#y has expired Compilation carousel has reagent.
and can not be expired.
used in this run.
%1:d is currently Compilation data to compile
in use on another a staining run
instrument (%0:s and the reagent
represents the is on another
reagent name and staining
%1:d represents instrument.
the reagent serial

Error Error
Class Code
number)
%1:d is currently and the reagent
in use on another is on another
instrument (%0:d staining
represents the instrument.
reagent product
code and %1:d
represents the
reagent serial
number)
6 80 Protocol # %d has Run Compiling a Correct the protocol.
more than %d Compilation staining run and
reagents in one finds a protocol
recipe step. (%d has more than 2
represents the reagents defined
protocol number for a staining
and the second procedure step.
%d represents the
maximum
reagents per
recipe step)
6 87 Manual application Run Selected Select a different Reagent
conflicts with the Compilation Reagent Access Access Point, or let the slide
selected Reagent Point is not run continue
Access Point, slide compatible with
run will be the manual
reattempted in application
%0:d minutes. slides
6 88 Dispense conflicts Run A dispense Select a different Reagent
with the selected Compilation operation Access Point
Reagent Access conflicts with the
Point, slide run will selected
be reattempted in Reagent Access
%0:d minutes. Point
7 1 %s has no Database Attempting to Contact Ventana.
associated cases. deactivate cases
(%s represents and no records
Case order name) exist.
7 4 This dispenser is Database Preparing to Wait for the other Host
owned by another refill a dispenser system to relinquish
host and cannot and the ownership. Force ownership
be filled at this dispenser is via access code from
time. owned by Ventana. Contact Ventana if
another Host the problem persists.
system.
7 5 This dispenser is Database Preparing to Wait for the other NexES
in use on an refill a dispenser Host system to relinquish
instrument and and the ownership.
cannot be filled at dispenser is
this time being used in a

Error Error
Class Code
staining run.
7 6 Product usage Database Attempting to Product has not been used.
data unavailable! generate a There is no data to be
Product Usage reported.
report and no
data is available.
7 7 There are no Database Attempting to log Set up the requestors.
preregistered cases when no
requesters case order
requesters are
set up.
7 13 There are no Database Attempting to log Register new bulks
preregistered bulk products
bulks and no
preregistered
consumables
are available.
7 14 There are no Database Attempting to log Register new probes
preregistered probe and no
probes pre-registered
probes are
available.
7 15 There are no Database Attempting to log Registere reagents.
preregistered reagents and no
reagents pre-registered
reagents are
available.
7 16 There are no Database Attempting to log Register control tissue
preregistered control tissue
blocks when no
preregistered
control tissue is
available.
7 17 There are no Database Attempting to Register new dispensers.
Active dispensers refill a
to fill dispensers when
no active
dispensers are
available.
7 18 There are no Database No pre- Register antibodies
preregistered registered
antibodies antibodies are
available and
attempting to log
antibodies.
7 19 There are no runs Database An attempt is Enter the control results
to QC at this time made to enter when there are executed
control results, staining runs.
and there are no
executed
staining runs.
7 21 Backup was Database User cancels the Do the backup again.
cancelled prior to backup before it

Error Error
Class Code
completion. is completed.
7 24 Incorrect Database The Select the correct frequency
Frequency in User maintenance
Maintenance frequency is not
Notes Daily, Monthly,
or Quarterly.
7 27 Inventory Database An attempt is Register product into
Database is Empty made to inventory
generate an
Inventory report,
and there are no
product records
in the inventory
database.
7 48 Database Integrity Database An error is Attempt to run database
Error: %s (%s encountered integrity check again.
represents data while performing Different actions will be
integrity error a database required depending on
message) integrity check. which tables get errors.
Send a screenshot to GTS
and the error log for further
analysis.
7 58 There is no Database There is no There is no system data to
system data to staining run data archive.
archive for the selected
archive date.
7 59 All staining run(s) Database Attempting to All staining run(s) must be
must be complete perform an complete before performing
before performing archive while a an archive.
an archive staining run is in
progress.
7 60 There are no runs Database Attempting to Change the date range or
to print at this time print a run report cancel the report.
and no data is
available for the
selected date
range.
7 61 No tests were run Database Attempting to Choose another dispenser
with this dispenser print a dispenser or cancel the report.
usage report
and the
dispenser has
not been used in
a staining run.
7 63 No runs have used Database Attempting to Choose another product or
this bulk fluid print a bulk cancel the report.
usage report
and the bulk
product has not
been used in a
staining run.
7 64 There were no Database Attempting to Change the date range.
runs which used print a bulk

Error Error
Class Code
bulk in the date usage report
range selected and the bulk
product has not
been used in a
staining run.
7 66 Keycode allocation Database No keycodes are Delete unused keycodes.
failed. Delete available within Change range of keycode
unused Keycodes the allocated allocation.
from Manage keycode range
Keycodes. Press and attempting
[Abort] to abort to print a case
print job. Press slide label with
[Ignore] to keycoding
generate a activated.
standard protocol
barcode
8 3 Both a Last and a Database Attempting to Re-enter data.
First Name are Access save contact
required information and
the first or last
name is blank.
8 6 File can not be Database The Host Database encryption got
opened, Call Access application is corrupted somehow. FTP
Ventana unable to open the NexES folder to Ventana
an encrypted for analysis.
database table.
8 7 Failed to Encrypt Database The Host Run database integrity
”%s” table with Access application is check. Retry. If it still fails,
Archive Password unable to re- gather the NexES folder and
(%s represents encrypt a FTP it to Ventana for
database table database table analysis.
name) with a NexES
Archive
encryption
during the
archive process.
8 8 Failed to copy Database The NexES Shutdown VSS and delete
tables to Access application fails all files and folders in
temporary folder to copy C:\VMSI\Private. Start VSS
database tables and try again. Check
to a temporary permissions to the
directory during C:\VMSI\Private folder.
the archive Check for antivirus
process. exclusions.
8 9 Failed to copy Database The NexES Shutdown VSS and delete
tables from Access application fails all files and folders in
temporary folder to copy C:\VMSI\Private. Start VSS
database tables and try again. Check
from a permissions to the
temporary C:\VMSI\Private folder.
directory to the Check for antivirus
NexES\Data exclusions.
directory during

Error Error
Class Code
the archive
process.
8 10 Error Deleting Database The NexES Restart VSS and retry. FTP
Runs Access application fails the dataset to Ventana for
to remove analysis if the problem
staining run data persists.
during the
archive process.
8 12 Error Deleting Database The NexES Restart VSS and retry. FTP
Dispensers Access application fails the dataset to Ventana for
to remove analysis if the problem
dispense data persists.
during the
archive process.
8 15 Could not gain Database Unable to gain Restart VSS and retry. FTP
ownership of Access ownership of a the dataset to Ventana for
Dispenser(s) reagent from analysis if the problem
another Host persists.
system when
attempting to
add or change
reagent
comments for
the kit.
8 15 Could not locate Database Unable to locate Restart VSS and retry. FTP
Kit Dispensers in Access the kit the dataset to Ventana for
table dispensers when analysis if the problem
attempting to persists.
add or change
reagent
comments.
8 37 Error Packing Database Unable to Restart VSS and retry. FTP
Table Access optimize the the dataset to Ventana for
database tables analysis if the problem
during the persists.
archive process.
8 43 Error Deleting Database Unable to delete Restart VSS and retry. FTP
Cases Access case requesters the dataset to Ventana for
from the analysis if the problem
database during persists.
the archive
process.
8 45 Error Deleting Database Unable to delete Restart VSS and retry. FTP
Blocks Access tissue blocks the dataset to Ventana for
from the analysis if the problem
database during persists.
the archive
process.
9 1 Probe: %s has Reagent Logging a 3rd Register a different probe.
already been Database party probe and Modify the current probe if
registered (%s the probe has data needs to be changed.
represents probe already been
name) registered in the

Error Error
Class Code
Host system.
9 2 Reagent: %s has Reagent Logging a 3rd Register a different reagent.
already been Database party reagent Modify the current reagent if
registered (%s and the reagent data needs to be changed.
represents reagent has already
name) been registered
in the Host
system.
9 6 Can not proceed Reagent A staining run is Register the product,
with staining run at Database started and no associate it with the
this time. You bulk reagents instrument, and start the
must register the are registered staining run.
following and associated
product(s) before with the
proceeding instrument.
10 2 There are no Printing You try to print a Set up the contacts.
contacts Recorded Contact report
and there are no
contacts set up
in the Ventana
software.
11 3 NexES Host Computer not Ensure USB drive is
Software Requires detecting USB working:
A Backup Disk To Flash drive 1. Double click on my
Run (Hardware) computer icon and double
click on the USB drive. If the
USB Drive is not shown,
remove the drive from the
PC, wait 3 seconds, then
reinstall the USB drive into
an available USB Port.
2. If USB drive is defective
at this point, replace it with a
Ventana approved USB
drive.
3. If site needs to start run.
1. Right click on NexES icon
on desktop, click on
properties 2. Click on
shortcut tab 3. add noback
to the following target path
C:\NexES\NexES.exe
11 4 XT Host could not Not defined Not defined
backup the
datafiles.
11 7 Com Port Error Communication Failed to Check connections and
(Message varies) with the initialize or retry. Contact ventana if the
Instrument utilize the com issue persists.
port for
instrument
communications
11 8 Out Of Memory in
ProcessResponse

Error Error
Class Code
11 9 Out Of Resources
in
ProcessResponse
11 10 Program
Exception -
Command:%d
Message:%s
11 12 Bad Short Date
Format: %s
11 18 Database
ownership update
failed.
11 20 Database version
update to table
failed.
12 0 Staining Remote The staining run Remove the slides.
instrument Software completes.
program ran to
completion
12 1 Invalid step found Remote Invalid step Contact Ventana
in RunStarting Software found in Run
macro. Call for start macro
service.
12 1 Slide heat is too Slide
high. temperature
reached a
potentially
damaging level
(125° C) for over
5 seconds.
Check slide
heater sensor,
fan.
12 2 Invalid step found Remote Invalid step Contact Ventana
in RunEnding Software found in Run
macro. Call for end macro
service.
12 3 Slide access door The slide door
was opened was opened,
during the run. possibly
compromising
the slide
temperature
during a run.
12 5 Low system air Remote The low Could be a compressor error
pressure was too Software pressure falls or a leak.
low. below the low
pressure low
limit.
12 5 Pressure is too Air pressure has
low. fallen below the
minimum (12.0
psi) over a 5

Error Error
Class Code
second period.
Do leak check.
Test compressor
and regulator.
12 6 Low system air Remote The low Could be a compressor
pressure is too Software pressure error.
high. exceeds the low
pressure high
limit.
12 6 Pressure is too Air pressure has
high. risen higher than
permitted (13.5
psi) over a 5
second period.
Check:
regulator, valves
(VRMIX and
BCBLO),
pressure sensor.
12 7 Pressurizing time
exceeded.
12 8 Purging failed to The purging
complete within operation
required time (dropping air
pressure to .5
psi) failed to
complete in the
time allotted (3
minutes). Check
zero calibration
of the pressure
sensor.
12 9 Time limit for A non-fatal error,
existing exception such as “Slide
expired was opened
during the run”
was not signed
off by the
operator within
the required 5
minute interval.
12 10 Power failed Remote The power to the Ensure the power
during run Software instrument is cut requirements are met from
off during a the lab's standpoint. Check
staining run. the power supply on the
instrument. Ensure the
power switch is on.
12 11 Slide heat Remote A slide heater on Could be not enough LCS
exceeded the Software the instrument on the slide at incubation, or
absolute maximum exceeds the a faulty slide heater.
temperature. maximum
allowable
temperature.

Error Error
Class Code
12 12 Slide heat Remote A slide heater Could be unplugged from
temperature Software sensor on the the banana board, or a faulty
sensor is bad or instrument heater
not connected. cannot be
detected.
12 15 Pressure Remote Air pressure has
exceeded the Software increased
absolute maximum beyond the
limit upper range of
the sensor (14.2
psi). Check:
regulator, valves
(VRMIX and
BCBLO),
pressure sensor.
12 16 Nozzle plate failed Remote The home faulty home sensor.
to find home Software sensor fails to Probably needs to be
position detect during the replaced
homing of the
nozzle plate.
12 16 Slide tray failed to
find home position.
12 17 Reagent tray failed Remote The home faulty home sensor.
to find home Software sensor fails to Probably needs to be
position detect during the replaced
homing of the
reagent tray
carousel.
12 17 Reagent tray failed Seek for home
to find home position failed.
position or tray is Possible
missing. problems with
motor controller,
motor, home
sensor. Also
check belts and
bearing pads.
12 18 Slide heat is too Slide
low. temperature
remained below
normal (-3° C)
for over 5
minutes. Check
slide heater
sensor, fan.
12 19 Fluid in tub Remote The excess fluid Drain could be clogged, or
exceeded Software level exceeds the sensor is faulty.
maximum level the sensor level
located on the
internal tub.
12 21 Depressurizing
time exceeded.
12 23 User aborted run Remote The User ends a Could be that the user

Error Error
Class Code
before normal Software staining run prior aborted the run manually, or
completion to its natural a VSS failed to detect the
completion. HASP key durign the start of
a run while other slides were
in progress
12 24 Nozzle plate Remote The nozzle plate Restart the runs from Sleep
position incorrect Software becomes mode. If the problem
during the run misaligned. persists, reboot the
instrument and try again.
12 24 Slide tray position
incorrect during
the run
12 25 Reagent tray Remote The reagent Restart the runs from Sleep
position incorrect Software carousel mode. If the problem
during the run becomes persists, reboot the
misaligned. instrument and try again.
12 36 LCS reservoir
failed to prime.
12 40 LCS reservoir
failed to prime.
12 41 Optional reservoir
failed to prime.
12 42 Vacuum trap is full
of fluid
12 44 LCS reservoir
failed to recharge
itself in time.
failed to recharge
itself in time.
12 48 LCS reservoir
failed to recharge
itself in time.
failed to recharge
itself in time.
12 50 Waste container is
full.
12 51 Slide heater error.
12 53 Nozzle plate check Remote The nozzle plate Contact Ventana to align
at end of run Software is slightly out of and check hardware
indicated minor alignment.
misalignment
12 53 Slide tray check at
end of run
indicated minor
misalignment
12 54 Nozzle plate check Remote The nozzle plate Contact Ventana to align
indicated major Software is seriously out and check hardware
misalignment of alignment.
12 54 Slide tray check at
end of run
indicated major

Error Error
Class Code
misalignment
12 55 Reagent tray Remote The reagent tray Contact Ventana to align
check at end of Software is slightly out of and check hardware
run indicated alignment.
minor
misalignment.
12 55 Reagent tray
check indicated
major
misalignment
12 56 Reagent tray Remote The reagent tray Contact Ventana to align
check at end of Software is seriously out and check hardware
run indicated of alignment.
major
misalignment.
12 56 Reagent tray
check indicated
major
misalignment
12 59 Priming operation
completed
12 60 Cleaning operation Remote A cleaning Go to the next step in the
completed. Software function has cleaning operation or
completed. resume using the instrument
12 61 Pressurizing time The standard 13
was exceeded psi air pressure
could not be
achieved at
startup in under
60 seconds.
Check
compressor,
relay, leakage
from fluid
bottles, etc.
12 63 Run stopped due Remote Slide drawer Replace heater.
to heater(s) Software heaters are too
abnormally hot. If hot for slide
this situation processing.
persists, call for
service.
12 65 High pressure Remote The high Dispatch FSE for service
exceeded Software pressure
exceeds the
maximum
allowable limit
for a specified
amount of time.
12 99 AFM left board is Remote The AFM control Could be bad board or
not responding Software board is not connection came loose.
normally to responding to Contact Ventana.
commands. If this commands.
situation persists,

Error Error
Class Code
call for service.
12 102 Exhaust fan is not Remote The exhaust fan Connection came loose.
operating properly. Software is not operating Dispatch FSE.
If this situation properly.
persists, call for
service.
12 103 Instrument Remote The instrument Instrument should restart
crashed due to Software crashes due to a automatically. Transfer
task hang. task hang. dataset to R&D for
investigation
12 106 High system air Remote The high Could be a bad sensor, or a
pressure was too Software pressure falls compressor error/leak
low. below the high
pressure low
limit.
12 107 High system air Remote The high Could be a bad sensor, or a
pressure is too Software pressure compressor error
high. exceeds the
high pressure
high limit
12 109 Failed to confirm Remote The system fails Slide may have moved, or
that the slide was Software to confirm that a slide may have gunk on it.
still present. slide is still Or Slide Detector is faulty
present.
12 111 Slide barcode Remote There is a slide Contact Ventana to check
reader Software barcode reader hardware
communications comm failure.
failure.
12 111 Barcode reader Remote Could not Could be a bad reader, or a
communications Software communicate connection came loose. Call
failure. with barcode Ventana
reader
12 112 Reagent barcode Remote There is a Contact Ventana to check
reader Software reagent barcode hardware
communications reader comm
failure. failure.
12 113 Slide processing Remote Commands Staining Procedure or Macro
time exceeded the Software attempted to error. Contact Ventana
limit of the slide process after the
tray dwell time. slide position's
Please notify dwell time
Ventana.
12 113 Slide processing
time exceeded the
limit of the nozzle
plate dwell time.
Please notify
Ventana.
12 116 Inactive slide Remote A slide requests Transfer dataset for analysis
attempted to start Software a submacro step
a sub macro. This while the nozzle
typically indicates plate is at
a software error stations 1, 7,8,

Error Error
Class Code
or 9, or an
inactive slide
requests the
macro step.
12 117 Inactive slide Remote An inactive slide Transfer dataset for analysis
attempted move Software or a slide that is
the reagent tray. not under nozzle
This typically plate station 6
indicates a requests a
software error. reagent carousel
move.
12 118 Slide heater error.
If this situation
persists, call for
service.
12 122 Slide barcode is Remote The instrument Make sure the slide barcode
unreadable, check Software can’t read the is readable and re-start the
slide and retry. barcode on the slide.
indicated slide.
12 125 High system air
pressure was too
low for an
extended period of
time.
12 126 Low system air
pressure was too
low for an
extended period of
time.
12 130 Slide #21 Remote The slide Could be a bad slide heater.
temperature Software position is Call FSE to run tests
control error (too unable to
low) achieve the
setpoint
temperature in
the timeout
duration.
low) achieve the
setpoint
temperature in
the timeout
duration.
low) achieve the
setpoint
temperature in
the timeout
duration.

Error Error
Class Code
low) achieve the
setpoint
temperature in
the timeout
duration.
low) achieve the
setpoint
temperature in
the timeout
duration.
low) achieve the
setpoint
temperature in
the timeout
duration.
low) achieve the
setpoint
temperature in
the timeout
duration.
low) achieve the
setpoint
temperature in
the timeout
duration.
low) achieve the
setpoint
temperature in
the timeout
duration.
low) achieve the
setpoint

Error Error
Class Code
temperature in
the timeout
duration.
temperature Software position Call FSE to run tests
control error (too temperature
high) exceeds the
maximum
allowable.
high) exceeds the
maximum
allowable.
high) exceeds the
maximum
allowable.
high) exceeds the
maximum
allowable.
high) exceeds the
maximum
allowable.
high) exceeds the
maximum
allowable.
high) exceeds the
maximum
allowable.
high) exceeds the
maximum
allowable.

Error Error
Class Code
high) exceeds the
maximum
allowable.
12 149 Slide #30 Remote The slide Send service rep to
temperature Software position investigate
control error (too temperature is
high) out-of-range or
disconnected.
12 150 Slide #21
temperature
sensor bad or
disconnected
sensor bad or temperature is
disconnected out-of-range or
disconnected.
disconnected.
disconnected.
disconnected.
disconnected.
disconnected.
disconnected.
disconnected.

Error Error
Class Code
disconnected.
temperature Software position is investigate
low). achieve the
setpoint
temperature in
the timeout
duration.
low). achieve the
setpoint
temperature in
the timeout
duration.
low). achieve the
setpoint
temperature in
the timeout
duration.
low). achieve the
setpoint
temperature in
the timeout
duration.
low). achieve the
setpoint
temperature in
the timeout
duration.
low). achieve the
setpoint
temperature in
the timeout
duration.

Error Error
Class Code
low). achieve the
setpoint
temperature in
the timeout
duration.
low). achieve the
setpoint
temperature in
the timeout
duration.
low). achieve the
setpoint
temperature in
the timeout
duration.
low). achieve the
setpoint
temperature in
the timeout
duration.
low). achieve the
setpoint
temperature in
the timeout
duration.
low). achieve the
setpoint
temperature in
the timeout
duration.
low). achieve the
setpoint

Error Error
Class Code
temperature in
the timeout
duration.
low). achieve the
setpoint
temperature in
the timeout
duration.
low). achieve the
setpoint
temperature in
the timeout
duration.
low). achieve the
setpoint
temperature in
the timeout
duration.
low). achieve the
setpoint
temperature in
the timeout
duration.
low). achieve the
setpoint
temperature in
the timeout
duration.
low). achieve the
setpoint
temperature in
the timeout
duration.

Error Error
Class Code
low). achieve the
setpoint
temperature in
the timeout
duration.
high). exceeds the
maximum
allowable.
high). exceeds the
maximum
allowable.
high). exceeds the
maximum
allowable.
high). exceeds the
maximum
allowable.
high). exceeds the
maximum
allowable.
high). exceeds the
maximum
allowable.
high). exceeds the
maximum
allowable.
high). exceeds the
maximum

Error Error
Class Code
allowable.
high). exceeds the
maximum
allowable.
high). exceeds the
maximum
allowable.
high). exceeds the
maximum
allowable.
high). exceeds the
maximum
allowable.
high). exceeds the
maximum
allowable.
high). exceeds the
maximum
allowable.
high). exceeds the
maximum
allowable.
high). exceeds the
maximum
allowable.
high). exceeds the

Error Error
Class Code
maximum
allowable.
high). exceeds the
maximum
allowable.
high). exceeds the
maximum
allowable.
high). exceeds the
maximum
allowable.
disconnected. out-of-range or
disconnected.
disconnected.
disconnected.
disconnected.
disconnected.
disconnected.

Error Error
Class Code
disconnected.
disconnected.
disconnected.
disconnected.
disconnected.
disconnected.
disconnected.
disconnected.
disconnected.
disconnected.
disconnected.

Error Error
Class Code
disconnected.
disconnected.
disconnected.
12 220 Waste container
was full during run.
12 225 Initializing
12 226 Draining Ventana
Fluids
12 227 Waiting for
Decontamination
Fluid
12 229 Incubating with
Decontamination
Fluid
12 230 Draining
Decontamination
Fluid
12 231 Waiting for DI
Water
12 233 Draining DI Water
12 234 Waiting for
Ventana Fluids
12 236 Priming lines with
Ventana Fluids
12 237 Disconnect tubing
manifold and
insert filled Bulk
bottles into
instrument.
12 241 Cleaning with
Disinfectant
12 243 Press button on
staining module to
continue the run.
12 245 Priming, please
wait
12 247 Press Ventana Remote A function test Press the button to resume
Bug button on Software has come to a the test.
staining module to stop and needs
continue test to be continued.
function
12 251 Press stainer Remote The system has Complete the application

Error Error
Class Code
button to open, Software paused for a and resume the staining run.
perform manual manual
application, press application.
and hold button
when complete
13 2 No slides found,
run terminated
13 3 Barcode read
Aborted with Error
Code %d, Please
Retry.
13 4 Barcode read Instrument Tray Attempting to Restart run.
timed out, Please Scan read barcodes
Retry. during the run
process and the
barcode
information is
formatted
incorrectly.
13 5 Barcode read
Aborted with Bad
Format error,
Please Retry.
13 6 Barcode Reader Instrument Tray Misread of slide Restart run.
Did Not Initialize, Scan label.
Please Retry.
13 7 Slide Barcode Instrument Tray Misread of slide Restart run.
Check Digit Error, Scan label.
Restart Run.
13 8 Invalid Barcode at Instrument Tray Attempting to Restart run.
position %d. Scan read reagent
barcodes during
the run process
and the reagent
barcode cannot
be decrypted.
13 9 (%d represents Instrument Tray Misread of slide Restart run.
the reagent Scan label.
position on the
reagent carousel).
13 10 %0:s with Serial
#%1:d at Position
%2:d is a duplicate
product, please
remove from tray.
13 11 Barcode Trigger Instrument Tray Misread of Restart run.
Failed, Please Scan Reagent label.
Retry.
13 12 Barcode read Instrument Tray Misread of Restart run.
Error Code %d, Scan Reagent label.
Retrying…
Barcode read
Timed Out,

Error Error
Class Code
Retrying…
13 13 Barcode read Bad Instrument Tray Misread of Restart run.
Format, Scan Reagent label.
Retrying…
13 14 Unknown Bar
Code Reader
Type, run
terminated
13 15 Keycode Bar Code Instrument Tray The keycode Check connectivity between
on Slide at Scan embedded in the the other hosts in the
Position %d could slide barcode replicated environment for
not be Resolved. could not be the ability to replicate case
read correctly slides.
during the
staining run
process.
13 17 Unknown error
text, but the error
is defined
13 18 (%d represents Instrument Tray Case slide Wait until other NexES Host
slide position Scan ownership could system is finished with case
Could not acquire not be acquired slide. Force ownership
Ownership of all from another acquisition with access code
Case Slide(s). Host system from Ventana.
during the
staining run
process.
13 21 [#] Slide Run Informational Information Only Information Only
Resumed after Message
being paused for 3
Mins 32 Secs
13 23 [#] Reagent Informational Information Only Information Only
Access occurred Message
during run.
14 3 Slide at position Staining Run The selected Replace the heater
#XXXX is on a protocol to be
faulty heater. used during the
run process was
not created for
the instrument
type.
14 4 Protocol #%0:s at Staining Run Communication Create protocol and restart
slide position with an staining run.
#%1:d is not instrument fails
defined for this during a staining
instrument type. run when
(%0:s represents information is
the protocol being
number and %1:d downloaded.
represents slide
position on the
carousel)).
14 5 Slide Barcode The number of An incorrect count was input

Error Error
Class Code
Count Mismatch - slides specified in the checklist or The
%d expected, but in the pre-run barcode reader is not
%d acquired. checklist did not functioning properly or The
match the barcode blow-off is not
number found. functioning.
Or The barcode reader is
not adjusted properly.
14 6 Run Aborted. Not Staining Run The staining Check communications path
acknowledged by instrument from instrument to host.
remote. Error encounters a
Code %d, Please timeout
Retry. (%d condition during
represents the a staining run.
error code).
14 7 Run download Staining Run The run Restart staining run
Timed Out, download
Restart Run. information is
formatted
incorrectly
during the run
process.
14 8 Run Download Staining Run A slide is seated Restart staining run
Aborted with Bad on a faulty
Format Code %d, heater during
Please Retry. (%d staining run.
represents the
format code).
14 9 The following slide Staining Run Communication Contact Ventana to replace
heater(s) are faulty between the faulty heaters
and require staining
service. Press [ instrument and
Abort ] to the host
terminate run. application is
Press [ Ignore ] to lost during the
continue. run information
download when
performing a
function test.
14 10 Run Download Staining Run Communication Restart the staining run.
Aborted, Restart to the staining
Run. instrument fails
while performing
a function test
when
downloading run
information to a
staining
instrument.
14 11 Run Download Staining Run Test Function Restart the test function run.
Aborted, Restart timed out while
Run attempting to run
14 12 Test Function Staining Run During a Restart the staining run.
Aborted, Restart function test the

Error Error
Class Code
Run. run download
information is
formatted
incorrectly.
14 13 The following slide Staining Run A slide is placed Contact Ventana to replace
heater(s) are faulty on a faulty faulty heaters
and require heater when a
service. Press [ function test is
Abort ] to run.
terminate run.
Press [ Ignore ] to
continue.
14 17 Press [ Ignore ] to
Continue anyway.
Press [ Ignore ] to
Continue anyway.
Press [ Abort ] to
abort Test
Function. Press [
Ignore ] to
Continue anyway.
14 18 Press [ Ignore ] to
Continue anyway.
Press [ Ignore ] to
Continue anyway.
Press [ Abort ] to
abort Test
Function. Press [
Ignore ] to
Continue anyway.
14 20 Run exceeds
desired delayed
start time. Run
starting
immediately.
14 21 Run exceeds
desired delayed
completion time.
Run starting
immediately.
14 22 Database version Staining Run The database Send attempt to fix code.
fields are out of version field of
date. Please the dispense
shutdown and record is
restart NexES. different than the
database
version in the
HASP key.
14 23 Database Staining Run The ownership Send attempt to fix code.
ownership version database
fields are out of version field of
date. Please the dispense
shutdown and record is

Error Error
Class Code
restart NexES. different than the
database
version field in
the dispense
record.
14 25 Slide Barcode
Check Digit Error,
Please re-label
slide at position:
%d
14 27 No reagents found
on reagent
carousel. Do you
wish to continue
anyway?
14 29 Protocol "%0:s" at
slide position
#%1:d is missing
Processing Steps.
14 31 %0:s dispenser
#%1:d missing
from Dispenser
database.
14 32 Duplicate %0:d
#%1:d dispensers
on tray.
14 33 %0:d dispenser
#%1:d missing
from Package.
14 34 %0:s, #%1:d
dispenser missing
from tray
14 35 %0:s, Serial
#%1:d is owned by
host #%2:d and
can not be used
14 36 Dispensers %0:s,
#%1:d at position
%2:d and a
dispenser of
"%3:s" must be
beside each other.
14 37 Dispensers %0:s,
#%1:d and %2:s,
#%3:d must be
beside each other.
14 38 Not enough of
reagent %s to
perform run
14 39 %0:s, #%1:d
dispenser missing
from tray
14 39 Reagent %s

Error Error
Class Code
missing from tray
14 40 Reagent missing
in Argument
database, product
code: %d.
14 41 %0:s, Serial
#%1:d has expired
and can not be
used
14 42 %0:s, Serial
#%1:d has been
Deactivated and
can not be used
14 43 %0:s, Serial
#%1:d has no
reagent in it and
can not be used
14 44 %0:s, Serial
#%1:d is not
enabled for this
instrument type
and can not be
used
14 45 %0:s, Serial
#%1:d is currently
in use on another
instrument
14 46 Continuing with
dispenser %0:s,
#%1:d missing
from tray
14 47 %0:s dispenser
missing from tray,
required adjacent
to dispenser
"%1:s", #%2:d at
position %3:d.
14 48 Inadequate waste
capacity to
continue.
14 49 Inadequate %s
bulk volume to
perform slide run.
14 51 A batch run is
starting on
instrument: %s.
For those slides,
the internal bulk
capacity must be
supplemented by
the external
bottles. Verify that
the following

Error Error
Class Code
amounts are
available in these
external bottles:
14 52 Protocol #%0:s at Staining Run Protocol is Check protocol names and
slide position defined for a numbers. Reprint labels
#%1:d is not different
defined for this instrument type
instrument type.
14 53 Protocol "%0:s" at Staining Run Protocol is Check protocol names and
slide position defined for a numbers. Reprint labels
#%1:d is not different
defined for this instrument type
instrument type.
14 54 Slide was detected Staining Run Barcode was Move the slide to a valid
on a faulty position acquired on a position. Call Ventana to fix
#%d, please malfunctioned the malfunctioned slide
reposition slide. slide position positions.
15 26 Run Compiler Customer tries A common cause of this
Terminated to start runs on error is characters have
Abnormally the ULTRA, after been used in the Instrument
slides are read friendly name. A single
the error quote (‘) and double quote
appears and (“) are not to be used in the
runs do not start. instrument name and will
cause the 15-26 error. An
example of an instrument
name that would cause the
error is: Bob’s ULTRA.
Rename the instrument
name without using the
single or double quotes. In
the example above you
could rename to: Bobs
ULTRA.
99 1 Unable to fix. The database FTP the NexES folder to
Table may be tables cannot be Ventana for analysis
Corrupted. fixed when
starting the host
application.
99 2 Fixing Archive Attempting to fix Restore from the most
data to your Live database tables recent backup. Archive files
system may cause that are mixed are not allowed to be run in
undesirable with Archive and the live system.
results. This action Live data when
is not starting the host
recommended!. application.
99 3 Unable to fix. Unable to re- FTP the NexES folder to
Table may be encrypt Ventana for analysis
Corrupted. database tables
while attempting
to repair the
table when
starting the host

Error Error
Class Code
application.
99 7 The Zip file Attempting to Rename the old file if you
already exists. create a zip wish to keep it. Otherwise,
Overwrite?. archive file and click Yes to automatically
the zip file overwrite the file.
already exists.
99 8 Error reading data Unable to read Retry. Reinstall Hasp drivers
from hardware the HASP key and reseat the Hasp key.
key. when creating a Replace the key if
zip archive necessary.

BenchMark XT Service Manual (New)

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BenchMark XT / DISCOVERY XT /

BenchMark LT Service Manual

Part Number 2000300 Revision E

VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page ii

VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page iii

5.3 Microcontroller IC .............................................................................................................. 28

VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page iv

10.12 Verify Instrument Level ..................................................................................................... 71

VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page v

12.0 Additional Tests and Adjustments.................................................................. 97

VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page vi

13.18 Slide Heater Assembly .................................................................................................... 145

VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page vii

VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page viii

Figure 54. Flex Cable Installed ............................................................................................................. 141

VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page ix

Figure 111. Motor Rotation Nozzle Plate Assembly ............................................................................... 208

VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page x

1.0 Safety Information

WARNING: UNPLUG THE UNIT BEFORE RELOCATING IT.

WARNING: FOR CONTINUED PROTECTION AGAINST THE

1.2.1 Caution: Hot Surface—Do Not Touch

Figure 1. Hot Surface Caution Label

1.2.2 Caution: Refer to Accompanying Documents

Figure 2. Document Reference Caution Label

VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page 1

1.2.3 Caution: Risk of Electric Shock

Figure 3. Electric Shock Caution Label

1.2.4 Caution: Disconnect Power Before Servicing

Figure 4. Disconnect Power Caution Label

1.2.5 Ground Connection

Figure 5. Ground Connection Label

VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page 2

1.2.6 Caution: LASER

Figure 6. LASER Caution Label

1.2.7 Caution: LASER

Figure 7. LASER Caution and Information Label

1.3 Safety Training

l The instrument must be connected to a voltage source that

VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page 3

¨ This includes the reagent carousel, dispensers, and

1.4 Safety Compliance

VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page 4

2.0 What the Instrument Does

2.2 Tissue Staining Process

VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page 5

2.3 How the Instrument Works

VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page 6

¨This is called barcode blow-off

VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page 7

3.0 Major System Modules

3.1 Stainer Subassembly

VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page 8

position below a plunger which presses down on a

3.2 Automated Fluidics Module (AFM)

3.3 Waste Subassembly

VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page 9

· The typical waste sensor has a gray cap. This sensor

3.4 Personal Computer

VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page 10

The entire instrument is monitored and controlled by the

VMSI CONFIDENTIAL INFORMATION P/N 2000300 REV E Page 11

4.0 Stainer Subassembly