IDEAS File Management Structure

Opening Data Files

There are three file types: Raw Image File (.rif), Compensated Image File (.cif), Data Analysis File (.daf).

To open a Raw Image File:

1. Select Open from the File menu and select a .rif file to open, or double click the icon.
2. To apply spectral compensation to the images, check Perform Compensation.
Quick Start Guide: IDEAS File Management

3. Choose a compensation matrix to use for spectral compensation. This file should be a
matrix generated from the controls used for the experiment. Click on the folder icon to
browse for the file. Compensation matrix files have the extension .ctm.
4. Select the number of objects to load.
5. To view the corrections that will be applied to the .rif file click Advanced. Most often, the
defaults will be adequate. On some older data files you may need to provide control files for
spatial alignment and camera background. Change Alignment Offsets and Change
Correction Offsets (Camera Background/Dark Current) buttons allow you to use values from
other .rif files if necessary. You may also turn on MTF correction.
6. Click OK.
7. Name the Compensated Image File that is created.
8. Choose a template file (.ast) to define the initial analysis state.
9. Save the file as a Data Analysis File.

To open a Compensated Image File:

1. Select Open from the File menu and select a .cif file to open, or double click the icon.
2. Select the name for the Compensated Image File that is created.
3. Choose a template file (.ast) to define the initial analysis state.
4. Click Open.
5. Save the file as a Data Analysis File.

To open a Data Analysis File:

1. Select Open from the File menu and select a .daf file to open, or double click the icon.
2. The state of IDEAS is restored to the state of the application when the .daf file was saved.

To open multiple .cif files:

1. Select Open Multiple Files from the File menu.
2. Click Add Files and select the .cif files to open. The files appear in the Files to Load list.
3. Enter the number of objects to load for each file.
4. A population is created for each file selected. You may change the default population names.
5. Enter the resulting .cif file name.
6. Browse to select a template.
7. Change the resulting .daf file name if desired.
8. Click OK to load the .cif files and create a single .daf file.

Copyright © 2007 Amnis Corporation. 800.730.7147 www.amnis.com

 File Management Procedures

To merge Raw Image Files:

1. Select Merge .rif Files from the Tools menu. The Merge .rif Files screen appears.
2. Click Add Files to browse for the .rif files to merge.
Quick Start Guide: File Management procedures

3. Click OK and name the file when the merge list is complete.
4. Enter a unique file name and click Save.

To Save a Data Analysis File:

1. Select Save as Data Analysis File from the File.
2. Enter a filename, and Click Save. Note that the default folder is where the .cif file is saved.

To save to a template file:

1. Select Save As Template File (.ast) from the File menu. A Save File screen appears.
2. Enter the name of the file to save and click Save.

To create a new data file from populations:

1. Select Create Data File from Population under the Tools menu.
2. Check the Raw Image File (.rif) box to create a .rif file and click the corresponding Browse
button to select a name.
3. Check the Compensated Image File (.cif) box to create a .cif.
4. Check the populations in the Select populations list to include in the new data file(s).
5. Click OK to create the new files.

File Structure Overview

1.) Open Raw Image File

2.) Navigate to compensation Matrix
3.) Save Corrected Image File

5.) Save Data Analysis File

4.) Navigate to analysis template

Copyright © 2007 Amnis Corporation. 800.730.7147 www.amnis.com