Académique Documents
Professionnel Documents
Culture Documents
http://rsb.info.nih.gov/ij
ImageJ
An adaptation of NIH image for the Java platform.
Can run on any computer systems that can run Java (Sun
Microsystems)
Open source
Two powerful scripting languages
Java Plugins
Macro Language
Continual Upgrades
Active community of several thousand users
Resources
ImageJ Web Site http://rsb.info.nih.gov/ij
Macbiophotonics: http://www.macbiophotonics.ca/imagej/
Wiki: http://imagejdocu.tudor.lu/
Burger and Burge (a real book!): Digital Image Processing,
An Algorithmic Introduction using Java; Springer Verlag, 2008
Image Menu
Process Menu
Analyze Menu
Plugins Menu
Help Menu
Log Scale
The histogram shows the number of pixels of
each value, regardless of location. The log
display allows for the visualization of minor
components. Note that there are unused pixel
values
In this case, the log display indicates that virtually all pixel values are used, even
though they are a small percentage of the total.
Brightness Adjustment
Contrast Enhancement
For contrast enhancement, a lower value, in this case, 88, is set at zero, and a higher
value, 166, is set at 255. The values of each of the pixels are adjusted proportionately.
Note that because of the integer values, not all of the pixel values are used.
Look-Up Tables
8-bit images have no inherent color values. We normally assign values to each
of the pixels according to a table. Because of earlier display devices, these
values were shades of gray. As displays improved, it became possible to
assign specific colors to given values. In ImageJ, there are three
representations of LUTs.
The other way to treat color is to assign a set of 3 values, for Red,
Green and Blue to each pixel. For common color images, each of the
three colors is represented as an 8-bit value.
The reason that the image is so dark is that the routine averages the three channels
(rgb) to generate the image. Since there is no data in g or b, the values for the red
channel are divided by 3, yielding a dark image.
We can overcome this by separating the three channels and discarding those
with no data.
8-bit
Channel separation
Because of the reduction in values in the 8-bit conversion, there are fewer values in the histogram.
Color Merge
Many fluorescence images are taken in single channel images which are
often merged to generate a single overlapped image.
What happened?
The value at any pixel is the sum of all four channels. Remember that the
gray channel actually has values for r,g, and b. These are added to the other
values, and exceed the 255 limit.
Since the image is a composite (i.e. each plane is
represented separately and the images are combined), we
can divide each of the planes, so that the maximum value
of the additions is less than 255. We can then adjust
brightness and contrast to compensate without exceeding
the limit.
red
green
blue
It appears that the greatest difference between the background and the
signal is in the red channel, but there are stripes on the image.
we can use the graph of the image to make a rough determination of the
threshold, and then tune it by looking as the selection.
We can change the unit of length to, say, mm, and the pixel width changes to
adjust. The results of the analysis, then, are presented in mm, rather than inches.*
*We have discovered that the camera we use for micrography also includes a value of 96 dpi in our images, which has
to be corrected. The value of 96 is, we assume, related to print size. At any rate, we have to restandardize each
image.