Hello
I have been using imageJ for a while and I am very comfortable using it.
I am trying to complete a research project that produces numerical results
that represent image slices as tab delimited text files.
Her is my question:
I have several hundreds of these text images. The following are some
information about the text image files:
1) All image have the same number of pixels along both dimensions.
2) Pixel values vary from 0-1.0
3) the pixel x dimension is different than the y dimension.
4) each image represent a z position
I wanted to stack these images and apply a LUT to them. I was able to
accomplish this task using the macro below:
//Get image directory name
dir = getDirectory("Choose a Directory ");
//Create file list of the QA Images & NumImagesToProcess
list = getFileList(dir);
NumImagesToProcess = list.length;
//Process one image at a time
for (i=0; i<list.length; i++) {
if (endsWith(list[i], "/")){
listFiles(""+SubDirNames[0]+list[i]);
}else{
Text1 = "open=["+dir+list[i]+"]";
//print(Text1);
run("Text Image... ",Text1);
run("16_colors");
}
}
//Make them into a stack and save
run("Images to Stack", "name=Stack title=-Group- use keep");
Text1 = "format=TIFF name=Stack start=0 digits=4 use save=["+
dir+"Stack0000.tif]";
run("Image Sequence... ", Text1);
This macro works. Is their a better way to do this?
My question:
1) Can I add these images to the stack without having to open them?
2) How can I modify the x and y dimension of the pixel (give the pixel
unit length value)
3) Rescale the pixel values and assign color to that value(currently
large number of values= 0 which are represented as black on the screen-->
light blue or anything else)
4) How to create a stack file from command line or a program.
Again thank very much for you help and support
Sincerely;
Mat M. Al-Tamimi, M.Sc.
E-mail:
[hidden email]
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