how to use imageJ to merge different channels and do a z stack average

Question

I have ten tiff files and each of them contains two channels imaging data, I want to labeling different colors for the two channels and after that do a z projection, anyone knows how to do it?

Answer 1

First of all, make yourself familiar with ImageJ's concepts of displaying pseudocolor and composite images.

Use File > Import > Image Sequence... to open your tiff files as a stack. You might need to use Image > Hyperstacks > Stack to Hyperstack... to convert your stack into a 2-channel, 10-slice hyperstack. Then use Image > Stacks > Z Project... to create the z projection.

Using the macro recorder while performing these commands will give you the code (needed to automate the task):

run("Image Sequence...", "open=/path/to/your/files file=tiff sort");
run("Stack to Hyperstack...", "order=xyczt(default) channels=2 slices=10 frames=1 display=Color");
run("Z Project...", "projection=[Average Intensity]");