I am new to ImageJ and here is my problem: I have a set of .ome.tiff images I would like to run this macro on:
run("Stack to Hyperstack...", "order=xyzct channels=4 slices=x frames=1 display=Color"); run("Split Channels"); close(); selectWindow("C1-imagename-0015.ome.tiff"); close(); run("Red"); run("Merge Channels...", "c1=[C3-imagename.ome.tiff] c2=[C2-imagename-0015.ome.tiff] create"); run("Subtract Background...", "rolling=50"); run("Detect Particles", " two=[Detect in both channels independently] ch1a=4 ch1s=3 ch2a=4 ch2s=3 calculate max=2 plot add=Nothing");
I would like to apply this macro to all images individually via batch processing, however I am struggling with these problems:
1.) Each image consists of 4 separate fluorescent channels, 1 timepoint and with different amounts of z-stacks. How, when the macro runs Stack to Hyperstack, can I run this command across all images so that I end up with 4 channels and a varying number of slices?
2.) After I have split the channels, I only would like to run the background correction on 2 channels, and so I close the other two. How can I make this occur in each image?
3.) Same problem as 2.) I would like to merge the remaining two channels into one. How do I do this across all images?
Thanks for the help!