thanks for stopping by.
I am trying to process ~50 images from .nd2 to .TIF, but the exported images are not what I expect and I'm not sure what is wrong. My .nd2's have two channels and I would like the final .TIF to be an image of both channels. However, the .TIF output of my code is an image of just one channel.
setBatchMode(true); //Batch mode processing setting in ImageJ
for (i=0; i<list.length; i++) {
showProgress(i+1, list.length);
filename = list[i];
setBatchMode(true); // prevents image windows from opening while the script is running
run("Bio-Formats Windowless Importer", "open=[" + dir1 + filename +"] autoscale color_mode=Composite rois_import=[ROI manager] view=DataBrowser stack_order=XYCZT");
selectWindow(filename);
run("Stack to RGB", "slices"); // convert to RGB stack
...after this part of code I split the z-stack, find the middle, and save that slice as a .TIFF.
Please let me know if anything isn't clear. Thanks again for reading.
