Dear Patriciody ,
If I understand you correct you have one nd2 file containing all the z-slices? If so, the macro below might do what you want (not tested).
dir1 = getDirectory("Select folder with nd2 files");
list = getFileList(dir1);
dir2 = getDirectory("Select folder to save the results");
for (i=0; i<list.length; i++){
// setBatchMode(true); // if all works fine you can remove the "// " at the start of this line to speed up the process; no images will be opened on the screen.
path = dir1 + list[i];
run("Bio-Formats Importer", "open="+path"+ autoscale color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");
getDimensions(width, height, channels, slices, frames);
run("Make Substack...", "delete slices=1-"+slices+"-2");
run("Z Project...", "projection=[Max Intensity]");
saveAs("tif", dir2+"C1"+list[i]+".tif");
close();
selectWindow(list[i]);
run("Z Project...", "projection=[Max Intensity]");
saveAs("tif", dir2+"C2"+list[i]+".tif");
run("Close All");
}
Best wishes
Kees
________________________________
Hi everyone,
I would like to know if someone could help me create a macro that will save
me a lot of time. I take photos of my fluorescent samples using 2 channels
and many z stacks, which gets saved as a .nd2 file. I would like to have a
macro that joins all Z stacks using Z project max intensity, then split the
2 channels into 2 individual pictures and save them as .tif
Would this be possible? I really appreciate if you could help me, and thanks
a lot in advance.
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