New in the forum and i hope I reach someone with more experience than me here.
What I have is an enormous folder with hyperstacks made of 4 channels with variable number of slices (single frames). What I need is to separate one of the channels (my selection marker) and run a maximum projection over it. Until here I’m good with the process in batch. What I want to do it to duplicate that MAX-projected image and re-concatenate it to match the specific number of slices that the original image had. That way I can re-merge it as an hyperstack with the other 3 channels.
Since my images do not have the same number of slices, I cannot define a specific number in my macro. Instead, I think I have to count the number of slices of each image so I get an “n” to later duplicate&concatenate that same number of Maximum projection images. But I dont know how to do this!
If I can get help to write this instructions in a macro in batch (PLEASE help me!!), I’m ready to run further macros to define ROIs and measure the MFI of independent channels in single planes.
I hope I didn’t make it too confusing and I’m eager to hear back