I have confocal images from optically clearing wholemount tissues, so are made of multiple Z slices and usually 4 colours. Typically, after doing some small brightness/contrast adjustments and removing outlier for background steps, I would use image 5d and make maximum intensity Z projections of each channel, plus overlays. Alternatively, I would do the same using hyperstack but I found this takes longer.
I now have quite a few images to get through and I feel like what I am doing is taking longer than it needs to, and can probably be done much more simply. I assume it could be automated but I apologise as I am a complete newbie to scripts.
Does anyone have any advice about how to process large amounts of images like this? Many thanks in advance.