I’d like to be able to fill in or crop irregular selections on a 3D stack of images. For example, in the fluorescent max projection below, I’d like to get rid of the part of the signal that I note with arrows. This signal is coming from tissue that is in the same plane as the desired signal but it’s labeling an unwanted structure. I’ve uploaded an example stack to dropbox too. https://upenn.box.com/s/p77hzbzd6ccm4sa4zgp4nt0hwwywv3vk
So far, I’ve dealt with this issue in two ways:
Scroll through the stack, draw selections around the unwanted signal, and push the delete key. This is effective but tedious.
I can open the stacks in 3D viewer, rotate the image so that I’m looking top/down, draw a selection around the unwanted signal then fill it. This is efficient but I’m not sure how to revert the edited image back to 2D stacks.
I know there are tools like 3D crop, but it seems like the unwanted signal must fit within a rectangular region. Unfortunately due to the nature of my tissue, each slice within a stack contains wanted and unwanted signal making this approach unfeasible.
max proj.tif (513.7 KB)