I am making a z project from a series of images I collected in a single z-stack and image J is doing a weird thing where when I create the project the resulting image is dark in regions that were bright in the original stack and when I go to look at the original stack certain slices are very dim, almost black in some cases. If I close the stack and reopen it the image slices are all back to their normal brightness but if I try to make a z-project again the same thing happens. This happens when I try a MAX, STD and AVG Z-project.
Basically, I take a number of slices from my original stack to make a Z-project. Prior to making the z-project every slice is the same brightness. Once I make the z project the resulting image is dark in regions it shouldn’t be and my original stack, that had images of the same brightness before, now has images in the stack that vary from their original brightness to completely black.
This is probably something simple in the program I have overlooked but if anyone can help me I would very much appreciate it!