I am trying to trace glial cells on a long-term basis in the adult zebrafish brain. As a living organism, fish cannot remain anesthesized under the microscope for long, which does not allow me to take long videos to check movement, as can be done with cell cultures. Instead, we develop different imaging sessions (once a day) and try to check cell movements between different time points. To allow a proper tracing, we therefore need stable landmarks that would allow us to see cell shifts from these structures. For this, I am using transgenic fish lines showing blood vessels in green and our cells of interest in red.
After the last imaging session, I end up with several Z-stacks showing blood vessels and cells throughout different time points. For the analysis of these images then, I would need to bring all the different time points into register using the blood vessels as landmarks. This means, I would need to set the first image (day0) as a fixed image and modify the later time points in order to match the blood vessels with the first one, which would allow me to see the corresponding movements in the cells.
The reason why I explain all the procedure here is because I am not able to find a proper and accurate plug-in/software/tool to get this done. The closest thing I managed to get has been 2D registration using the maximal projection of the stacks through the bUnwarpJ plug-in in ImageJ. However, this does not allow me to detect cell shifts or movements on the Z axis.
I would really appreciate any help any of you could give me and I thank you all beforehand for it!