I am imaging mammalian embryonic jaws at the biphoton microscope (SP8 DIVE from Leica). To be able to image this jaws, I tile the entire jaw (between 8 and 20 tiles depending on the developmental stage), each tile being a stack of file (500 to 1500 µm thick ~300 image per stack). My files are between 6 and 20 Go.
These jaws have been treated with EdU to detect cell division, so all the nucleus of dividing cells are labelled (with a 647 dye). I now want to see where the cells division occur and the local density of them within the jaws. My plan was to:
- visualize the jaws in 3D to locate the cell division within the jaw
- count the nucleus using 3D OC
Here are the issues that I have:
*despite having a powerful workstation (xeon gold proc and 128 Go of RAM), I sometimes have issue with the 3D viewer. Is there a way to allocate more memory? Would an ImageJ based software like Icy would be better for 3D visualization?
*I have trouble running 3D OC because the images are obviously big. Is there a way to reduce the file size or to make it better handled? Is there another plugin that would be better for this type of task?
Thanks a lot for your help!