I’m working with yeast cells and want to quantify cell volume using signals from a GFP-tagged membrane protein. I’m using a Zeiss confocal microscope. The membrane-associated GFP shows the borders of my cells. Using pictures from the whole Z stack, I want to calculate exactly how large my cells are. I’m aware of tools that calculate volume based on surface area in different Z layers, but the tool I’m thinking of would have to fill in the holes, as only the mambrane is marked.
I already downloaded 3d imageJ suite, which has 3D Mathematical Morphology tools. However, I’m not sure how to use it. The “3d fill holes” function produces an error, apparently it cannot handle my .czi files. Can anybody tell me how to use that tool (in case it’s the right one) or which tool to use?
Thanks in advance!