Volume measurement using membrane protein signal



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!


What is the size of your 3D stack and how many cells are there? If there aren’t that many, you might be able to just use the flood fill tool to fill-in the volumes.


Hi @s.vanselow , do you have a sample 3D stack by any chance ?


Thanks for the reply. The 3d stack contains 20 slices in 0.5µm intervals.For each strain (there are two) I took 15 photos which contain around 30-100 yells each. Would I have to fill in every cell in every slice manually? That’s what I was trying to avoid…


I do, but one channel is 50 MB in size. I attached five sample slices from the stack in jpg format so you can have a look at it. If you need the original file, I can post a link to dropbox maybe.


Yes, I was referring to manually filling them. So that won’t be practical for your purposes.