I can adjust the threshold function and lasso a cell outline, but I would like Fiji to automatically recognized and lasso the same cell outline through the z stack so I don't have to manually do it and then make the measurement. I got it to work once, but then could not replicate it, so I know it is possible. Or, if there is an easier way to do it, I'd be happy to try it.
Hi Amanda, maybe you could try with the 3D suite for imageJ/Fiji: http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:start
You can get the volume of 3D objects from there.
Hope it helps,
Manel.
I am working with images like this that are in a z stack. I am having a hard time getting the 3 D plugin to recognize the individual cells.
Which method are you using, Simple segmentation, iterative thresholding, hysteresis?
Walk us through your process and we should be able to provide feedback to tweak it.
I also have the same issue. I want to measure the change in volume of vacuoles after we add a particular peptide in the medium. So, I have z-stacks (around 20-30 images of the entire cell with vacuoles fluorescently labeled) for before and after treatment. However, I am confused about what to use to calculate the volumes for each case.
Any help in this regard would be greatly appreciated!
Thanks.
the above link is not working, and I am also interested in using imageJ to analyze the 3D volume of defined cells in a z-stack.
Does any one has a solution or suggestions ?
you can use voxel counter plugin in image j. After thresholding the stack, you can get the number of voxels for all the images of the z-stack. Since the size of each voxel is known you can get the volume by multiplying them.
Thank you Luv Kishore Srivastava for your answer. Indeed, this is a really easy solution to calculate cell volume.
Just to expand a bit,
1- make a thresholding on the z-stack
2- using ROI manager, select the area containing the cell (I used the square to draw the interest area as the cell should always be contained in this area all along the z-stack). You can make different areas for different cells
3- use the voxel counter plugin for Fiji (https://imagej.nih.gov/ij/plugins/voxel-counter.html)
4- Look at the value obtained for the Thresholded volume.
Good luck
If looking for an open-source approach, Voxel counting in Fiji is the way to go. I use the approach described here, turning the voxel count into a unit of volume (e.g., um^3): https://visikol.com/2018/11/blog-post-loading-and-measurement-of-volumes-in-3d-confocal-image-stacks-with-imagej/
Happy measuring!
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