Count cells in z-stacked 3D images with dual-channels

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I’m now using Fiji ImageJ to count the cells in 3D. I have already known how to count it in single channel images. Now I’m facing problems in dual-channel images. I split channels into green and red images after I z-stacked dozens of images and repeat the same procedure of single channel images but it didn’t show the result I want. I think it only counts the cells in the first layer of the z-stacked image. Does anyone know how to solve the problem?




Welcome to the Forum!

So… to start I think we need a bit more information from you. Would you be able to describe in more detail the workflow you are using? Too - when you say:

… what is it that you ‘want’? What do you want to measure exactly? If it is to segment and count the number of cells in your z-stack… you can take a look at the plugin MorpholibJ, specifically how it is able to visualize segmented components in 3D. This plugin can help you segment your cells in 3D for sure… so take a look.

Also - if you can provide your original images - that would be great for us to better help you.



Hi Eta,

I’m going to count the cell numbers in a 3D scaffold. I can count the cell numbers if I take the image by using one channel, for example, green channel. However, when I took the images of live and dead cells (two channels) and followed the same procedure of the single channel images, it can only count one layer cell numbers instead of the 3D scaffold.

I’ll try MorpholibJ then.

Thank you,