How to Count Cells in 3D using ImageJ (Fiji)

[@carl-johanhorberg1399]

Nice! Had a review comment that I had to resolve, and this saved me from having to do it by hand or writing something myself. Thanks a lot!

[@mcammer]

I have been watching a lot of ImageJ videos. This is one of the better ones. And I learned something. Thank you.

[@WK_UWO]

This is super helpful, Mike. Really appreciate your contribution.

[@davidjones9976]

Excellent work！I wonder that the tissue section you displayed is dorsal root ganglion?

[@kinzakhan9456]

you are doing great thanks for helping me with my project :)

[@raphaelrispal4732]

Life saving video, cheers Mike !

[@MiketheMichael]

Appreciate the support!

[@alguienjuandelpueblo5630]

Nice video! Is there any way to use this same analysis pipeline to count cells with different stains separately and later looking at whether they colocalize or not?

[@Dragonquest87]

Hi Mike! This is extremely helpful. Do you know of there is a way you can have this 3D counter count double positive cells? (Red and green colocalization)

[@ooddessaa]

Thanks for the vid! Have you tried using this method to count marker colocalizations?

[@johanmartinez-fuentes3319]

*bump* super good question, I think colocalization is a simple form of analysis that should be possible! Just ask the program if a smaller object's centroid XYZ point is "inside" the labeled 3D object... How can we do this? Anyone?

[@fatemehbahari1293]

Fantastic video! VERY VERY helpful! Thank you! I have a question though: how much is your computer's memory? I'm trying to fit my computer to be able to do this kind of analysis and am not sure how much memory I should have.

[@krishnamohan62]

Very useful...I am aware of real facts through this video...thanks

[@livviibb]

thanks - this was helpful! Is this a TEB from a mammary duct out of interest?

[@MiketheMichael]

Very Good Eye. Yes Terminal End Buds from mouse mammary whole mounts.

[@zachladwig8359]

super helpful video thank you!!!!

[@franciscomunozcarvajal9839]

Thanks for the video its really helpfull, but i doesnt work in really tight cellclusters. :(

[@swordfish2059]

Hi Mike Awesome Video. been trying to convert my 2D SEM images to 3D projections. 1. Is it possible to do that using Fiji 2. If Yes, is is possible to measure tortuosity of a certain phase using Image J with Fiji. Thanks

[@MiketheMichael]

Thank you Waqas, I've heard that tortuosity can be difficult to quantify, with that said it shouldn't be impossible. I would give the website ResearchGate a try and see if anyone there can answer your question. Also, Wichai Shanklin wrote a short review on the idea of turning 2D SEM images into 3D models titled "2D SEM images turn into 3D object models". I hope this helps.

[@swordfish2059]

Thanks alot. I will look into it. Keep up the good work. thumbs up

[@joshuakuruvilla]

Note : ImageJ representative Images (nice green, red contrast, great for powerpoint)

[@michaelanderson2249]

Awesome video! Thank you.

[@mariaquintero5807]

Has anyone tried doing this on a mac book air? Is it normal for it to take a very long time even with a new one? does it not have good processing power for this?

[@dahuhait]

Can i do this kind of analysis only in a ROI ?

[@bladethirst1]

Is there recent advances on this topic with AI tools?

[@jonascampos1895]

Trying it out here! It seems really demanding (computationally speaking).

[@MiketheMichael]

VERY demanding. If you are at a university try using one of the higher end computers on campus.

[@hypeyourlife840]

Can you also get the percentage of the volume

[@jakepanten]

Thank you!

[@h40738880]

Useful video. Thanks a lot.