Counting cells in a z-stack

[osama aldalahmah]

Hello,

Thank you for the wonderful work in bringing Icy to life! I am new to image analysis, and I have 54 z-stacks of GFP labelled cells (neurons, glia, neuroblasts) which I need to count. I tried automated counting in ImageJ (3D object counter), but it could not find all the cells, and it had serious problems in segmenting cell clusters. I am hoping to use Icy to do that, but I have not found a way yet. 

I appreciate any help, I can also provide image samples if that helps. 

Many thanks

Osama 

[Alexandre Dufour]

Hi Osama,

Would you have a sample z-stack (or portion therefor) that you could submit to this forum (as a 3D tiff file for instance)? That would help us figure out the best place for you to start from.

Cheers

Alexandre

---

Alexandre Dufour, Ph.D.

Institut Pasteur - Quantitative Image Analysis Group

25, rue du Docteur Roux, Paris, France

Research: http://www.bioimageanalysis.org/dufour

Software: http://www.bioimageanalysis.org/icy

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[osama aldalahmah]

Hi Alexandre,

Thank you very much for your reply.

I attached a zipped version of the stack. I counted it manually and got 114 cells, then- after 3 days of pulling my hair out- I managed to use volocity software (commercial) and do a semi-automated count, that gave me 122 objects (fairly good for semi-automated counting). But this is a demo version. So If i can do something like that with Icy, it would be great!! Any help is much appreciated.

Many thanks

Osama