Colocalization analysis of cells - What's the best way? (ImageJ, Photoshop?)

Experimental Techniques
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Hi all,

I want to do some colocalization analysis in the spinal cord. I’ve done a combo of immunohistochemistry and in situ hybridazation and I have four colors:

DAPI = Blue
White = Gene 1
Red = Gene 2
Green = GFP transgene

I want to quantitate the co-occurrence of these signals, so for example (GFP+/Gene1+/Gene2-) etc in an efficient manner. I’ve used Photoshop in the past and used the selection too. But I know ImageJ must have a good way to do this. I’ve shied away from ImageJ in the past because I found it buggy and slow, but I’m willing to use it if it can do what I want. Are there any specific tutorials on how to do? I’m looking around, but the documentation for ImageJ is pretty verbose.

Thanks!

Here’s an example of what I’m looking at.

Screen Shot 2017-01-13 at 1.05.16 PM.png622×746 94.5 KB

@tberta @fmoehring @Ale @zhzhj131421 @LegakisL @tonellor @mwc19 @lfqueme @YawarJQ

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Hello,

I have used JACop, it’s a colocalisation plug in for ImageJ/FIJI.

Download here:
https://imagej.nih.gov/ij/plugins/track/jacop.html

Paper reference:
http://onlinelibrary.wiley.com/store/10.1111/j.1365-2818.2006.01706.x/asset/j.1365-2818.2006.01706.x.pdf;jsessionid=3CEBCC024702EE60161738FDF41BBB97.f02t02?v=1&t=iz72kb28&s=049cabd7894c209ed3cd15a3168f6ffe46478370

I have done integrated density using thus plug in. Although, I think it only allows to do two channels at the time.

I hope it helps!
Marta

1 Like
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Thanks Marta! I’ll give it a try.

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CellProfiler recently came on my radar for cell counting. It looks very powerful.

http://forum.cellprofiler.org/t/rnascope-in-spinal-cord-neurons-quantitation-of-overlap-between-different-in-situ-probes/5355

I recently saw a paper describe using CellProfiler for automated counting of DRGs

https://www.nature.com/articles/s41598-017-01004-y#Sec13

22 PM
22 PM705×516 73 KB

Hopefully we can come up with a reproducible pipeline that works. This would be a huge time saver.

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