# Colocalization analysis of cells - What's the best way? (ImageJ, Photoshop?) **URL:** \ **Category:** Experimental Techniques\ **Created:** [January 13, 2017, 6:03pm UTC](https://forum.painresearcher.net/t/colocalization-analysis-of-cells-whats-the-best-way-imagej-photoshop/152 "2017-01-13T18:03:27Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![achamess](https://yyz2.discourse-cdn.com/flex030/user_avatar/forum.painresearcher.net/achamess/32/534_2.png) [@achamess](https://forum.painresearcher.net/u/achamess)\ **Post date:** [January 13, 2017, 6:03pm UTC](https://forum.painresearcher.net/t/colocalization-analysis-of-cells-whats-the-best-way-imagej-photoshop/152/1 "2017-01-13T18:03:27Z")
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. ![](https://canada1.discourse-cdn.com/flex030/uploads/painresearcher/original/1X/c22519d6578af6e096e0fc5bba1f325634f54649.png) @tberta @fmoehring @Ale @zhzhj131421 @LegakisL @tonellor @mwc19 @lfqueme @YawarJQ ---
**Author:** ![MAlves\_Simoes](https://avatars.discourse-cdn.com/v4/letter/m/ea5d25/32.png) [@MAlves\_Simoes](https://forum.painresearcher.net/u/MAlves_Simoes)\ **Post date:** [February 15, 2017, 2:48pm UTC](https://forum.painresearcher.net/t/colocalization-analysis-of-cells-whats-the-best-way-imagej-photoshop/152/2 "2017-02-15T14:48:02Z")
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](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](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 ---
**Author:** ![achamess](https://yyz2.discourse-cdn.com/flex030/user_avatar/forum.painresearcher.net/achamess/32/534_2.png) [@achamess](https://forum.painresearcher.net/u/achamess)\ **Post date:** [February 17, 2017, 3:22pm UTC](https://forum.painresearcher.net/t/colocalization-analysis-of-cells-whats-the-best-way-imagej-photoshop/152/3 "2017-02-17T15:22:32Z")
Thanks Marta! I’ll give it a try. ---
**Author:** ![achamess](https://yyz2.discourse-cdn.com/flex030/user_avatar/forum.painresearcher.net/achamess/32/534_2.png) [@achamess](https://forum.painresearcher.net/u/achamess)\ **Post date:** [November 19, 2017, 1:36am UTC](https://forum.painresearcher.net/t/colocalization-analysis-of-cells-whats-the-best-way-imagej-photoshop/152/4 "2017-11-19T01:36:20Z")
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](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](https://www.nature.com/articles/s41598-017-01004-y#Sec13) ![22 PM](https://canada1.discourse-cdn.com/flex030/uploads/painresearcher/original/1X/1d380d336402d199d579217674da289124eee660.png) Hopefully we can come up with a reproducible pipeline that works. This would be a huge time saver. ---
**Author:** ![achamess](https://yyz2.discourse-cdn.com/flex030/user_avatar/forum.painresearcher.net/achamess/32/534_2.png) [@achamess](https://forum.painresearcher.net/u/achamess)\ **Post date:** [February 21, 2019, 8:36pm UTC](https://forum.painresearcher.net/t/colocalization-analysis-of-cells-whats-the-best-way-imagej-photoshop/152/5 "2019-02-21T20:36:51Z")
> **[Be a histology hero with CellProfiler](https://blog.cellprofiler.org/2017/01/30/be-a-histology-hero-with-cellprofiler/)** > > Thanks to the rapid advancement in image processing, we now have so many techniques to characterize cellular and subcellular objects (hooray CellProfiler!) Measuring cultured cells in monolayers is…