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Bug 1082 - Issues with colocalisation analysis
Issues with colocalisation analysis
Status: RESOLVED INVALID
Product: Fiji
Classification: Unclassified
Component: ImageJ2
unspecified
PC Windows
: P5 enhancement
Assigned To: Curtis Rueden
Depends on:
Blocks:
 
Reported: 2015-06-08 14:57 CDT by Ann Wheeler
Modified: 2015-06-11 10:47 CDT
1 user (show)

See Also:
Description Ann Wheeler 2015-06-08 14:57:28 CDT 
Something seems to have happened to the colocalisation functionality in Fiji. In WCIF ImageJ there were a range of plugins for looking at colocalisation but these appear not to have been implemented in Fiji. Coloc2 seems unstable and is also not able to analyse colocalisation data the way we need, JaCoP, which does work also had this issue. Further since we have a lot of data we would like to script our analysis but the colocalisation plugins seem not to get on well with the macro writing. 

We need to set the thresholds for channel 1 and channel 2 ourselves for the colocalisation analysis we are carrying out for scientific reasons. We are using FRET to see whether there is a interaction between the proteins labelled in channel 1 and channel 2. However we're intereted in finding out if the two proteins are overlapping (colocalising) if they are not FRETing. I am aware that there are known issues with colocalisation functionality in Fiji.

Thanks for having a look

Ann Wheeler
Comment 1 Curtis Rueden 2015-06-11 10:47:17 CDT 
> In WCIF ImageJ there were a range of plugins for looking at
> colocalisation but these appear not to have been implemented in Fiji.

MBF ImageJ shipped with two colocalization plugins:

* http://fiji.sc/Colocalization_Threshold
* http://fiji.sc/Colocalization_Test

Both are still shipped with Fiji, but they are deprecated. We recommend using the newer Coloc 2 plugin instead:

* http://fiji.sc/Coloc_2

Also, if you haven't read it yet, please read the Colocalization Analysis guide from the Fiji Cookbook:

* http://fiji.sc/Colocalization_Analysis

> Coloc2 seems unstable and is also not able to analyse colocalisation
> data the way we need

You will have to be more specific. I suggest sending a mail to the ImageJ mailing list (http://imagej.net/Mailing_Lists), so that one of the Coloc 2 plugin maintainers can assist you.

> Further since we have a lot of data we would like to script our
> analysis but the colocalisation plugins seem not to get on well with
> the macro writing. 

Coloc 2 is supposed to work from a macro. If not, again, please write to the ImageJ list with a specific description of your issue.

Here is a guide to writing good ImageJ issue reports:

* http://imagej.net/Bug_reporting_best_practices

I am closing this issue, since it does not raise any specific bugs, but please feel welcome to contact the community mailing lists for assistance. There are many friendly people on the ImageJ mailing list.