[ImageJ-bugs] [Bug 1082] Issues with colocalisation analysis

[bugzilla at fiji.sc]

http://fiji.sc/bugzilla/show_bug.cgi?id=1082

Curtis Rueden <ctrueden at wisc.edu> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|---                         |INVALID

--- Comment #1 from Curtis Rueden <ctrueden at wisc.edu> ---
> 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.

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