Re: Colocalization plugin development

[Daniel James White]

Hi  Lenny,

>
> On Fri, 9 Sep 2011, Leonardo Guizzetti wrote:
>
>> I've taken the liberty of updating the Colocalization Threshold plugin
>> (part of the rolled-up plugins in the MacMaster Biophotonics plugin
>> package). As someone completely new to version control systems, how do
>> you suggest I put forth the new plug-in code? Should I just email the
>> author(s) ?
>
> Yep, that is one good idea. Speaking of the Colocalisation Threshold
> plugin, we also made some (miniscule) changes to unbreak it for newer
> ImageJ versions in Fiji:
>
> http://fiji.sc/Colocalisation_Threshold.java
>
> (you can see the history of that file within Fiji's version control system
> by clicking on the 'history' link, first in the second line on that page)
>
> Ciao,
> Johannes

further to the advice of Johannes,
you can see that the macmaster biophotonics version of the colocalization threshold plugin
is now old and broken, and we had to fix it to make it mostly work in modern imageJ and Fiji.

If you are serious about developing better tools for colocalization analysis
then this is a warm invitation to leave behind that old and hard to maintain/fix plugin,
and join development  of the next generation colocalization plugin in Fiji called
Coloc 2
http://fiji.sc/Colocalization_Analysis

there is a design and discussion document here:
http://bit.ly/mUBHg4

I can grant you write access to that if you have good ideas to add.

Right now we have a nasty bug to fix in Coloc 2,
in the code for Manders coefficients above thresholds
(gives results > 1 which is impossible....)
but this should be easier to spot and fix in Coloc2 than similar bugs in the hard to follow code of the
old Colocalization Threshold plugin which Coloc 2 replaces.
Can you spot it in the Fiji source code?

The invitation to join in goes out to all interested,
and we will be writing a nature methods paper on it before too long,
with as many authors as people who contribute something useful.

cheers

Dan


Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Processing and Analysis
Light Microscopy Facility
Max Planck Institute of Molecular Cell Biology and Genetics
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01307 DRESDEN
Germany

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