[ImageJ-bugs] [Bug 1100] Coloc2 apparently no longer being supported

[bugzilla at fiji.sc]

http://fiji.sc/bugzilla/show_bug.cgi?id=1100

Curtis Rueden <ctrueden at wisc.edu> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEEDSINFO                   |RESOLVED
         Resolution|---                         |MOVED

--- Comment #3 from Curtis Rueden <ctrueden at wisc.edu> ---
Thanks for the details, Ann.

> (i) menu functionality e.g. selecting what to colocalise and which
> coefficients are needed. This is implemented in colocalisation
> threshold (set options checkbox), though this is mathematically weaker
> than Coloc2 and colocalisation threshold can't colocalise ROIs from
> the ROI manager.

Filed at:
https://github.com/fiji/Colocalisation_Analysis/issues/7

> (ii) Results display. In the output results file one needs to know
> what slice and ROI the colocalisation coefficients correspond to and
> be able to only chose the ones of interest for the study . 

Filed at:
https://github.com/fiji/Colocalisation_Analysis/issues/8

> (iii) This all needs to be scriptable so if one has 100 - 200 images
> Fiji can munch through them and generate an results file exportable to
> Excel with:
> 
> Columns corresponding to:
> 
> Slice, ROI, Threshold, 'My favourite colocalisation coefficient', 'Other colocalisation coefficient', 'AN OTHER parameter as desired'
>
> Rows corresponding to:
> Slice 1, ROI1
> Slice 1, ROI2
> Slice 2, ROI1
> Slice 2, ROI2 etc
>
> Not dissimilar to the output of multimeasure for analysing particles.
> Manders Coefficient and ICQ in IJ1 can do all of this and are
> scriptable easily.

Filed at:
https://github.com/fiji/Colocalisation_Analysis/issues/9

However, it would be helpful if you could clarify what you mean by "Manders
Coefficient" and "ICQ" in IJ1. Are these plugins? If so, where did you get
them? Are they part of the MBF ImageJ distribution?

Doing a quick web search, I see that ICQ is a statistic available as part of
the old Colocalization Analysis plugin -- is that what you mean?

> (iv) Another thing is the x and y axis of the plots in Coloc2 are not
> labeled so it sin't clear which axis corresponds to channel 1 and
> channel 2 in the output. I assume it's always consistent. I guess this
> is a easy fix. 

Filed at:
https://github.com/fiji/Colocalisation_Analysis/issues/10

> (v) A more delicate matter, These issues have been outstanding for
> over a year, which is the reason for additional fuss. Generally all
> issues of 'plugin not playing' are promptly addressed in updates,
> since Fiji as a group of developers are really good at maintaining
> tools. So perhaps these Coloc2 coding issues may be easier to resolve
> than the 'finding a person who has time to do the coding' issue..

Please understand that your "additional fuss" comes off as an attitude of
entitlement, which may negatively motivate those involved in the project from
addressing your wishes. It is always best to be polite. The open source
software development is radically different from more traditional goods and
services; here is a nice summary:

http://jeremyckahn.github.io/blog/2014/10/19/open-source-does-not-mean-free-labor/

The traditional open source mantra is "scratch your own itch" -- because with
OSS, you _can_. Like I said before, if you have development resources available
to you, and you need the above features to be addressed, this is a perfect
opportunity to give back to the OSS community.

If you have additional comments on any of the issues above, you are very
welcome to create a GitHub account and comment on the issue(s) in question.
Your feedback is very helpful here!

Lastly, it may interest you to know that I'll be visiting the HHMI Janelia
campus in a couple of weeks, where we are planning to discuss future
development directions of Coloc 2 with one of the main developers. Please
understand that AFAIK, no one is actually funded to work on this project right
now, so any progress will probably be slow. But obviously we do want it to be a
high quality, useful piece of software for the scientific community, so
hopefully that discussion will be fruitful for planning and next steps.

-- 
You are receiving this mail because:
You are the assignee for the bug.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://imagej.net/pipermail/imagej-bugs/attachments/20150717/e59331e5/attachment-0001.html>