[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
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             Status|NEW                         |NEEDSINFO
                 CC|                            |ctrueden at wisc.edu

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

Thank you for continuing to engage the ImageJ community in this discussion!

However, please note that this is an issue tracker, not a general discussion
forum. It would be much better to discuss these social issues on the ImageJ
mailing list.

> I have now discovered that the person who was writing and supporting
> Coloc2 in Fiji is no longer doing so. They have apparently left the
> MPI in Dresden and are now working for a company.

If you refer to Dan White, the project lead: he is still active in the
community and tries to help with Coloc 2 issues when he has time (e.g., just
today: http://imagej.net/pipermail/imagej-devel/2015-June/002605.html). Dan is
one of the most talented, friendly and helpful members of the community with
whom I have had the pleasure of working.

If you refer to Tom Kazimiers, the main developer: AFAIK he currently works at
HHMI Janelia Research Campus, as part of Albert Cardona's group. He is also an
asset to the community and as you can see from his GitHub profile
(https://github.com/tomka), he is still very active in development of related
software projects.

> This is a major issue for those in the community who need
> colocalisation analysis for their scientific research. Since the
> plugin is effectively half finished and the writer of the plugin has
> little intention of completing the work apparently.

These statements are not constructive. Please understand that ImageJ and Fiji
are open source software projects, not commercial software products. The ImageJ
community supports the software largely on a volunteer basis, as time and
energy permits. As such, it is important for users to be patient when reporting
issues; see this FAQ entry for details:
http://imagej.net/FAQ#I_reported_an_issue.2C_but_it_is_still_not_fixed.21_Why_not.3F

You will have to be very specific about:
* What exactly you are trying to accomplish;
* What exactly is insufficient about the Coloc 2 plugin;
* How you envision the software working, such that Tom or others could improve
things

Your mail to the ImageJ list a few days ago
(https://list.nih.gov/cgi-bin/wa.exe?A2=IMAGEJ;956552e2.1506) was a big step in
the right direction; we should continue the discussion from there to identify
specific ways the colocalization support in ImageJ can be improved for your use
cases.

> Likely the MPI-Dresden will be taken up coding plugins for SPIM, such
> as Big data viewer and presumably wouldn't have personnel to finish
> the project.

Rather than make assumptions, why not have a respectful, public discussion
which engages all relevant parties appropriately?

> Colocalisation was reliably and robustly implemented in IJ1 and needs
> must IJ2 / FIJI should at least be able to reproduce the functionality
> available in IJ1 in newer versions. 

As I said before (http://fiji.sc/bugzilla/show_bug.cgi?id=1082#c1), Fiji ships
both of the old MBF ImageJ colocalization-related plugins:
Colocalization_Threshold and Colocalization_Test. You will need to be more
specific about exactly what functionality is missing from Fiji that was present
in MBF ImageJ and/or ImageJ 1.x.

Fiji tries very hard to be backwards compatible with ImageJ 1.x -- anything
missing in that regard is very likely an oversight and readding old components
which are still needed is almost always extremely straightforward. But from
your description, I honestly do not know which plugins you are talking about.

> I can see if my image informaticist might be interested as a last
> recourse.

I encourage you to engage the technical resources available to you to best
achieve your goals. ImageJ and Fiji are available to you as free and open
source (FOSS) software, thanks to the efforts of many software developers
worldwide over a course of many years. If your group contributes back to the
project for the benefit of all, that is not a "last recourse" but rather a
wonderful thing, and how Fiji was built. We're all in this together.
http://imagej.net/Philosophy

>From a technical perspective: I will leave this issue open hoping you will
point me to the plugin(s) you want to see made available. Then we can close
this issue after they have been added to the Fiji distribution.

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