Colocalization analysis in Fiji/ImageJ Coloc_2 plugin updated with several fixes.

Posted by Daniel James White on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Colocalization-analysis-in-Fiji-ImageJ-Coloc-2-plugin-updated-with-several-fixes-tp6955853.html

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Dear colocalization analysis fans.

Thanks the keen eyes and astute minds of users
(Thanks to all of you!!!)
of the new working prototype
Coloc_2 plugin for Fiji (is just imageJ - batteries included)
we have identified and fixed an number of bugs and design problems in the code:

1) A problem in the design of how regions of interest/mask were implemented
caused a bug in the thresholded Manders coefficient calculation that gave values greater than 1.
This should now be fixed. Please test it as tell us if you feel it does the right thing.  
(JACoP might give different numbers due to a different interpretation of the maths in the original Costes paper.
After asking Dr. Costes, we believe Coloc_2 is correct)

2) Some further fixes were made in how masks/ROIs are handled for the
Costes statistical significance randomization test.

3) We added test code that uses Gaussian shaped spot images of various patterns
as per Manders' original paper, in order to recapitulate his tests and to identify
problems in our implementations of algorithms which calculate Pearsons and Manders coefficients etc.

There are also various little tweaks and redesigns,
that should make it easier for any programmer to read, follow and understand
and then extend the code with new functionality
(Spearman correlation anyone? Objects based analysis like in JACoP - anyone?)

Look in the GIT log to see all the code revision commit messages from Tom and Johannes.
The ideas/design document is still viewable at
https://docs.google.com/document/d/1bEJyXdGyKx4J_G6WlsABpcl3cn-kI5CQs57qU-3Gx7Y/edit


Thanks to all involved,
and please let us know how you would like the user interface and the standardized output PDF to look.

happy colocalizing... update Fiji and you will get the new version of Coloc_2.

cheers

Dan



Dr. Daniel James White BSc. (Hons.) PhD

Leader - Image Processing Facility,
Senior Microscopist,
Light Microscopy Facility.

Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
[phone] (Work phone at MPI-CBG)
[phone] (Fax MPI-CBG LMF)
chalkie666 Skype
http://www.bioimagexd.net  BioImageXD
http://fiji.sc                                        Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk                Dan's Homepages
https://ifn.mpi-cbg.de  Biopolis Dresden Imaging Platform (BioDIP)
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )