http://confocal-microscopy-list.275.s1.nabble.com/Colocalization-analysis-in-Fiji-ImageJ-Coloc-2-plugin-updated-with-several-fixes-tp6955853p6957675.html
coefficients is dead. See PubMed 21809413 - do you have nearest neighbor
> *****
> To join, leave or search the confocal microscopy listserv, go to:
>
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> *****
>
> 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
>
> +49 (0)15114966933 (German Mobile)
> +49 (0)351 210 2627 (Work phone at MPI-CBG)
> +49 (0)351 210 1078 (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 )
>
>