Posted by
Daniel James White on
Jun 11, 2010; 10:25am
URL: http://imagej.273.s1.nabble.com/Colocalization-analysis-w-ICA-and-JACoP-tp3687953p3687954.html
Dear Veronica and Bryan,
It really looks like we are gathering some useful information on all these plugins,
which is really important, since we are trying to design the next generation coloc tool for ImageJ2.
Thanks for sharing your observations!
Here are some I recently found out:
1) The Colocalization Threshold plugin uses a rearranged form of the Person's correlation equation,
the should be more numerically precise and faster to compute than the
way the equation is written in the classic Manders paper.
(Well done (Tony Collins?) whoever implemented that!)
2) I didn't find an implementation in java yet of the Costes statistical significance test (P-value)
(See Colocalization Test plugin and JACoP)
that follows the letter of the description of the algorithm in the Costes et al Paper.
It seems that the Coloc Test generates new random data that looks a bit like the image
but does not reshuffle the original image,
and the JACoP plugin does reshuffle the original image,
but it does it in a destructive way.
Maybe Fabrice can comment?
I really think we should pool all this information in a place where we can
all see it, contribute more and discuss the details.
This can be a place to pool info, and to add wishes to the list of potential features
for the next generation coloc tool for imageJ2
This list is great for sharing info of course,
but maybe we can also make a home for a coherent list of stuff we have found out.
... in fact thats easy with google docs...
and I will send you an invite to a google docs document that have just started.
It would be great if you can copy paste the info you have already sent to this list
that you think fits.... there.....
Bryan, Please send me the email address you use on your google account
so i can invite you to also edit the document.
The others seemed to exits in google already.
The doc can also be viewed by anybody here:
http://docs.google.com/View?id=df66rgc7_2dtqkv3dxmore below....
On Jun 11, 2010, at 6:00 AM, IMAGEJ automatic digest system wrote:
>
> Date: Thu, 10 Jun 2010 13:00:52 -0700
> From: sibert <
[hidden email]>
> Subject: Re: Colocalization analysis w/ ICA and JACoP
> I'm in the process of trying to expand my knowledge of Java and go through
> the ICA and JACoP plugins. At this point, I've only been able to find the
> source for JACoP v. 1, not the current version, but the changelog does not
> indicate any changes to the ICQ calculation.
is the source code in the .jar you downloaded?
It was in the one i recently got!
just unzip the jar (rename it to .zip of you need)
>
>
> I'm trying to write some new plugins to mimic the behavior of each plugin to
> confirm that I am correct. I'm also trying to check for differences in the
> other values (Pearson's, Mander's). It's possible that I have missed
> something in the code and these differences are incorrect or not
> comprehensive.
You seem keep to write some code....
so we should work together!
>
> I will continue my efforts to nail this down, I welcome any
> confirmation/correction by others.
Lets put all this info, arguments, agreements, disagreements on the google docs document.
and use that asa forum for pinning things down, explaining what we think is the right way to do stuff,
and recording our wishes for the next generation plugin.
Many heads a re better then one!
cheers
Dan
Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
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)
http://www.bioimagexd.net BioImageXD
http://pacific.mpi-cbg.de Fiji - is just ImageJ (Batteries Included)
http://www.chalkie.org.uk Dan's Homepages
https://ifn.mpi-cbg.de Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )