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Hi George, 

On Nov 3, 2011, at 6:03 AM, CONFOCALMICROSCOPY automatic digest system wrote:

> Date:    Wed, 2 Nov 2011 22:04:39 -0400
> From:    George McNamara <[log in to unmask]>
> Subject: Re: Colocalization analysis in Fiji/ImageJ Coloc_2 plugin updated with several fixes.
> 
> Hi Dan,
> 
> Too bad red + green = yellow pixel colocalization and its many 
> coefficients is dead. See PubMed 21809413 - do you have nearest neighbor 
> analysis in yet/

No! Do you want to implement it!?

Ha Ha! Long live pixel based intensity correlation colocalization analysis. 

Seriously though.... yes this is a sensible method that they outline here...
pity the actually workflow/code they used is nowhere to be seen, 
despite the software they used being open source (its from Finland! )
http://csbi.ltdk.helsinki.fi/anduril/site/.

So they got it half right.... the script they used should be published also though... maybe I should ask for them...

General point (which George makes obliquely here)
is that coloc analysis only makes sense if you define the spatial scale you are talking about. 

If the universe is 1 single voxel - then everything is colocalised. 
If my voxels are smaller than electrons... then _Nothing_ colocalizes!

Pauli's exclusion principle says that 2 particles can't have the same wave mechanical description. 
So i cant have 2 atoms in the same place.... So i can't have a GFP and a mCherry in the same place either. 

BUT... so long as we define the spatial scale we are measuring the correlations over... ie the 
spatial sampling rate and the optical resolution .... which we always should. 
Then it does make sense for things to "be" in the same physical location,
so long as they are much smaller then the space scale or resultion we are working in. 

Of course, many biological "coloc" problems are actually situations where
the spatial correlation or overlap is never full, rather blobs site "next to" other blobs, 
and we need a good method of quantifying that.... how close are the blobs?

.....and the above mentioned paper has a method for that!
Great... so who wants to implement that as a module in Coloc_2
... we tried to make it easy for others to contribute modules...

Spearman correlation anyone?

cheers
Dam



> 
> George
> 
> On 11/2/2011 10:54 AM, Daniel James White wrote:
>> *****
>> 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:

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 )