http://confocal-microscopy-list.275.s1.nabble.com/Colocalization-analysis-in-Fiji-ImageJ-Coloc-2-plugin-updated-with-several-fixes-tp6955853p6961393.html
At the single molecule scale, colocalization is dead. I am now busy
p.s. sorry Jay - I am unable to figure out how to use your ImageJ plugin
see Phasor in the plugins list of names). I am unsure whether
much empty in ImageJ). I tried one of your commands with a FLIM image,
> Is it (coloc) still hot in the age of single molecu
> *****
> To join, leave or search the confocal microscopy listserv, go to:
>
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> *****
>
> Hi George and Dan,
>
> Is it (coloc) still hot in the age of single molecule fluorescence and raster ICS.
>
> Why not propagating xyztc imaging, which is also supported technologically, where c is biomolecule concentration per voxel?
>
> Cheers,
>
> Vitaly
>
>
> ________________________________
> From: Daniel James White<
[hidden email]>
> To:
[hidden email]
> Sent: Thursday, November 3, 2011 11:03 AM
> Subject: Re: Colocalization analysis in Fiji/ImageJ Coloc_2 plugin updated with several fixes.
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
>
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> *****
>
> 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<
[hidden email]>
>> 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 )
>
>