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-tp6955853p6962322.html
*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy*****
Hi George and Vitaly,
On Nov 4, 2011, at 6:02 AM, CONFOCALMICROSCOPY automatic digest system wrote:
> Date: Thu, 3 Nov 2011 21:14:22 -0400
> From: George McNamara <
[hidden email]>
> Subject: Re: Colocalization analysis in Fiji/ImageJ Coloc_2 plugin updated with several fixes.
> Hi Vitaly,
>
> At the single molecule scale, colocalization is dead.
there never was anything to measure at that scale....
except perhaps a FRET/FLIM measured or other wide measured distance between molecules.
But, lets not get ahead of ourselves....
we can talk about fancy new methods,
but most folks doing biological fluorescence imaging
dont have access to these advanced methods yet,
and very much still rely on looking for yellow stuff (wrong approach at that is)
for colocalization. The first step it got get them using
better analysis methods for the kind of images data they get
from "conventional" confocal and widefield+deconvolution images.
Pixel intensity correlation over space and object based colocalization are still vastly under used.
> I am now busy
> trying to figure out how to get internal funding for simFCS to do Phasor
> analysis, re: PMID: 21808026 and PMID: 21858900.
>
> George
> p.s. sorry Jay - I am unable to figure out how to use your ImageJ plugin
> to do Phasor analysis with B&H SPCm / SPCimage TCSPC FLIM data (I don't
> see Phasor in the plugins list of names). I am unsure whether
> ImageJ/Bio-Formats is opening the data files correctly (they look pretty
> much empty in ImageJ). I tried one of your commands with a FLIM image,
> crashed ImageJ.
If we can get it working,
we can also add it to the Fiji distribution of ImageJ,
so folk just get it and dont have to install anything.
THe plugin author can take ownership of that plugin in Fiji
and maintain it, and its docs.
Documentation can like on the Fiji wiki or linked to an external site from there.
QuickPALM is already there in Fiji, for instance.
cheers
Dan
>
>
> On 11/3/2011 1:15 PM, Vitaly Boyko wrote:
>> 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
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 )