Re: Colocalization analysis w/ ICA and JACoP

Posted by Daniel James White on Jun 02, 2010; 3:42pm
URL: http://imagej.273.s1.nabble.com/Colocalization-analysis-w-ICA-and-JACoP-tp3687953p3687960.html

Hi there "Sibert"

On Jun 2, 2010, at 6:00 AM, IMAGEJ automatic digest system wrote:

>
> Date:    Tue, 1 Jun 2010 09:28:55 -0700
> From:    sibert <[hidden email]>
> Subject: Colocalization analysis w/ ICA and JACoP
>
> Hello,
>
> I would like to analyze the colocalization of two proteins in some
> fluorescent images.  Based on what I've read, I'd like to use the ICA method
> by Li et al. (J. Neurosci. 24:4070, 2004)

it seems like a good method,
but you might as well also give the Manders (thresholded) and Pearsons (total and thresholded) measurements.

Remember to use a region of interest where the biology is, not the whole image.

>
> So far, I've tried the
> http://www.uhnresearch.ca/facilities/wcif/software/Plugins/ICA.html
> Intensity Correlation Analysis plugin  and
> http://rsbweb.nih.gov/ij/plugins/track/jacop.html JACoP .
>
> These plugins always provide different values for the Intensity Correlation
> Quotient (ICQ) as well as the Pearson's coefficient and Mander's
> coefficients for the same images.  I've tried both plugins with identical
> thresholds and without thresholds.  Adjusting the threshold does not appear
> to have any effect on the ICQ from JACoP.

Not sure if thresholds are used in ICQ....

but i am looking very hard at all these methods at the moment,
with the aim of making the next generation colocalization tool for ImageJ2...

I hope to do this in collaboration with Fabrice C and others who have contributed the current plugins.
Maybe Fabrice and comment on the difference between the results of the two plugins?
For sure we need to find out why they are different and implement it correctly in any new plugin.

>
> The ICQ from JACoP seems to be excessively high, even when minimal
> colocalization is visible the value given is generally > 0.3.  Whereas the
> ICA plugin returns values of ~.28 when the proteins appear highly
> colocalized (such an image returns ~.44 in JACoP).
>

it might be due to differences in the precision of the numbers used in the calculations,
but i expect that would not give differences this large.

Please can you send me a sample image that gives you different ICQs in the 2 plugins so i can verify the problem?

> The Pearson's and Mander's coefficients are also generally higher in JACoP
> than ICA.

by how much? Third significant figure differing by 1 is ok... larger than that is a problem...

>
> Unfortunately, I don't know Java well enough to determine how these
> calculations are being done in the source code.  It isn't clear to me from
> any documentation why the values are not identical between the two plugins.

One of the missions i have set myself is to make the code understandable
for a non expert, so they can understand the mathds being done,
and verify it agains the description in the original publiucations....

lets say... thats not always easy with the current crop of plugins, and that can be improved.

>
> Can anyone provide some insight as to why these plugins are providing
> different values for the same analysis and how I may discern which of the
> plugins is providing accurate calculations?

if you send me a sample image, I will be happy to investigate,
since i need to check both implementations anyway....


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

[phone] (German Mobile)
[phone] (Work phone at MPI-CBG)
[phone] (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 )