Re: Colocalization analysis w/ ICA and JACoP

Posted by Daniel James White on Jun 09, 2010; 8:18am
URL: http://imagej.273.s1.nabble.com/Colocalization-analysis-w-ICA-and-JACoP-tp3687953p3687959.html

Dear Veronica,


On Jun 9, 2010, at 6:00 AM, IMAGEJ automatic digest system wrote:

> Date:    Tue, 8 Jun 2010 12:30:41 -0400
> From:    Veronica Labrador Cantarero <[hidden email]>
> Subject: Re: Colocalization analysis w/ ICA and JACoP
>
> Hello everyone,
>
>     I have also found differences in Pearson and ICQ coefficients betwee=
> n JACoP and
> ICA plugins. Please, have a look at the document "JACoP vs ICA" where
> the same image was used with different grades of overlap.

thanks for sharing  that. It see what you mean.... i will also have  closer look.
It loks like you have done sensible tests there....
Maybe i can use something similar for unit testing of the next generation coloc tool we are designing.
Maybe you might like to also help with that?

>
>     In addition, I have found that Overlap coefficients are higher than =
> expected,
> in my opinion, after applying a threshold even if the degree of colocaliz=
> ation
> is low.

I cant see how to do thresholded ICQ in JACoP?
How did you do that?

>
>     I also compared Overlap and K coefficients obtained for several imag=
> es with MS
> Excel and with JACoP plugin. When no threshold was applied the results we=
> re
> exactly the same but as I applied thresholds values became different (see=
> the
> document "Test 2").

again, i dint know how JACoP can use thresholds for that?????

>
>
>
> We would really appreciate any help on this subject.=20

Well, I hope we can help each other a a community and find the problems,
and work on more robust tools for the future.
JACoP is a big step forward in usability from the older stand alone plugins,
and we need to work hard to make the next generation toold even better for imageJ2

>
>
> Here is the link to download the documentation:
>
> http://rapidshare.com/files/396731811/Documentation.zip.html

many thanks for sharing, its really helpful!

cheers

Dan

>
>
>
> Thank you in advance,
>
> Veronica Labrador Cantarero
>
> Servicio de Microscopia Optica y Confocal=20
> Centro de Biologia Molecular Severo Ochoa
> C/Nicolas Cabrera,1
> Universidad Autonoma de Madrid
> Madrid (Spain)
> http://www.cbm.uam.es/confocal

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

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