Posted by
Daniel James White on
Aug 01, 2011; 6:23pm
URL: http://imagej.273.s1.nabble.com/Fwd-Running-coloc2-in-a-script-fwd-tp3683645.html
Hi Kurt,
Begin forwarded message:
> ---------- Forwarded message ----------
> Date: Fri, 29 Jul 2011 15:58:36 -0700
> From: Kurt Thorn <
[hidden email]>
> Reply-To: ImageJ Interest Group <
[hidden email]>
> To:
[hidden email]
> Subject: Running coloc2 in a script?
>
> Hi All -
>
> I'm trying to analyze the colocalization present of a large number of images so
Make sure you read, absorb, re read and grow to understand the many technical points described at
http://fiji.sc/wiki/index.php/Colocalization(i really need to tidy that up a bit....)
Coloc analysis is a minefield, and you need to be super careful,
esp. if its gonna be a medium/high through put job.
Background subtraction and selection of appropriate biological ROIs
is always challenging.
> I'm trying to figure out how to call the coloc2 plugin in a script in such a way
> that I can get access to the returned Manders coefficients in my script.
Coloc2 is a a working prototype, and I'm not sure if we can use it from the imageJ macro language yet.
A proper plugin could probably automate it.
For the methods we are using the Manders coefficients only make sense with background subtracted
images where the background is at 0 (as per Manders original paper)
The thresholded Manders coefficients, as per Costes 2004 are better for technical reasons
BUT, we seem to have a nasty bug in that calculation right now
and tese are being over estimated.
We need to fix that right away.
>
> I have a couple hundred images, so what I'd like to do is loop over all of them,
> determining appropriate ROIs,
How?
Manual? Automated?
> calling coloc2 for each two channel image for the
> current ROI, and then record the returned Manders coefficients associated with
> that image and ROI.
THresholded Manders are what you probably want.
> Any help would be most appreciated. I'm still pretty new
> to ImageJ scripting, so it's quite likely I'm overlooking something.
Not sure if Coloc2 can be run correctly from imageJ macro lang...
you could try recording a macro to see what happens.
But, presently I'm not sure what the best approach is to do what you want...
but its something we should certainly make possible.
you input is very welcome.
cheers
Dan
>
> Thanks,
> Kurt
Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Processing and Analysis
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)
http://www.bioimagexd.net BioImageXD
http://pacific.mpi-cbg.de Fiji (is just ImageJ - batteries included)
http://www.chalkie.org.uk[hidden email]
(
[hidden email] )