Posted by
Daniel James White on
Mar 12, 2011; 7:23am
URL: http://imagej.273.s1.nabble.com/JACoP-parameter-and-PSF-tp3685080p3685092.html
Hi Gauri
On Mar 12, 2011, at 6:08 AM, IMAGEJ automatic digest system wrote:
>
> Date: Fri, 11 Mar 2011 08:03:11 -0800
> From: gauri <
[hidden email]>
> Subject: JACoP parameter and PSF
>
> Hi,
> I am looking at colocalization of two proteins on confocal microscope. I am
> using JACoP plugin to find Pearson
> 's coefficient and mander's coefficient. I had a few questions about setting
> parameters for JACoP. For the microscope parameter it asks about XY
> calibration and Z calibration. I am not sure what does that mean and what
> will be the correct value for it. The other problem i had was does JACoP
> calculate PSF. What PSF does it use. it never asks anythiong about PSF.
> Thanks
> Gauri
Email the authors directly if you want fine details... but....
you will find more info here
http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:jacop_2.0:just_another_colocalization_plugin:startand here
http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2818.2006.01706.x/pdf.mpi-cbg.de/cgi-bin/gitweb.cgi?p=fiji.git;a=blob_plain;f=src-plugins/Colocalisation_Analysis/Colocalisation_Test.java;hb=HEADin a nutshell....
x y and z calibration is the pixel spacing of the image. How far apart are the pixels with respect to the sample.
PSF approximate size is used for the image randomisation of the Costes significance test.
So it knows how big the chunks of image are to shuffle.
Excluding the object based coloc, all this stuff has now been redone... with fast image randomisation
standardised pdf result output and more,
in the upcoming Coloc_2 plugin for Fiji / imageJ2 / imglib
I am writing the docs now.... and the new plugin will be released to the Fiji updater
as soon as we verify that recent changes to imglib dont break it.
Do you want to test it and give me feedback?
cheers
Dan
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]
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