Colocalization test and Macro

[Daniel White]

Hi Olivier,

Colocalization Test plugin is very old, buggy, and not really maintained
anymore, but thanks Jan for the fix....
Also it doesn't do the image randomisation as described by Costes... it
just uses a white noise image to compare.

Please use the Coloc2 plugin instead, its tested, maintained and improved.
http://imagej.net/Coloc_2

In Coloc2 the maths is implemented as described by Costes et al, as per the
documentation on the imagej wiki.

below is a macro that works for me as an example.

cheers
Dan


***********************************************
open("/home/dan/Downloads/150707_WTstack.lsm");
run("Split Channels");
selectWindow("C3-150707_WTstack.lsm");
selectWindow("C1-150707_WTstack.lsm");
makeRectangle(237, 327, 148, 132);
run("Coloc 2", "channel_1=C1-150707_WTstack.lsm
channel_2=C3-150707_WTstack.lsm roi_or_mask=[ROI(s) in channel 2]
threshold_regression=Costes show_save_pdf_dialog display_images_in_result
display_shuffled_images li_histogram_channel_1 li_histogram_channel_2
li_icq spearman's_rank_correlation manders'_correlation
kendall's_tau_rank_correlation 2d_instensity_histogram
costes'_significance_test psf=3 costes_randomisations=10");
****************************************************




Dear ImageJ list,

I am trying to call "Colocalization test" function from a Macro but I am
not able to.

"Colocalization test" function is working fine, I get expected results when
I use it manually (Analyze > Colocalization > Colocalization test).
But if the Macro recorder is open, in order to get the macro command line,
when I run "colocalization test" function, I get an error message from the
recorder :

Duplicate keyword :
Command "Colocalization Test"
Keyword "Channel"
Value: <name of my 2nd channel image>
Add an underscore to the corresponding label in the dialog to make the
first word unique.

At the end, I still get a command line in the recorder :

run("Colocalization Test", "channel=red.tif channel=green.tif roi=None
randomization=[Costes approximation (smoothed noise)] pixel=0.040
channel=520 na=1.40 iterations=75 psf=10");

But this command does not run the "Colocalization Test" function, it seems
nothing happen.
If anyone knows how to call this function from a macro, this would be very
helpful.
With Best regards,

Olivier

******************************************************
Olivier Leroy

Plateau d'imagerie cellulaire et tissulaire<
http://ugbdd.curie.fr/fr/imagerie>
Unité de génétique et biologie du développement<http://ugbdd.curie.fr/fr>

Centre de Recherche de l'Institut Curie
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