Re: 3D ObjectCounter

Posted by Fabrice Cordelières on Nov 19, 2008; 11:04pm
URL: http://imagej.273.s1.nabble.com/3D-ObjectCounter-tp3694459p3694460.html

Hi Johannes,

I indeed have a good idea about how to make this work: first, use the  
new version of 3D-OC, available from the wiki: http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:3d_object_counter:start
Now, looking at the macro, am I right thinking that all your images  
carry the same name ?!!! Surely, renaming images either while running  
the macro or prior to analysis, may help. The resutsTable is  
identified by its name which itself is build from the image title.  
Analysing twice the same image or two images with the same name will  
result in replacing the content of the resultsTable with the new  
analysis results. Here is a modified version of the macro:

index=0;
do {
selectWindow("FL-1.tif");
rename("Image"+index);
run("Object Counter3D", "threshold=100 slice=3 min=10 max=358974  
new_results dot=3 font=12 summary");
//selectWindow("FL-1.tif");
selectWindow("Image"+index);
close();
index++;
} while (nImages>=1);


Fabrice


Le 19 nov. 08 à 16:37, Johannes-P. Koch a écrit :

> Hi all,
>
> I am running the 3D ObjectCounter semiautomatically by calling it  
> from a macro. The macro cycles through the open images and the  
> Counter analyzes the objects. So far, so good.
> If I decide to show no summary and if I do not click on "New  
> results" in the 3D Object Counter, the plugin adds new results to  
> the results tab. The problem is, that I cannot distinguish any  
> longer which results is from which object. Is it possible to add a  
> line in between which just tells you e.g. the name of the open  
> image, or just "next window".
>
> I have already tried an - for me - "easier" solution; if you select  
> "summary", but not "New results" in the 3D Object Counter plugin,  
> the Summary is displayed in the Log-file, and new objects are always  
> added, however, the Results window (which also pops up) is always  
> updated and the new -individual- results replace the old ones (which  
> means that the individual results from the previous image are lost).  
> I tried to add a command line to my macro to Duplicate the results  
> and give this window a new name+index; however this did not work out.
>
> Here is my macro (just the interesting part of it): (FL-1.tif is the  
> name of all open images!)
>
> do {
> selectWindow("FL-1.tif");
> run("Object Counter3D", "threshold=100 slice=3 min=10 max=358974  
> new_results dot=3 font=12 summary");
> selectWindow("FL-1.tif");
> close();
> } while (nImages>=1);
>
> Does anybode has an idea on that? Is any of my ideas plausible and  
> possible to implement in my macro???
>
> Thanks in advance
> Johannes
>
> _________________________________
> Johannes-P. KOCH
> University of Vienna
> MFPL, Center of Molecular Biology
> Department of Biochemistry
> Dr. Bohrg. 9/5
> A-1030 Vienna
> Austria
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Fabrice Cordelières, PhD

Institut Curie - Section de recherche/ CNRS UMR 146
Plateforme d'Imagerie Cellulaire et Tissulaire
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