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3D ObjectCounter

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Johannes-P. Koch

3D ObjectCounter

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
phone +431427752809
fax +43142779528

[hidden email]

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Fabrice Cordelières

Re: 3D ObjectCounter

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
> phone +431427752809
> fax +43142779528
>
> [hidden email]
>
>
>
>
> --
> Ich verwende die kostenlose Version von SPAMfighter für private
> Anwender,
> die bei mir bis jetzt 5186 Spammails entfernt hat.
> Rund 5,6 Millionen Leute nutzen SPAMfighter schon.
> Laden Sie SPAMfighter kostenlos herunter: http://www.spamfighter.com/lde
>

Johannes-P. Koch

Re: 3D ObjectCounter

Thank you so much! Works really fine now. It is certainly a good idea to
rename the images. I have thought of that before, but it is not possible to
do that in the macro before. Doing it in the "do"-loop is just perfect! :-)

Johannes
_________________________________
Johannes-P. KOCH
University of Vienna
MFPL, Center of Molecular Biology
Department of Biochemistry
Dr. Bohrg. 9/5
A-1030 Vienna
Austria
phone +431427752809
fax +43142779528

[hidden email]

----- Original Message -----
From: "Fabrice Cordelières" <[hidden email]>
To: <[hidden email]>
Sent: Thursday, November 20, 2008 12:04 AM
Subject: Re: 3D ObjectCounter

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
> phone +431427752809
> fax +43142779528
>
> [hidden email]
>
>
>
>
> --
> Ich verwende die kostenlose Version von SPAMfighter für private Anwender,
> die bei mir bis jetzt 5186 Spammails entfernt hat.
> Rund 5,6 Millionen Leute nutzen SPAMfighter schon.
> Laden Sie SPAMfighter kostenlos herunter: http://www.spamfighter.com/lde
>

Fabrice Cordelières, PhD

Institut Curie - Section de recherche/ CNRS UMR 146
Plateforme d'Imagerie Cellulaire et Tissulaire
Bâtiment 112 - Centre universitaire
91405 Orsay Cedex
FRANCE

Tél. : +33 1 69 86 31 30
Fax. : +33 1 69 86 17 03

Consultez mes disponibilités sur
http://www.google.com/calendar/embed?src=fabrice.cordelieres%40gmail.com

--
Ich verwende die kostenlose Version von SPAMfighter für private Anwender,
die bei mir bis jetzt 5190 Spammails entfernt hat.
Rund 5,6 Millionen Leute nutzen SPAMfighter schon.
Laden Sie SPAMfighter kostenlos herunter: http://www.spamfighter.com/lde