D
DocBadwrench
I am an administrator at a research institute that specializes in
graphical/figure solutions for my investigators. Recently, I've come
to discover ImageJ and, after committing the cardinal sin of displaying
competence and enthusiasm, am now the possessor of a new job -
processing hundreds upon hundreds of histology images. I've consulted
the documentation, the one wiki I found dedicated to the software, and
many other miscellaneous sources.
WHAT I'M TRYING TO DO
Each image is opened. Then, the macro entitled "AUTODECON" is run. This
is a custom macro that utilizes the custom filter entitled COLOR
DECONVOLUTION (found elsewhere) to produce the results. My DESIRE is
to automate this process so that result tables can be accessed along
with the source image. As it stands now, ImageJ overwrites result
tables making normal batch procedures insufficient.
The aforementioned macro follows:
run("Colour Deconvolution", "vectors=[H DAB]");
close();
setAutoThreshold();
//run("Threshold...");
setThreshold(0, 140);
run("Analyze Particles...", "size=2-100 circularity=0.20-1.00
show=Nothing clear summarize");
saveAs("Text", "D:\\Temp\\DAB.txt");
close();
setAutoThreshold();
setThreshold(0, 230);
run("Analyze Particles...", "size=0-infinity circularity=0.00-1.00
show=Nothing clear summarize");
saveAs("Text", "D:\\Temp\\hematox.txt");
close();
close();
THE PLUGINS/MACROS I'M TRYING TO USE
For completeness' sake, I will list all the "elements" that I'm trying
to coordinate together with one large "over-macro" (assuming it can be
done).
MACRO: AUTODECON
Mentioned previously, this is macro listed above. It utilizes the Color
Deconvolution filter and then analyzes the particles which results in
two small, stacked windows that contain the Result Table.
FILTER: COLOR DECONVOLUTION
Adjusts the color so that the particle analysis works properly.
PLUGIN: EXCEL TOOLBAR
My hope was to use this so that I could somehow dump the result tables
into a new worksheet. While I can use the Excel toolbar manually with
little problem, I can't seem to make the macro recorder note the
choices I make within the plugin window itself. If there's a way to get
the result tables to be written to unique filenames (perhaps based on
the title of the image) rather than using this plugin, I'm certainly
willing to try.
PLUGIN: MULTIPLE IMAGE PROCESSOR
This was to be the main tool used to get the cycle of opening, running
macros, and closing working.
FINAL THOUGHTS (AT THIS POINT)
Those of you who read this list regularly are probably wondering what
the heck this newbie thinks he is with the long messages? Though I am
new to ImageJ, I am *not* new to graphic processors, macro writing or
light coding, and know that there must be some way to pull this off,
though likely in ways I haven't yet encountered.
Thanks so much for your attention.
graphical/figure solutions for my investigators. Recently, I've come
to discover ImageJ and, after committing the cardinal sin of displaying
competence and enthusiasm, am now the possessor of a new job -
processing hundreds upon hundreds of histology images. I've consulted
the documentation, the one wiki I found dedicated to the software, and
many other miscellaneous sources.
WHAT I'M TRYING TO DO
Each image is opened. Then, the macro entitled "AUTODECON" is run. This
is a custom macro that utilizes the custom filter entitled COLOR
DECONVOLUTION (found elsewhere) to produce the results. My DESIRE is
to automate this process so that result tables can be accessed along
with the source image. As it stands now, ImageJ overwrites result
tables making normal batch procedures insufficient.
The aforementioned macro follows:
run("Colour Deconvolution", "vectors=[H DAB]");
close();
setAutoThreshold();
//run("Threshold...");
setThreshold(0, 140);
run("Analyze Particles...", "size=2-100 circularity=0.20-1.00
show=Nothing clear summarize");
saveAs("Text", "D:\\Temp\\DAB.txt");
close();
setAutoThreshold();
setThreshold(0, 230);
run("Analyze Particles...", "size=0-infinity circularity=0.00-1.00
show=Nothing clear summarize");
saveAs("Text", "D:\\Temp\\hematox.txt");
close();
close();
THE PLUGINS/MACROS I'M TRYING TO USE
For completeness' sake, I will list all the "elements" that I'm trying
to coordinate together with one large "over-macro" (assuming it can be
done).
MACRO: AUTODECON
Mentioned previously, this is macro listed above. It utilizes the Color
Deconvolution filter and then analyzes the particles which results in
two small, stacked windows that contain the Result Table.
FILTER: COLOR DECONVOLUTION
Adjusts the color so that the particle analysis works properly.
PLUGIN: EXCEL TOOLBAR
My hope was to use this so that I could somehow dump the result tables
into a new worksheet. While I can use the Excel toolbar manually with
little problem, I can't seem to make the macro recorder note the
choices I make within the plugin window itself. If there's a way to get
the result tables to be written to unique filenames (perhaps based on
the title of the image) rather than using this plugin, I'm certainly
willing to try.
PLUGIN: MULTIPLE IMAGE PROCESSOR
This was to be the main tool used to get the cycle of opening, running
macros, and closing working.
FINAL THOUGHTS (AT THIS POINT)
Those of you who read this list regularly are probably wondering what
the heck this newbie thinks he is with the long messages? Though I am
new to ImageJ, I am *not* new to graphic processors, macro writing or
light coding, and know that there must be some way to pull this off,
though likely in ways I haven't yet encountered.
Thanks so much for your attention.