Re: Batch processing images with custom threshold values

Posted by Pascal Lorentz on
URL: http://imagej.273.s1.nabble.com/Batch-processing-images-with-custom-threshold-values-tp3698896p3698898.html

Hi Wayne

your plugin is really great.
I'm still working with the version 1.37v and therefore I get a summary window
for each image and can not save them in a single file.
On the ImageJ website I can not get a newer version than 1.37v for PC.
What can I do.

Pascal


Zitat von Rasband Wayne <[hidden email]>:

> Here is a macro that runs the particle analyzer on all the images in
> a folder using custom threshold values and saves the results as a
> text file. It requires ImageJ 1.38o or later. The particle analyzer
> in earlier versions created a "Summary" window for each image.
>
>      requires("1.38o");
>      dir = getDirectory("Choose a Directory ");
>      list = getFileList(dir);
>      setBatchMode(true);
>      for (i=0; i<list.length; i++) {
>          showProgress(i, list.length);
>          open(dir+list[i]);
>          getStatistics(area, mean, min, max, std);
>          threshold = mean + 2.5*std;
>          setThreshold(threshold, 255);
>          run("Analyze Particles...", "size=10-1000 summarize");
>          close;
>      }
>      selectWindow("Summary");
>      saveAs("Text", getDirectory("home")+"Summary.txt");
>
> -wayne
>
> On Jul 4, 2007, at 5:37 PM, Adem Can wrote:
>
> > Dear List members,
> >
> > I am working on a project which requires cell counts from thousands of
> > images. Obviously, batch processing is the right way to work on these
> > images. I am not a programmer but still managed to reverse engineer
> > some
> > batch processing macros originally written for other functions for
> > myself.
> > But still there are problems that I need your expertise to solve.
> >
> > These are 8-bit images of immunoreactive neurons to be counted. I
> > can't use
> > the built-in autothresholding or entropy methods. Instead for each
> > image a
> > different threshold value is calculated according to the following
> > formula:
> > mean gray values+(2.5xSTD). I can calculate these values en masse
> > with batch
> > statistics macro. But after that, I have to do actual cell counting
> > one by
> > one, entering the appropriate threshold value for each image, a
> > process
> > which is, needlessly to say, unproductive.
> >
> > The ideal macro will batch process the following steps:
> >
> > -Open each image from a folder
> > -Calculate the threshold value for that image, according to a user
> > defined
> > algorithm (e.g. mean gray values+(2.5xSTD))
> > -Calculate number and total area of cells according to user defined
> > parameters (e.g. min-max pixel size) using the threshold value from
> > the
> > previous step
> > -Export these cell number and area values with the file name of the
> > image
> > into an Excel sheet (or a text file)
> >
> > So far I could not write such a macro. Thank you in advance for
> > your help.
> >
> >
> > Adem Can
> > The University of Texas at Austin, Department of Psychology
>

--
Pascal Lorentz
Centre for Biomedicine
Department of Clinical-Biological Sciences
University of Basel


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