http://imagej.273.s1.nabble.com/Batch-processing-images-with-custom-threshold-values-tp3698896p3698899.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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