batch process question

[Fabrice Senger]

Dear all,

hereafter I send you a peace of code.
I have an image with nuclei.
I roughly segment them (this is not a problem)
Next I convert the generated ROI's to new images and save them into a
specified directory.
To keep track of all the images (using the name of the image without the
"." and the extension), i used this nice code I got from the list some
time ago.
But now I would like to batch process whole folders of such images.
Usually I simply use the macro "BatchProcess" where I insert a function,
but here due to the fact that I call the name of the image this doesn't
work.

Has someone suggestions about this ?

Thank you very much,

Fabrice.


name = getTitle;
           dotIndex = indexOf(name, ".");
           title = substring(name, 0, dotIndex);


// Get path to aurelien directory
 aurelien = getDirectory("aurelien");
 if (aurelien=="")
     exit("No aurelien directory available");

// Create a directory in temp
 myDir = aurelien+title+File.separator;
 File.makeDirectory(myDir);
 if (!File.exists(myDir))
     exit("Unable to create directory");

setBatchMode(true);

// Segmentation process

run("Duplicate...", "title=one.tif");
run("Gaussian Blur...", "sigma=2");
run("Make Binary");
run("Watershed");
run("Analyze Particles...", "size=8000-Infinity circularity=0.00-1.00
show=Nothing exclude clear add");
close();

// Convert ROI's to new images and save to corresponding folder

myID = getImageID();
n = roiManager("count");
for (i=0; i<n; i++) {
    selectImage(myID);
    roiManager("select", i);
    run("Copy");
newImage(title+"_"+i+1, "8-bit Black", 400, 400, 1);
run("Paste");
saveAs("tiff", myDir+getTitle);
 close();
run("Select None");

}

--
Senger Fabrice

------------------------------------------------------------------------

The original MIME headers for this attachment are:
Content-Type: image/tiff;
 name="stable controle 1.tif"
Content-Transfer-Encoding: base64
Content-Disposition: inline;
 filename="stable controle 1.tif"


--
Senger Fabrice

[dpoburko]

Hi Fabrice,
 
  Have you had a look at the BatchProcessFolders.txt or
BatchProcessFolders_onlyTifIn Subfolder.txt  macros in the ImageJ macro
examples? They layout the basic outline of how to set up a macro to step
through the files in a given directory or a set of subdirectories. These
examples should be pretty easy to merge into your current code.

Cheers,
Damon


Senger Fabrice wrote:

> Dear all,
>
> hereafter I send you a peace of code.
> I have an image with nuclei.
> I roughly segment them (this is not a problem)
> Next I convert the generated ROI's to new images and save them into a
> specified directory.
> To keep track of all the images (using the name of the image without
> the "." and the extension), i used this nice code I got from the list
> some time ago.
> But now I would like to batch process whole folders of such images.
> Usually I simply use the macro "BatchProcess" where I insert a
> function, but here due to the fact that I call the name of the image
> this doesn't work.
>
> Has someone suggestions about this ?
>
> Thank you very much,
>
> Fabrice.
>
>
> name = getTitle;
>           dotIndex = indexOf(name, ".");
>           title = substring(name, 0, dotIndex);
>
>
> // Get path to aurelien directory
> aurelien = getDirectory("aurelien");
> if (aurelien=="")
>     exit("No aurelien directory available");
>
> // Create a directory in temp
> myDir = aurelien+title+File.separator;
> File.makeDirectory(myDir);
> if (!File.exists(myDir))
>     exit("Unable to create directory");
>
> setBatchMode(true);
>
> // Segmentation process
>
> run("Duplicate...", "title=one.tif");
> run("Gaussian Blur...", "sigma=2");
> run("Make Binary");
> run("Watershed");
> run("Analyze Particles...", "size=8000-Infinity circularity=0.00-1.00
> show=Nothing exclude clear add");
> close();
>
> // Convert ROI's to new images and save to corresponding folder
>
> myID = getImageID();
> n = roiManager("count");
> for (i=0; i<n; i++) {
>    selectImage(myID);
>    roiManager("select", i);
>    run("Copy");
> newImage(title+"_"+i+1, "8-bit Black", 400, 400, 1);
> run("Paste");
> saveAs("tiff", myDir+getTitle);
> close();
> run("Select None");
>
> }
>

--

Damon Poburko, PhD
Postdoctoral Research Fellow
Stanford University School of Medicine
Dept. of Molecular & Cellular Physiology
279 Campus Dr., Beckman B103, Stanford, CA 94305
Ph: 650 725 7564, fax: [phone]