Re: Help with macro for stack segmentation

Posted by Peter Haub on Nov 03, 2019; 11:11am
URL: http://imagej.273.s1.nabble.com/Solved-Help-with-macro-for-stack-segmentation-tp5022617p5022619.html

Hi Mario,

I have created a stack
     newImage("Untitled", "32-bit black", 200, 200, 12);
     run("Invert", "stack");

and draw some black objects on slice 2, 6 and 10.

I copied your macro code into the Process>Batch>Macro window 1:1
and run it ('Input path' = location of the created stack).

Here ('old' ImageJ 1.49u) it works as expected for one or more images in
the input folder.
For each image the different mask images (3 in my case) are stored in
the subfolder 'mask'.

Maybe you can run this as a test.

Regards,
Peter

On 01.11.2019 19:38, mariob wrote:

> Hi, everyone,
>
> I've just started with Fiji. I've written a code for cell segmentation that
> works when I run from the "Script editor" window, but not when I run from
> the "Process>Batch>Macro" menu, and I was hoping someone could advise me as
> to how to solve it.
>
> I have a bunch of stacks (9 slices x 4 channels) with single-cell images,
> and I want to segment the cell in each slice to take some measurements with
> another portion of the script. In my case, channel 2 is used for
> segmentation, and the script is supposed to go through Ch2 in each slice,
> segment it and save the mask as a separate image for later use (I also like
> to keep the mask as a record in case I have to check anything in the
> future).
>
> As I said, the macro bellow works fine in the script editor window (I test
> it with one single file at a time) and 9 different masks are generated
> corresponding to each slice. But when I run the exact same thing through
> Process>Batch>Macro I get 9 identical masks corresponding to the first slice
> (i.e., 9 different files with the expected names but with identical images).
> If there is more than one file in the parent folder, I get one set of 9
> identical masks for each original file.
>
> {
> frames=nSlices;
> title=getTitle();
> ImgName=substring(title, 0, lengthOf(title)-4);
> dir=getDirectory("image");
> dirOut1= dir + File.separator + "mask";
> dirOut2= dir + File.separator + "tiff";
> setMinAndMax(0, 65535);
> File.makeDirectory(dirOut1);
> File.makeDirectory(dirOut2);
> saveAs("TIFF",dirOut2 + File.separator + title);
>
> //to create the masks
> run("Gaussian Blur...", "sigma=1 stack");
> run("Convert to Mask", "method=Mean background=Light calculate");
> run("Fill Holes", "stack");
> run("Open", "stack");
> for (i=0; i<frames; i+=4) {
> setSlice(i+2); //mask is based on 2nd channel
> saveAs("PNG",dirOut1 + File.separator + ImgName + "_" + i+2);
> }
> close();
> }
>
> Any input would be much appreciated.
>
> Mario
>
>
>
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>
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