Re: Analyze Particles macro in headless mode

Posted by gankaku on Mar 08, 2014; 11:45am
URL: http://imagej.273.s1.nabble.com/Analyze-Particles-macro-in-headless-mode-tp5006825p5006829.html

Hi Nick,

@ Question 1:
I would guess that the problem lies in the following line:

run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Overlay
Outlines display record slice");

you need to put the show option in [] like this because due to the space
inbetween it will otherwise not be recognized as correct command and then
also the consecutive commands are potentially not recognized anymore.

run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00
show=[Overlay
Outlines] display record slice");

@ Question 2:

This is because during saving the image as PNG the shown overlays are
destructively integrated into the image and thus are visible in the final
output image. Saving the image as TIFF stores your outlines still as
overlays which will be present when you reopen the TIFF image but they are
not visible when you check the image e.g. watching it in the windows image
galery or any other  program.
So, actually you save the outlines as overlays.
In the case you want to save TIFF files and integrate the outlines
destructively then you need to integrate a flattening beforehand:

run("Flatten");

This gives you a copy of your image which you then can save.

hope this works out for your images.
regards,
Jan


2014-03-07 22:41 GMT+01:00 Nick X. Tsui <[hidden email]>:

> Dear ImageJ fellows:
>
> Many many thanks for your time reading my email. I am trying to do Analyze
> Particles in macro, using Fiji headless mode. I have two questions, and I
> am showing my code first, which will followed by the questions:
>
> Code:
>
> for (i=0; i<list.length; i++) // go through files in the folder
>     {
>         showProgress(i+1, list.length);
>
>         if (endsWith(list[i], ".tif")) // process tiff
>         {
>             open(input_dir+list[i]);
>             print(list[i]);
> run("Invert LUT");
> run("8-bit");
> setAutoThreshold();
> run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00
> show=Overlay Outlines display record slice");
> run("16-bit");
>             dotIndex = lastIndexOf(list[i], ".");
>             if (dotIndex != -1) output_file = substring(list[i], 0,
> dotIndex); //remove extension
>             saveAs("PNG", output_dir+output_file);
>             close(output_file);
>             close(list[i]);
>             check++;
>         }
> else if (list[i] == "Experiment.xml") // Experiment.xml file copied into
> output folder for review in ThorImageLS
> {
> print(list[i]);
> src = input_dir + list[i];
> dst = output_dir + list[i];
>  print(src);
> print(dst);
>  exec("cmd", "/c", "copy", src , dst);
> }
>     }
>
>
> Questions 1:
> In my results, I can only see the Invert LUT works, but I cannot see run
> Analyze Particles work, because there is neither outline, nor object count
> showing on the result images. However, when I use the memu on Fiji UI to do
> the same thing, I can see outlines and object counts on the results images.
> I am wondering something wrong with my script?
>
>
> Questions 2:
> Even if I can show outlines and object counts with Fiji UI, I cannot save
> the outlines and object counts together with result images when they are
> saved as .TIFF, however, when the results are saved as .PNG, or .JPEG, I
> can see the outlines and objects counts saved together. I am wondering is
> there anyway to save outlines and object counts even when result images are
> saved as .TIFF?
>
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>

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