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EMBL BioImage Data Analysis



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RT @CornellBiotech: Join us for the Fiji (ImageJ) Summer Workshop Aug 10-12
About 3 days, 11 hours ago by: Kota Miura (@cmci_)

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RT @christlet: Extending the classic full-width at half-maximum (FWHM) method for estimating image resolution on sub-resolutive structures…
About 1 week, 4 days ago by: Kota Miura (@cmci_)

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RT @CiminiLab: I've made a Twitter Community for Bioimage Analysis- feel free to join and share widely! I'll fully admit this is an experim…
About 1 week, 6 days ago by: Kota Miura (@cmci_)

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RT @kjaMartens: We created a very simple method to get high precision and density in spectrally-resolved single-molecule localization micro…
About 1 month ago by: Kota Miura (@cmci_)

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RT @random_walker: There’s a reproducibility crisis brewing in almost every scientific field that has adopted machine learning. On July 28,…
About 1 month ago by: Kota Miura (@cmci_)

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@AthaleLab @IISERPune @serbonline @DBTIndia @IFCPAR @OfficialSICI @boschindia Congrats Prof. Chait!
About 1 month, 1 week ago by: Kota Miura (@cmci_)

ImaegJ Macro Headless Limitations

There are two ways to run ImageJ “Headless”ly.

1. Real-Headless: running ImageJ without any display. 2. Pseudo-Headless: running ImageJ without physical display, but with a virtual display that is hidden - virtual frame buffer. xvfb-run command is often used for this purpose.

With the second method, you can run ImageJ macro just like you do with GUI. The speed of processing is similar to that you experience with normal GUI. With the first method, as there is no GUI drawing involved, the processing becomes much faster - but there are some problems. As some of the windows often used in ImageJ macro, such as ROI Manager and Results table cause “headlessexception” error and you will fail in the successful execution of that macro. (If you use xvfb-run, this does not happen).

There is some workaround as shown below.

ROI Manager

Don't use ROI Manager in a pure-headless environment. Instead, use Overlay function like the example below.

run("Blobs (25K)");
run("Analyze Particles...", "  show=Overlay");
newImage("Untitled", "8-bit ramp", 256, 254, 1);
for (i=0; i<Overlay.size; i++) {
  mean = List.getValue("Mean");
  print(i+"  "+mean);

Results Table

You can see the results table by saveAs(“Results”, path) command, but the renaming of the results table becomes impossible in the pure-headless environment. Avoid renaming, and instead, try to save the results table as soon as the results are filled in the table with a specific file name.

documents/200720ijmacro_headless.txt · Last modified: 2020/07/20 23:39 by kota