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EMBL BioImage Data Analysis



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RT @dgaboriau: Nice #bioimageanalysis with @Fiji protocol
About 20 hours, 6 mins ago by: Kota Miura (@cmci_)

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RT @tbyhdgs: The @swcarpentry workshop (Bash, #python, git, reproducible research) we’ve been running with @EMBLEvents & @denbiOffice is ta…
About 1 day, 12 hours ago by: Kota Miura (@cmci_)

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RT @J_Cell_Sci: Read our Editorial about the launch of FocalPlane– a meeting place for the microscopy minded @focalplane_jcs:
About 5 days, 15 hours ago by: Kota Miura (@cmci_)

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RT @KuglerElisabeth: 🔥Preprint #3🔥 "3D #quantification of #zebrafish cerebrovascular architecture by automated image analysis of #lightShe…
About 5 days, 15 hours ago by: Kota Miura (@cmci_)

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RT @lmescu: Let's tile a bit the 3D space!!!!
About 5 days, 15 hours ago by: Kota Miura (@cmci_)

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RT @ferrandoelisa: Are you tired of searching through piles of image files? And do you want to start your working days here? Then apply for…
About 1 week, 5 days 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