User Tools

Site Tools


Sidebar

Top
Seminar
Courses -2016
Courses 2018-
Textbooks
Documents
Downloads (-2016)
Downloads (2016-)
Weblog
RSS aggregates
Discussions
Archives


EMBL BioImage Data Analysis

EuBIAS

NEUBIAS

—- Contact
CMCI Alumni
ALMF
EMBL Heidelberg
EMBL Intranet


Popularity Ranking


Timeline of @cmci_

cmci_ avatar

RT @dgaboriau: Nice #bioimageanalysis with @Fiji protocol https://t.co/ZJvbbUlnaY
About 20 hours, 6 mins ago by: Kota Miura (@cmci_)

cmci_ avatar

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_)

cmci_ avatar

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

cmci_ avatar

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_)

cmci_ avatar

RT @lmescu: Let's tile a bit the 3D space!!!! https://t.co/kQBiRG5TRs
About 5 days, 15 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

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_)
documents:200720ijmacro_headless

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.

https://github.com/imagej/imagej-legacy/issues/153

run("Blobs (25K)");
setAutoThreshold("Default");
run("Analyze Particles...", "  show=Overlay");
Overlay.copy
newImage("Untitled", "8-bit ramp", 256, 254, 1);
Overlay.paste
for (i=0; i<Overlay.size; i++) {
  Overlay.activateSelection(i);
  List.setMeasurements;
  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