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EMBL BioImage Data Analysis



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Anna getting ready for her talk @NEUBIAS_COST workshop starting in 3 min.
About 6 hours, 1 min ago by: Kota Miura (@cmci_)

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RT @MIAP_Freiburg: @MIAP_Freiburg @UniFreiburg will host another basic Fiji @FijiSc/#ImageJ workshop on November 14th-15th 2018 with Kota M…
About 6 hours, 2 mins ago by: Kota Miura (@cmci_)

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RT @haesleinhuepf: Let's measure with @laure_plantard and #ImageJ at #NEUBIAS #TS8 🤘
About 1 day ago by: Kota Miura (@cmci_)

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RT @haesleinhuepf: Tracking cells on steroids: @jytinevez introducing #Mamut just next door #NEUBIAS #TS9
About 1 day ago by: Kota Miura (@cmci_)

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RT @haesleinhuepf: Anna Klemm from @scilifelab lifting us to the next level: tracking objects #NEUBIAS #TS8
About 1 day ago by: Kota Miura (@cmci_)

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RT @dn_mason: Check out our latest @biorxivpreprint (/w @Rosalierrr @ViolaineSee, @raphavisses & Rachel Bearon)! A workflow for imaging, tr…
About 1 day, 2 hours ago by: Kota Miura (@cmci_)

Drop Script

Drop Script Interface in ImageJ


Kota Miura (


2011-07-25 First release
2012-02-19 Additional capability for dropping jython files. Fixed a bug: Drop Script window was listed in the menu “windows” even after closing, but now it disappears as it should be.
2012-11-24 “Auto Run” feature. When the script file is saved in the editor, the script is automatically executed.



Download Drop_Script-1.0.x.jar from the link below, and place it under the plugin folder of Fiji or ImageJ.

Jar file

In case of ImageJ, you need Jython interpreter (Fiji already comes with the Jython interpreter so you don't need to install it). To get the interpreter, you need to run a test jython script (whatever you could just write, something like “print 'test'”) and “evaluate python” in ImageJ. Automatic Jython installation then starts.

If you are using Fiji:
Instead of installing manually, you could also set automatic download & updates by registering our update site. <code> </code> For managing update site, see this page.


ImageJ ver 1.44h or higher (ImageJ, upgrade page).


The aim of this plugin is to synchronize the script editing using external editors such as Notepad++ (windows only), Coteditor (osx) or Vim (universal) and quickly run the script in ImageJ or Fiji. Start the plugin, drag and drop the script file to the plugin window, and edit the file in the editor of your choice. Then clicking the “Run” button in the Drop-Script window will run the script.

DropScript plugin only keeps the path to the dropped files and accesses the code in the saved file every time when “Run” is clicked. For this reason, you could edit the code in external editor while the macro/script is keep on being listed in the DropScript drop-down menu.

To be more efficient: Turning on “Auto Run” option will let you automatically trigger to run the script as soon as the script is “Save”ed in the editor. With “auto-run”, the Drop script plugin continuously monitor changes in the script file, and automatically executes the script in ImageJ or Fiji whenever any change is detected.

This plugin will appear under menu tree Plugins > EMBLtools > Drop Script. The plugin opens a small window titled “Drop Script” where you drag and drop ImageJ macro (.ijm), Javascript (.js) and Jython (.py) script files. You could drag & drop as many files as you want directly from filesystem browser such as “Windows explorer” or “Finder (osx)”.

Dropped files will be appended as a list to the drop-down menu. “Clear” button will clear the list. “Code” button will open the code (Only for Javascript and ImageJ macro) in ImageJ macro editor.

known bugs

Only with Jython script, running a code with infinit loop will freeze ImageJ. This is because outputs from Jython interpretor is currently kept in a buffer (ByteArrayOutputStream), converted to a String and then printed in the log window at once (IJ.log(String)). Infinite loop causes the buffer to never reaching the log window.

Additional Information

Syntax Highlighter for ImageJ Macro is available in following editors.

downloads/drop_script.txt · Last modified: 2016/07/14 04:12 by kota