Setting up a scripting environment

Learning Objectives

After completing this lesson, learners should be able to:
  • Set up a scripting environment for your platform


In order to run bioimage analysis scripts you need a platform where you can both run and develop those scripts. There is a range of solutions where especially the development of script ranges from a simple text editor to a full integrated development environment (IDE).

Concept map

graph TD S("Script") -->|contains| C("Code") E("Environment") -->|executes| C S("Script editor") -->|modifies| C S("Script editor") -->|may have| A("Auto-completion") S("Script editor") -->|may have| B("Break-points")


Fiji script editor with auto-completion and Run button


Install a scripting environment for your bioimage analysis platform.

Show activity for:  

Fiji script editor (IJ Macro, Groovy, Jython, ...)

  • Install Fiji
  • Start Fiji and install update site(s)
    • IJPB-Plugins (MorpholibJ)
  • Restart Fiji
  • File > New > Script...</kbd>
  • Run button to execute the code.
  • [ Script Editor > Language ]
    • IJ1 Macro
    • Javascript
    • Jython
    • Groovy
    • and some more…
  • Choose a language
  • Test autocompletion
    • IJ1 Macro
      • Type IJ. (you should see completion options)
        • Select freeMemory(); and press TAB

Napari python script editor plugin

  • Install python, napari and the script editor; see here
  • Auto-completion
  • Break-points



Follow-up material

Recommended follow-up modules:

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