https://github.com/elevans/fiji-scripts

A repository for image processing scripts for ImageJ2/Fiji.
https://github.com/elevans/fiji-scripts

image-analysis image-processing

Last synced: about 1 year ago
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A repository for image processing scripts for ImageJ2/Fiji.

• Host: GitHub
• URL: https://github.com/elevans/fiji-scripts
• Owner: elevans
• Created: 2023-03-23T12:53:39.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2024-10-28T15:58:13.000Z (over 1 year ago)
• Last Synced: 2024-10-28T17:48:46.834Z (over 1 year ago)
• Topics: image-analysis, image-processing
• Language: Python
• Homepage:
• Size: 157 KB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

          
# fiji-scripts

This repository contains various image processing and image analysis scripts written

in languages supported by Fiji (_e.g._ Groovy, Python (Jython), ImageJ Macro, etc...).

# How to run a script in Fiji

To run a script in Fiji, open the _script editor_ with the `[` hotkey or

**New** > **Script...** from the menu. Copy or open a script in the _script editor_

and then click **Run** to execute the script.

![script editor](docs/images/script_editor.png)

# Notes

- Scripts starting with the `ijo` prefix utilize [ImageJ Ops](https://imagej.net/libs/imagej-ops/index)

  to perform the image processing.

    - **ImageJ Ops** ships with Fiji, no additional installation is required.

- Scripts starting with the `sjo` prefix utilize [SciJava Ops](https://ops.scijava.org/en/latest/)

  to perform t he image processing.

    - **SciJava Ops** must be installed first before using scripts that use the `OpEnvironment`.

    - See these instructions on [how to install SciJava Ops](https://ops.scijava.org/en/latest/Installation.html).