pyimagej-fiji-bridge
CommunityBridge Python to ImageJ/Fiji for image analysis.
Authorjaechang-hits
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This Skill enables seamless integration between Python and ImageJ/Fiji, allowing you to leverage powerful Java-based image processing plugins and workflows directly from your Python scripts.
Core Features & Use Cases
- Fiji Plugin Execution: Run ImageJ plugins like Bio-Formats, TrackMate, and Analyze Particles from Python.
- Data Exchange: Bidirectionally convert NumPy arrays to ImageJ's ImagePlus/ImgLib2 objects and back.
- Headless Operation: Automate Fiji workflows for batch processing without manual GUI interaction.
- Use Case: Process a large collection of microscopy images using Fiji's advanced segmentation and tracking algorithms, then analyze the results using Python's data science libraries.
Quick Start
Initialize PyImageJ in headless mode and print the ImageJ version.
Dependency Matrix
Required Modules
pyimagejscyjavanumpypandas
Components
scriptsreferences
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: pyimagej-fiji-bridge Download link: https://github.com/jaechang-hits/SciAgent-Skills/archive/main.zip#pyimagej-fiji-bridge Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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