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Instruction File Index

This index shows the relationships between instruction files and when to use them.

Quick Selection Guide

Working on SciJava Projects

Start with: scijava-foundation.md (shared concepts for all projects)

By Task Type

Image Processing Development

  • Core library work: imglib2.md (data structures), imagej-common.md (ImageJ2 data model)
  • Algorithm development: imagej-ops.md (ops framework)
  • Format I/O: scifio.md (image file formats)

Application Development

  • ImageJ2 app: imagej2.md (gateway), imagej-common.md (data model)
  • Fiji distribution: fiji.md (distribution), imagej2.md (core)
  • Original ImageJ compatibility: imagej-legacy.md (bridge layer), imagej1.md (IJ1 specifics)

Scripting & Editor

  • Script editor development: scijava-script-editor.md (editor UI), scijava-common.md (plugin system)
  • Script examples/templates: imagej-scripting.md (example patterns)
  • Python scripting (Jython): scijava-scripting-python.md (JSR-223 bridge)
  • Python wrapper (CPython): pyimagej.md (PyImageJ library)

User Interface

  • Swing UI components: imagej-ui-swing.md, scijava-ui-swing.md
  • App launcher: scijava-app-launcher.md

Special Features

  • Update system: imagej-updater.md
  • ImageJ1 patching: ij1-patcher.md
  • Tutorial examples: imagej-tutorials.md

Non-ImageJ Projects

  • LLM application development: langchain4j-core-module.md

File Dependency Map

Foundation Layer

scijava-foundation.md (shared concepts)
└── scijava-common.md (core framework)
    ├── imagej-common.md (ImageJ data model)
    │   ├── imagej2.md (application gateway)
    │   ├── imagej-ops.md (algorithm framework)
    │   ├── imagej-legacy.md (IJ1 bridge)
    │   └── imagej-ui-swing.md (Swing UI)
    ├── scijava-script-editor.md (editor)
    ├── scijava-scripting-python.md (Python bridge)
    ├── scijava-ui-swing.md (Swing components)
    ├── scijava-app-launcher.md (launcher)
    └── scifio.md (I/O framework)

Image Data Layer

imglib2.md (core data structures)
└── imagej-common.md (ImageJ wrapper)
    ├── All ImageJ libraries depend on this
    └── pyimagej.md (Python wrapper uses this)

Application Layer

imagej2.md (core application)
└── fiji.md (extended distribution)

imagej1.md (original ImageJ)
└── imagej-legacy.md (compatibility bridge)
    └── ij1-patcher.md (bytecode modification)

Scripting Layer

scijava-common.md (script service)
├── imagej-scripting.md (example scripts)
├── scijava-scripting-python.md (Jython via JSR-223)
├── scijava-script-editor.md (editor GUI)
└── pyimagej.md (CPython via JPype)

Recommended File Combinations

Developing a Script Editor Plugin

  1. scijava-foundation.md - Plugin system basics
  2. scijava-script-editor.md - Editor architecture
  3. scijava-common.md - Service details (if needed)

Building ImageJ2 Algorithms

  1. scijava-foundation.md - Plugin system basics
  2. imglib2.md - Data structures
  3. imagej-common.md - ImageJ data model
  4. imagej-ops.md - Ops framework (if using ops)

Creating Format Readers

  1. scijava-foundation.md - Plugin system basics
  2. imglib2.md - Image data structures
  3. scifio.md - Format architecture

Working on Fiji Distribution

  1. scijava-foundation.md - Plugin system basics
  2. imagej2.md - Core application
  3. fiji.md - Distribution specifics

Python Integration Work

  • Jython (in-JVM): scijava-scripting-python.md, scijava-common.md
  • CPython (external): pyimagej.md, imagej-common.md, imglib2.md

ImageJ1 Compatibility

  1. imagej1.md - Original ImageJ
  2. imagej-legacy.md - Bridge architecture
  3. ij1-patcher.md - Bytecode patching (if modifying patcher)

Project Characteristics

Libraries vs Applications

Libraries (reusable components):

  • imglib2, imagej-common, imagej-ops, scifio
  • scijava-common, scijava-script-editor
  • Focus on APIs and extension points

Applications (end-user):

  • imagej2, fiji
  • Focus on dependency aggregation and entry points

Plugin Types by Project

  • Services: scijava-common, imagej-common, scifio
  • Commands: imagej-ops, imagej-legacy, script-editor
  • Formats: scifio
  • Languages: scijava-scripting-python
  • UI Components: imagej-ui-swing, scijava-ui-swing

Completeness Status

✅ Complete - Comprehensive coverage:

  • scijava-common, imagej-common, imglib2
  • imagej2, fiji, scifio
  • scijava-script-editor, pyimagej
  • langchain4j-core-module

✅ Good - Covers main workflows:

  • imagej-legacy, imagej-ops
  • scijava-scripting-python, imagej-scripting
  • imagej-updater, ij1-patcher

⚠️ Partial - May need expansion:

  • imagej-ui-swing, scijava-ui-swing
  • scijava-app-launcher
  • imagej-tutorials, imagej1

Generation Notes

All files in copilot/ were generated using GitHub Copilot by analyzing the respective project repositories. They reflect project state as of late 2024 / early 2025.

Maintenance: Update these files when projects undergo major architectural changes or version bumps.