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LLM Interactive Documentation for smite

This file bootstraps Claude (or other LLMs) to provide interactive assistance with smite (Single Molecule Imaging Toolbox Extraordinaire).

🤖 FOR LLMs: Read This First

You are now assisting with smite, a MATLAB package for fluorescence single molecule imaging analysis (SMLM and SPT).

Documentation Access

If you have filesystem access:

  • Entry point: doc/llm-guide/index.md (in this repository)
  • Catalog: doc/llm-guide/manifest.json

If using URLs:

  • Entry point: https://raw.githubusercontent.com/LidkeLab/smite/main/doc/llm-guide/index.md
  • Catalog: https://raw.githubusercontent.com/LidkeLab/smite/main/doc/llm-guide/manifest.json

How to Help Users

  1. Read the index first: Load doc/llm-guide/index.md to understand available documentation
  2. Load specific documents based on user questions:
    • Installation → getting-started/installation.md
    • Architecture → core-concepts/architecture.md
    • SMLM workflow → workflows/smlm-analysis.md
    • Examples → examples/basic-localization.md
  3. Provide working code - All examples are tested MATLAB code
  4. Follow cross-references - Documents link to related topics

⚠️ Documentation Status

This documentation was generated by Claude Sonnet 4.5 and has not been extensively reviewed by human domain experts.

For users: If you find errors, unclear explanations, or missing content, please open a GitHub issue.

Your Capabilities

With documentation loaded, you can:

  • ✅ Answer questions about smite installation, usage, and architecture
  • ✅ Explain SMF/SMD data structures
  • ✅ Guide users through SMLM and SPT workflows
  • ✅ Provide working code examples
  • ✅ Troubleshoot common issues
  • ✅ Help tune parameters and optimize performance

If you have write access to files:

  • ✅ Create/modify analysis scripts
  • ✅ Update configuration files
  • ✅ Generate test data
  • ✅ Fix bugs in user code

Documentation Structure

doc/llm-guide/
  ├── index.md                    # START HERE
  ├── manifest.json               # Document catalog
  │
  ├── getting-started/            # Installation & first steps
  ├── core-concepts/              # SMF/SMD architecture
  ├── workflows/                  # Complete SMLM & SPT pipelines
  ├── how-to/                     # Task-based guides
  └── examples/                   # Runnable code examples

Coverage: Phase 1 complete (12 docs, ~19k words). Phase 2 planned (40+ additional docs).

👤 FOR HUMANS: How to Use This Documentation

Option 1: Local Filesystem (Recommended for Development)

✅ Best for: Active development, writing code, file manipulation ⚠️ Requires: One-time setup (~5 minutes)

What You Get:

  • Claude can read AND write your files (create scripts, fix code, modify data)
  • Works offline
  • Always uses your latest local changes
  • Faster than URL access

Setup Steps:

  1. Open Claude Desktop

  2. Go to File → Settings → Extensions

  3. Add the Filesystem extension:

    • Click to add/enable the Filesystem extension
    • You'll be prompted to add a folder

  4. Add your smite folder:

    • Browse to your smite repository location
    • Example: C:\Users\klidke\Documents\MATLAB\smite
    • Click to add/allow access

  5. Done! Claude now has read/write access to your smite folder

  6. Verify: Look for 🔨 hammer icon in the chat input showing filesystem tools available

Usage:

Start any conversation with:

Read the file: C:/Users/klidke/Documents/MATLAB/smite/LLM_DOCS.md

Claude will bootstrap from this file, load the documentation, and you can then discuss smite naturally.

Example session:

You: Read the file: C:/Users/klidke/Documents/MATLAB/smite/LLM_DOCS.md

Claude: [reads file and loads documentation]

You: How do I install smite?

Claude: [provides installation guide from getting-started/installation.md]

You: Create a script to localize molecules in test data

Claude: [writes a working MATLAB script to your smite directory]

Option 2: GitHub URLs (Zero Setup)

✅ Best for: Quick questions, learning, browsing ⚠️ Limitation: Read-only (Claude cannot write files)

What You Get:

  • No setup required
  • Works with any LLM (web-based or desktop)
  • Always shows latest from main branch
  • Works anywhere with internet

Usage:

After pushing to GitHub, start any conversation with:

Read this URL: https://raw.githubusercontent.com/LidkeLab/smite/main/LLM_DOCS.md

Claude will fetch and load the documentation.

Example session:

You: Read this URL: https://raw.githubusercontent.com/LidkeLab/smite/main/LLM_DOCS.md

Claude: [fetches and reads documentation]

You: Show me SMLM workflow step-by-step

Claude: [provides detailed workflow from workflows/smlm-analysis.md]

You: Give me code for basic localization

Claude: [provides working MATLAB example from examples/basic-localization.md]

Option 3: Manual Browsing

If you just want to read the docs yourself:

Local: Open doc/llm-guide/index.md in any markdown viewer or IDE

Online: https://github.com/LidkeLab/smite/blob/main/doc/llm-guide/index.md

What You Can Ask

Once Claude has loaded the documentation:

Installation & Setup:

  • "How do I install smite?"
  • "What MATLAB toolboxes do I need?"
  • "How do I set up GPU acceleration?"
  • "Help me compile mex files"

Understanding smite:

  • "Explain the SMF structure"
  • "What's the difference between SMLM and SPT?"
  • "How does smite's architecture work?"
  • "What are the main namespaces?"

Running Analysis:

  • "Walk me through SMLM analysis step-by-step"
  • "How do I load .h5 data files?"
  • "Show me drift correction workflow"
  • "How do I do frame connection?"

Writing Code: (requires filesystem access)

  • "Create a script to localize molecules"
  • "Write batch processing code for all my datasets"
  • "Generate a complete SMLM analysis pipeline"
  • "Fix this error in my script"

Optimization:

  • "How do I tune localization parameters?"
  • "My results look wrong, what should I check?"
  • "How can I improve precision?"
  • "Speed up my analysis"

Troubleshooting:

  • "I'm getting GPU errors"
  • "Why are my localizations scattered?"
  • "Help me debug this MATLAB error"
  • "Explain this warning message"

Quick Start Summary

Claude Desktop (with filesystem MCP setup):

Read the file: /path/to/smite/LLM_DOCS.md

Any LLM (via URL after pushing to GitHub):

Read this URL: https://raw.githubusercontent.com/LidkeLab/smite/main/LLM_DOCS.md

Then just talk naturally about smite!

Documentation Maintenance

For contributors using Claude Code, documentation is maintained using slash commands:

  • /smite_docs_status - Check documentation status and health
  • /smite_update_llm_docs - Update docs after code changes
  • /smite_validate_llm_docs - Validate documentation quality
  • /smite_build_llm_docs - Build Phase 2+ documentation

See .claude/README.md for the complete documentation build system.

Feedback & Issues

If you encounter problems with the documentation:

Ready to get started? Tell Claude to read this file (local or URL) and start asking questions! 🔬