bigstitcher-skills

Claude Code skills for working with BigStitcher, BigStitcher-Spark and multiview-reconstruction.

A skill is a SKILL.md instruction file plus optional scripts and reference docs. Claude Code keeps every skill's name and description in context and loads the rest when a task matches. These skills drive the installed CLI tools; they do not need the Java source trees.

Skills

Skill	What it does
skills/bigstitcher-xml	Edit SpimData XML projects safely: filter to selected channels / tiles / angles / illuminations / timepoints / views (bundled filter_bigstitcher_xml.py), clear or repair interest points and strip registrations via BigStitcher-Spark's filter-views, clear-interestpoints, clear-registrations. Locates an existing BigStitcher-Spark install (BIGSTITCHER_SPARK_HOME, BIGSTITCHER_SPARK_JAR) and documents install-release, which downloads the latest release instead of building.
skills/bigstitcher-tune-alignment	Workflow for finding good interest-point detection, matching and solver parameters. Skeleton for now.

All skills are prefixed bigstitcher- so they stay unambiguous when installed as bare user skills.

Use locally (current setup)

Symlink each skill into your user skills directory. Claude Code loads user skills in every session, regardless of working directory:

cd /path/to/bigstitcher-skills
ln -s "$PWD/skills/bigstitcher-xml"            ~/.claude/skills/bigstitcher-xml
ln -s "$PWD/skills/bigstitcher-tune-alignment" ~/.claude/skills/bigstitcher-tune-alignment

Edits in the repo are picked up at the next session start.

Publishing as a plugin (not done yet, on purpose)

The skills/ layout is already the one Claude Code plugins use. To let others install this repo:

1. Add .claude-plugin/plugin.json (name, version, description) and .claude-plugin/marketplace.json listing this plugin with source ./.
2. Users run /plugin marketplace add JaneliaSciComp/bigstitcher-skills followed by /plugin install.

Nothing is distributed until that metadata exists and someone explicitly adds the marketplace. Once installed, Claude Code pulls plugin updates at session start, so from that point on treat pushes to the default branch as releases.

Layout

skills/<name>/
├── SKILL.md        # frontmatter (name, description) + instructions
├── scripts/        # executable helpers (optional)
└── references/     # docs loaded on demand (optional)