BrainDeer — Developer Documentation

BrainDeer is a scriptable neuroimaging viewer: orthogonal 2D slices, a VTK 3D scene, BIDS-aware data loading, and a plugin host you can extend in Python — with optional bridges to Blender and AI tooling.

This site is the technical documentation: architecture, plugin development, subsystem deep-dives, ADRs, and the full API reference. Guides, videos, and screenshots for end users live in the user documentation.

Status — active development (v2.0.0a1)

The viewer core, plugin host, WarpDrive, ROI Studio, BIDS panel, and Blender bridge are in daily use. APIs under plugin_api.v1 are the stable surface for extension authors; internal modules may still move as the 2.0 restructure lands.

What’s inside

Area	What it does	Where to start
Plugin host	Discover, load, and host Qt plugins under plugins/	Plugin development
Plugin API v1	PluginBase, metadata, facade to the running app	API map by layer
Commands & events	Shared actions + pub/sub between UI, plugins, and scripts	Architecture overview
Warp engine	Manual warp correction (RBF fields, session I/O)	Warp engine (warp/)
Rendering	VTK 3D scene, surfaces, tracts, slice planes	Rendering (rendering/)
I/O & BIDS	NIfTI, lazy volumes, BIDS mapping	Infrastructure: I/O & BIDS
API reference	Auto-generated from src/brain_deer	sidebar → API Reference

Documentation map

Foundations

• Architecture overview
  • The layers
  • Design rationale
  • Core mechanisms
  • Data flow (load → view → render)
  • See also
• Contributing
  • Dev setup
  • Building the docs
  • Commit conventions

Extending

• Plugin development
  • Conventions
  • Tutorial: your first plugin
  • Best practices
• Subsystems in detail
  • Warp engine (warp/)
  • Rendering (rendering/)
  • Infrastructure: I/O & BIDS

Reference

• API map by layer
  • Stable extension surface
  • Core layers
  • Bundled plugins
  • How to read the generated pages

Project

• Architecture decision records (ADRs)
  • ADR-0001: Docs as a duo — MkDocs Material + Sphinx
  • ADR-0002: AutoAPI instead of autodoc
  • ADR-0003: Plugin model — PluginBase, allowlist, widget split
  • ADR-0004: Event bus + command registry as integration surfaces
• API Reference
  • brain_deer

Indices

• Index

• Module Index