AniMouse

Blender tools for the AniBody mouse biomechanical model.

Built at HHMI Janelia Research Campus, Johnson Lab.

What This Does

AniMouse provides a Blender add-on and command-line scripts for working with the mouse musculoskeletal model:

• Mesh catalog rendering — render isolated thumbnails of every body part with tissue-type coloring and transparent backgrounds
• Metadata extraction — compute volume, surface area, bounding box, tissue type, and anatomical classification for all 583 meshes
• Whole-body rendering — multi-view renders of the complete model
• Version compatibility — works with Blender 4.1+ and 5.0+

Quick Start

As a Blender Add-on (recommended)

1. Open Blender
2. Go to Edit > Preferences > Add-ons
3. Click Install from Disk and select the animouse/ folder
4. Enable "AniMouse" in the add-on list
5. In the 3D Viewport, press N to open the sidebar, find the AniMouse tab

From the Scripting Tab

Open any script from scripts/ in Blender's Scripting tab and run it with Alt+P.

From the Command Line

# Render 8 test parts
blender --background model.blend --python scripts/batch_render.py

# Render all 583 meshes
blender --background model.blend --python scripts/batch_render.py -- --mode all

# Extract metadata
blender --background model.blend --python scripts/extract_catalog.py

Requirements

• Blender 4.1+ or 5.0+
• No additional Python packages needed (uses Blender's bundled Python)

Project Structure

animouse/           Blender add-on
  __init__.py       Add-on registration and UI panel
  compat.py         Blender version compatibility helpers
  tissue_types.py   Material-to-tissue mapping and color palette
  mesh_metadata.py  Geometric and anatomical metadata extraction
  render_catalog.py Isolated mesh rendering engine
scripts/            Standalone CLI scripts
  batch_render.py   Command-line batch rendering
  extract_catalog.py Command-line metadata extraction
data/               Shared data files
tests/              Validation scripts

Related Projects

• janelia-anibody — AniBody project organization
• janelia-anibody/fruitfly — Virtual biomechanical fly
• flybody — Whole-body fly simulation (Vaxenburg et al., Nature 2025)
• mimic-mjx — Imitation learning for biomechanical models
• dm_control — MuJoCo export pipeline

License

BSD-3-Clause. See LICENSE.