Cheese3D

Cheese3D is a pipeline for tracking mouse facial movements built on top of existing tools like DeepLabCut/DeepLabCut and lambdaloop/anipose. By tracking anatomically-informed keypoints using multiple cameras registered in 3D, our pipeline produces sensitive, high-precision facial movement data that can be related internal state (e.g., electrophysiology).

Cheese3D output can be visualized interactively.

Using a combination of hardware synchronization signals and a multi-stage pipeline, we are able to precisely synchronize video and electrophysiology data. This allows us to relate spikes recorded in the brainstem to various facial movements (here, we highlight two example units correlated with ipsilateral ear movements).

If you use Cheese3D, please cite our preprint:

@article {Daruwalla2024.05.07.593051,
    author = {Daruwalla, Kyle and Martin, Irene Nozal and Zhang, Linghua and Nagli{\v c}, Diana and Frankel, Andrew and Rasgaitis, Catherine and Zhang, Xinyan and Ahmad, Zainab and Borniger, Jeremy C. and Hou, Xun Helen},
    title = {Cheese3D: Sensitive Detection and Analysis of Whole-Face Movement in Mice},
    elocation-id = {2024.05.07.593051},
    year = {2025},
    doi = {10.1101/2024.05.07.593051},
    publisher = {Cold Spring Harbor Laboratory},
    URL = {https://www.biorxiv.org/content/early/2025/03/01/2024.05.07.593051},
    eprint = {https://www.biorxiv.org/content/early/2025/03/01/2024.05.07.593051.full.pdf},
    journal = {bioRxiv}
}

Guides

• Installation
  • Requirements
  • Setup
  • Platform-specific support
• Hardware setup guide
  • Cheese3D rig part list
  • Synchronization
  • Head-fixation
  • Recording protocol
• Quick-start guide
  • Organizing Cheese3D projects
  • Creating a new project
  • Adding video data to the project
  • Extracting and labeling frames
  • Training a new model
  • Tracking 3D keypoints
  • Visualizing the results

How-to examples

• Regex guide
  • What is a regular expression?
  • Common regex patterns
  • Named groups in Python regex
  • Cheese3D configuration dictionary format

Reference

• Configuration file
  • Main configuration options
  • Model options
  • Ephys options
  • Sync options
  • Recording session options
  • Triangulation options
  • View options
  • Keypoint options

Indices and tables

• Index

• Module Index

• Search Page