| --- |
| task_categories: |
| - keypoint-detection |
| license: cc-by-nc-4.0 |
| tags: |
| - biology |
| - pose-estimation |
| - mouse |
| - lightning-pose |
| pretty_name: Facemap |
| size_categories: |
| - 1K<n<10K |
| --- |
| |
| # Facemap — Lightning Pose Single-View Dataset |
|
|
| Single-camera orofacial pose estimation dataset for mice, packaged for use with [Lightning Pose](https://github.com/paninski-lab/lightning-pose). |
|
|
| ## Dataset Description |
|
|
| Mice were head-fixed and recorded with a close-up camera of the face during neural activity experiments. **15 keypoints** are labeled around the eyes, nose, mouth, whiskers, and lower lip; a paw keypoint is also included for frames in which the paw enters the camera field of view. Several keypoints (e.g., paw) are frequently occluded or absent. |
|
|
| Sessions were recorded from two camera angles (cam0 and cam1), both treated as a single view. |
|
|
| Source data: original archive at https://doi.org/10.25378/janelia.23712957. |
|
|
| ## Data Splits |
|
|
| | Split | Labeled frames | Sessions | |
| |-------|---------------:|---------:| |
| | In-distribution (InD) | 2,400 | 57 | |
| | Out-of-distribution (OOD) | 100 | 6 | |
|
|
| - `CollectedData.csv` — InD labels; `videos/` — InD videos |
| - `CollectedData_test.csv` — OOD labels; `videos_test/` — OOD videos |
|
|
| ## Keypoints |
|
|
| 15 keypoints total. |
|
|
| | Region | Keypoints | |
| |--------|-----------| |
| | Eye | eye_back, eye_bottom, eye_front, eye_top | |
| | Nose | nose_bottom, nose_r, nose_tip, nose_top, nosebridge | |
| | Mouth | lowerlip, mouth | |
| | Whiskers | whisker_c1, whisker_c2, whisker_d1 | |
| | Paw | paw | |
| |
| ## Directory Structure |
| |
| ``` |
| facemap/ |
| ├── labeled-data/ # Extracted frames per session; includes ±2 context frames |
| ├── videos/ # InD session video clips |
| ├── videos_test/ # OOD session video clips |
| ├── CollectedData.csv # InD 2D keypoint labels (x,y per keypoint) |
| ├── CollectedData_test.csv # OOD 2D keypoint labels |
| ├── config_facemap.yaml # Sample Lightning Pose training config |
| └── project.yaml # View and keypoint definitions (required by LP App) |
| ``` |
| |
| See the Lightning Pose documentation for full details on the [single-view data directory structure](https://lightning-pose.readthedocs.io/en/latest/source/directory_structure_reference/singleview_structure.html). |
| |
| ## Usage with Lightning Pose |
| |
| The included `config_facemap.yaml` is a ready-to-use training config. Key settings: |
| |
| - **Image resize:** 256 × 256 |
| - **Backbone:** `resnet50_animal_ap10k` |
| - **Keypoints:** 15 |
| |
| Update `data.data_dir` to an absolute path on your machine before training. |
| |
| ```bash |
| litpose train config_facemap.yaml |
| ``` |
| |
| ## Citation |
| |
| If you use this dataset, please cite: |
| |
| ```bibtex |
| @article{syeda2024facemap, |
| title = {Facemap: a framework for modeling neural activity based on orofacial tracking}, |
| author = {Syeda, Atika and Zhong, Lin and Tung, Renee and Long, Will and |
| Pachitariu, Marius and Stringer, Carsen}, |
| journal = {Nature Neuroscience}, |
| volume = {27}, |
| number = {1}, |
| pages = {187--195}, |
| year = {2024}, |
| publisher = {Nature Publishing Group US New York} |
| } |
| ``` |
| |
| Original data archive: https://doi.org/10.25378/janelia.23712957. |
| |
