| --- |
| task_categories: |
| - keypoint-detection |
| license: cc-by-4.0 |
| tags: |
| - biology |
| - pose-estimation |
| - mouse |
| - lightning-pose |
| pretty_name: Mirror Mouse |
| size_categories: |
| - 1K<n<10K |
| --- |
| |
| # Mirror Mouse — Lightning Pose Multi-View Dataset |
|
|
| Multi-camera pose estimation dataset for mouse locomotion keypoints, packaged for use with [Lightning Pose](https://github.com/paninski-lab/lightning-pose). |
|
|
| ## Dataset Description |
|
|
| Head-fixed mice run on a circular treadmill while avoiding a moving obstacle (Warren et al., *eLife* 2021). The treadmill has a transparent floor and a mirror mounted inside at 45°, allowing a single camera to capture two roughly orthogonal views — a side view and a bottom view via the mirror — simultaneously at **250 Hz**. Each frame is labeled with **14 keypoints**: 7 body keypoints visible from the side (top) and the same 7 keypoints from the bottom (mirror) view. This dataset splits these mirrored frames into separate top and bottom images/videos, each with 7 keypoints. |
|
|
| > **Note:** The original dataset contains keypoints on the moving obstacle; this version removes those keypoints. |
|
|
| Source data: Warren et al., *eLife* 2021 — original archive at https://doi.org/10.6084/m9.figshare.24993315. |
| Data collected by Richard Warren and Qianyun Zhang in the Sawtell Lab, Columbia University. |
|
|
| ## Data Splits |
|
|
| | Split | Labeled instances | Sessions | |
| |-------|---------------:|---------:| |
| | In-distribution (InD) | 789 | 17 | |
| | Out-of-distribution (OOD) | 253 | 5 | |
|
|
| InD and OOD sets contain **different sessions / animals** (no overlap). |
|
|
| - `CollectedData_{cam}.csv` — InD labels; `videos/` — InD videos |
| - `CollectedData_{cam}_test.csv` — OOD labels; `videos_test/` — OOD videos |
|
|
| ## Keypoints |
|
|
| 7 body keypoints per view: |
|
|
| - paw1LH |
| - paw2LF |
| - paw3RF |
| - paw4RH |
| - tailBase |
| - tailMid |
| - nose |
|
|
| ## Directory Structure |
|
|
| ``` |
| mirror-mouse-separate/ |
| ├── labeled-data/ # Extracted frames per session; includes ±2 context frames |
| ├── videos/ # InD session video clips |
| ├── videos_test/ # OOD session video clips |
| ├── videos-for-each-labeled-frame/ # 51-frame videos centered on each OOD labeled frame |
| ├── CollectedData_{cam}.csv # InD 2D keypoint labels (x,y per keypoint) for each camera view |
| ├── CollectedData_{cam}_test.csv # OOD 2D keypoint labels for each camera view |
| ├── config_mirror-mouse-separate.yaml # Sample Lightning Pose training config |
| └── project.yaml # View and keypoint definitions (required by LP App) |
| ``` |
|
|
| The `videos-for-each-labeled-frame/` directory contains 51-frame video clips with the labeled frame at the center, intended for use with temporal smoothers such as the [Ensemble Kalman Smoother](https://github.com/paninski-lab/eks). |
|
|
| See the Lightning Pose documentation for full details on the [multi-view data directory structure](https://lightning-pose.readthedocs.io/en/latest/source/directory_structure_reference/multiview_structure.html). |
|
|
| ## Usage with Lightning Pose |
|
|
| The included `config_mirror-mouse-separate.yaml` is a ready-to-use training config. Key settings: |
|
|
| - **Image resize:** 256 × 128 |
| - **Backbone:** `vits_dino` |
| - **Keypoints:** 7 |
|
|
| Update `data.data_dir` to absolute paths on your machine before training. |
|
|
| ```bash |
| litpose train config_mirror-mouse-separate.yaml |
| ``` |
|
|
| ## Citation |
|
|
| If you use this dataset, please cite the original paper: |
|
|
| ```bibtex |
| @article{warren2021rapid, |
| title = {A rapid whisker-based decision underlying skilled locomotion in mice}, |
| author = {Warren, Richard A and Zhang, Qianyun and Hoffman, Judah R and Li, Edward Y and |
| Hong, Y Kate and Bruno, Randy M and Sawtell, Nathaniel B}, |
| journal = {eLife}, |
| volume = {10}, |
| pages = {e63596}, |
| year = {2021}, |
| publisher = {eLife Sciences Publications, Ltd} |
| } |
| ``` |
|
|
| Original data archive: https://doi.org/10.6084/m9.figshare.24993315. |
|
|
