| --- |
| task_categories: |
| - keypoint-detection |
| license: cc-by-4.0 |
| tags: |
| - biology |
| - pose-estimation |
| - fish |
| - lightning-pose |
| pretty_name: Mirror Fish |
| size_categories: |
| - n<1K |
| --- |
| |
| # Mirror Fish — Lightning Pose Single-View Dataset |
|
|
| Single-camera pose estimation dataset for mormyrid fish body keypoints, packaged for use with [Lightning Pose](https://github.com/paninski-lab/lightning-pose). |
|
|
| ## Dataset Description |
|
|
| Weakly-electric mormyrid fish (*Gnathonemus petersii*) swim freely in and out of an experimental tank, capturing worms from a well. The tank has a side mirror and a top mirror, both at 45°, allowing a single camera to capture three views simultaneously — a direct view and two mirror views — at **300 Hz**. Each frame is labeled with **51 keypoints**: 17 body parts across all three views. |
|
|
| Source data: original archive at https://doi.org/10.6084/m9.figshare.24993363. |
| Data collected by Federico Pedraja, David Ehrlich, and Dillon Noone in the Sawtell Lab, Columbia University. |
|
|
| ## Data Splits |
|
|
| | Split | Labeled frames | Sessions | |
| |-------|---------------:|---------:| |
| | In-distribution (InD) | 373 | 28 | |
| | Out-of-distribution (OOD) | 94 | 10 | |
|
|
| InD and OOD sets contain **different sessions / animals** (no overlap). |
|
|
| - `CollectedData.csv` — InD labels; `videos/` — InD videos |
| - `CollectedData_test.csv` — OOD labels; `videos_test/` — OOD videos |
|
|
| ## Keypoints |
|
|
| 51 keypoints total: 17 body parts × 3 views (`_main`, `_top`, `_right`). |
|
|
| | Body part | Main view | Top view | Right view | |
| |-----------|-----------|----------|------------| |
| | Chin tip | chin_tip_main | chin_tip_top | chin_tip_right | |
| | Chin ¾ | chin3_4_main | chin3_4_top | chin3_4_right | |
| | Chin half | chin_half_main | chin_half_top | chin_half_right | |
| | Chin ¼ | chin1_4_main | chin1_4_top | chin1_4_right | |
| | Chin base | chin_base_main | chin_base_top | chin_base_right | |
| | Head | head_main | head_top | head_right | |
| | Mid | mid_main | mid_top | mid_right | |
| | Tail neck | tail_neck_main | tail_neck_top | tail_neck_right | |
| | Caudal ventral | caudal_v_main | caudal_v_top | caudal_v_right | |
| | Caudal dorsal | caudal_d_main | caudal_d_top | caudal_d_right | |
| | Pectoral L base | pectoral_L_base_main | pectoral_L_base_top | pectoral_L_base_right | |
| | Pectoral L | pectoral_L_main | pectoral_L_top | pectoral_L_right | |
| | Pectoral R base | pectoral_R_base_main | pectoral_R_base_top | pectoral_R_base_right | |
| | Pectoral R | pectoral_R_main | pectoral_R_top | pectoral_R_right | |
| | Dorsal | dorsal_main | dorsal_top | dorsal_right | |
| | Anal | anal_main | anal_top | anal_right | |
| | Fork | fork_main | fork_top | fork_right | |
| |
| ## Directory Structure |
| |
| ``` |
| mirror-fish/ |
| ├── 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.csv # InD 2D keypoint labels (x,y per keypoint) |
| ├── CollectedData_test.csv # OOD 2D keypoint labels |
| ├── config_mirror-fish.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 [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_mirror-fish.yaml` is a ready-to-use training config. Key settings: |
| |
| - **Image resize:** 256 × 384 |
| - **Backbone:** `resnet50_animal_ap10k` |
| - **Keypoints:** 51 |
| - **Mirror columns:** `[0–16]` (main), `[17–33]` (top), `[34–50]` (right) |
| |
| Update `data.data_dir` to an absolute path on your machine before training. |
| |
| ```bash |
| litpose train config_mirror-fish.yaml |
| ``` |
| |
| ## Citation |
| |
| If you use this dataset, please cite: |
| |
| ```bibtex |
| @article{biderman2024lightning, |
| title = {Lightning Pose: improved animal pose estimation via semi-supervised |
| learning, Bayesian ensembling and cloud-native open-source tools}, |
| author = {Biderman, Dan and Whiteway, Matthew R and Hurwitz, Cole and |
| Greenspan, Nicholas and Lee, Robert S and Vishnubhotla, Ankit and |
| Warren, Richard and Pedraja, Federico and Noone, Dillon and |
| Schartner, Michael M and others}, |
| journal = {Nature Methods}, |
| volume = {21}, |
| number = {7}, |
| pages = {1316--1328}, |
| year = {2024}, |
| publisher = {Nature Publishing Group US New York} |
| } |
| ``` |
| |
| Original data archive: https://doi.org/10.6084/m9.figshare.24993363. |
| |
