---
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.