---
task_categories:
  - keypoint-detection
license: cc-by-4.0
tags:
  - biology
  - pose-estimation
  - marmoset
  - primate
  - lightning-pose
pretty_name: Marmoset3k
size_categories:
  - 1K<n<10K
---

# Marmoset3k — Lightning Pose Single-View Dataset

Top-down pose estimation dataset for common marmosets (*Callithrix jacchus*), packaged for use with [Lightning Pose](https://github.com/paninski-lab/lightning-pose).

## Dataset Description

Marmosets were recorded from a top-down camera in two configurations: alone (single) and in pairs. For pair sessions, individual animals are tracked — each labeled frame contains one focal animal cropped from a scene with two marmosets. **16 full-body keypoints** are labeled per animal.

Source data: original archive at https://zenodo.org/records/14672425.

## Data Splits

| Split | Labeled frames | Sessions |
|-------|---------------:|---------:|
| In-distribution (InD) | 3,920 | 4 (2 pair, 2 single) |
| Out-of-distribution (OOD) | 824 | 2 (1 pair, 1 single) |

InD and OOD sessions contain **different animals**.

- `CollectedData.csv` — InD labels; `videos/` — InD videos
- `CollectedData_test.csv` — OOD labels

## Keypoints

16 full-body keypoints.

| Region | Keypoints |
|--------|-----------|
| Head | head, leftear, rightear |
| Torso | neck, spinemid |
| Forelimbs | leftelbow, rightelbow, lefthand, righthand |
| Hindlimbs | leftknee, rightknee, leftfoot, rightfoot |
| Tail | tailbase, tailmid, tailend |

## Directory Structure

```
marmoset3k/
├── labeled-data/              # Extracted frames per session; includes ±2 context frames
├── videos/                    # InD session video clips
├── CollectedData.csv          # InD 2D keypoint labels (x,y per keypoint)
├── CollectedData_test.csv     # OOD 2D keypoint labels
├── config_marmoset3k.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_marmoset3k.yaml` is a ready-to-use training config. Key settings:

- **Image resize:** 256 × 256
- **Backbone:** `resnet50_animal_ap10k`
- **Keypoints:** 16

Update `data.data_dir` to an absolute path on your machine before training.

```bash
litpose train config_marmoset3k.yaml
```

## Citation

If you use this dataset, please cite:

```bibtex
@article{cheng2025real,
  title     = {A real-time, multi-subject three-dimensional pose tracking system
               for the behavioral analysis of non-human primates},
  author    = {Cheng, Chaoqun and Huang, Zijian and Zhang, Ruiming and Huang, Guozheng
               and Wang, Han and Tang, Likai and Wang, Xiaoqin},
  journal   = {Cell Reports Methods},
  volume    = {5},
  number    = {2},
  year      = {2025},
  publisher = {Elsevier}
}
```

Original data archive: https://zenodo.org/records/14672425.