upload labels and configs

README.md

@@ -1,3 +1,96 @@
 ---
+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.

config_marmoset3k.yaml

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+data:
+  image_resize_dims:
+    height: 256
+    width: 256
+  data_dir: ${LP_ROOT_PATH:}/data/mirror-mouse-fused
+  video_dir: ${data.data_dir}/videos
+  csv_file: CollectedData.csv
+  num_keypoints: 16
+  keypoint_names:
+    - head
+    - leftear
+    - rightear
+    - neck
+    - leftelbow
+    - rightelbow
+    - lefthand
+    - righthand
+    - spinemid
+    - tailbase
+    - leftknee
+    - rightknee
+    - leftfoot
+    - rightfoot
+    - tailmid
+    - tailend
+  columns_for_singleview_pca: null
+
+training:
+  imgaug: dlc-top-down
+  train_batch_size: 8
+  val_batch_size: 32
+  test_batch_size: 32
+  train_prob: 0.95
+  val_prob: 0.05
+  train_frames: 1
+  num_gpus: 1
+  unfreezing_epoch: 20
+  min_epochs: 400
+  max_epochs: 400
+  log_every_n_steps: 10
+  check_val_every_n_epoch: 5
+  rng_seed_data_pt: 0
+  rng_seed_model_pt: 0
+  optimizer: Adam
+  optimizer_params:
+    learning_rate: 1e-3
+  lr_scheduler: multisteplr
+  lr_scheduler_params:
+    multisteplr:
+      milestones: [150, 200, 250]
+      gamma: 0.5
+  uniform_heatmaps_for_nan_keypoints: true
+
+model:
+  losses_to_use: []
+  backbone: resnet50_animal_ap10k
+  model_type: heatmap
+  heatmap_loss_type: mse
+  model_name: test_model
+
+dali:
+  general:
+    seed: 123456
+  base:
+    train:
+      sequence_length: 32
+    predict:
+      sequence_length: 64
+  context:
+    train:
+      batch_size: 16
+    predict:
+      sequence_length: 64
+
+losses:
+  pca_singleview:
+    log_weight: 10.7
+    components_to_keep: 0.99
+    epsilon: null
+  temporal:
+    log_weight: 10.7
+    epsilon: 10.0
+    prob_threshold: 0.05
+
+eval:
+  predict_vids_after_training: false
+  save_vids_after_training: false
+  test_videos_directory: ${data.video_dir}
+  confidence_thresh_for_vid: 0.90
+
+callbacks:
+  anneal_weight:
+    attr_name: total_unsupervised_importance
+    init_val: 0.0
+    increase_factor: 0.01
+    final_val: 1.0
+    freeze_until_epoch: 60
+

project.yaml

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+keypoint_names:
+- head
+- leftear
+- rightear
+- neck
+- leftelbow
+- rightelbow
+- lefthand
+- righthand
+- spinemid
+- tailbase
+- leftknee
+- rightknee
+- leftfoot
+- rightfoot
+- tailmid
+- tailend
+schema_version: 1
+view_names: []