license: cc0-1.0
language:
- en
tags:
- biology
- animal-behavior
- collective-behavior
- animal-tracking
- object-detection
- mosaic
pretty_name: 'Golden shiners: point-model training and TREx tracking'
size_categories:
- 1M<n<10M
Golden shiners — POLO point-model training and TREx tracking example
A mosaic dataset for a complete tracking workflow: published tracks become point pseudo-annotations, those train a POLO point detector, and TREx tracks with it — or, with no model at all, with its own background subtraction.
Worked end to end in
notebooks/shiners-polo-tracking.ipynb.
What is in it
| File | Size | Contents |
|---|---|---|
shiners-polo.tar.gz |
1.09 GB | dataset.yaml, media_raw/ (3 concatenated recordings), media/frames/kmeans/ (80 frames per recording), tracks/ (the published SchoolTracker tables) |
The POLO training tree is not shipped: it is a rearrangement of the frames and the tables under different filenames, so it would enlarge the download to carry nothing new. Section 2 of the notebook rebuilds it in seconds.
The tables under tracks/ were produced by a converter that lives in
collective-motion-shiners.ipynb,
not inside mosaic, so their src_format is one no installed mosaic knows. Reading
them works; re-converting from source needs that notebook's converter cell.
Contents
shiners-polo.tar.gz unpacks to shiners-polo/, a mosaic dataset:
| Root | What |
|---|---|
media_raw/ |
3 re-encoded H.264 recordings, one per group size (10 / 30 / 70 fish), ~24,600 frames each |
media/frames/ |
80 k-means-selected PNG frames per recording (240 total) |
tracks/ |
the published SchoolTracker tables, identity-corrected |
dataset.yaml |
the manifest |
tar xzf shiners-polo.tar.gz
Then point the notebook's LOCAL_DATASET at shiners-polo/, or let it download this
archive itself.
No model weights
None are included. The trainer, Ultralytics, is AGPL-3.0; rather than work through what distributing a model produced by it requires, this dataset carries none. The notebook's model-free TREx route needs no weights, and its training section prints the command to produce your own.
Provenance and licence
Free-swimming golden shiners (Notemigonus crysoleucas) in a 2.1 x 1.2 m tank, filmed from above, tracked with SchoolTracker and manually identity-corrected.
Source data CC0 1.0 from Dryad, doi:10.5061/dryad.sbcc2fr2h. The recordings here are re-encoded (each trial's segments concatenated, first frame of each segment dropped to match the track tables) and the tables converted to mosaic's schema; both are derivatives of that record and carry the same licence.
Please cite the original work:
Davidson JD, Sosna MMG, Twomey CR, Sridhar VH, Leblanc SP, Couzin ID (2021) Collective detection based on visual information in animal groups. Journal of the Royal Society Interface 18: 20210142. doi:10.1098/rsif.2021.0142
A note on X/Y
In these tables X/Y is the fish's head, not its body centre — SchoolTracker
reports it that way. It matters when training a point model on them, and the notebook
says why.