| --- |
| 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](https://github.com/EcodylicScience/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`](https://github.com/EcodylicScience/mosaic/blob/main/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`](https://github.com/EcodylicScience/mosaic/blob/main/notebooks/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 | |
|
|
| ```bash |
| 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](https://doi.org/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](https://doi.org/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. |
|
|
