EcodylicScience/mosaic-example-shiners

Golden shiners, collective motion across group size

Pose tracks for ten trials of free-swimming golden shiners (Notemigonus crysoleucas) at four group sizes, converted to mosaic parquet tables and ready to analyse without a conversion step.

Worked example: notebooks/collective-motion-shiners.ipynb. Set SOURCE = "download" (the default) and it fetches both files below.

Read this before comparing against another tracker

X / Y is the fish's HEAD, not its body centre. SchoolTracker measures no centroid. It locates the head, within 2 px of the midpoint between the two eyes, and that is what these tables carry. Every other tracker mosaic converts (TRex, SLEAP, Ultralytics, DeepLabCut) puts a body centroid in X / Y, so a feature reading X across this dataset and one of those is comparing two landmarks about half a body length apart, with nothing in the numbers to say so.

The same warning travels with the data: it is written into the schooltracker_v1 schema description recorded in tracks/index.csv.

There are no poseX* / poseY* columns. The head is the one point measured and it is already in X / Y; a keypoint pair would be a verbatim copy under a name promising a second, separately detected landmark.

Files

File	Size	What it is
shiners-tracks.tar.gz	350 MB	A complete mosaic dataset: dataset.yaml + tracks/. Ten trials, 10,827,539 rows.
shiners-raw-sample.tar.gz	8.9 MB	One trial (10-fish/0066, 7 segments) of raw SchoolTracker _fov.h5, reduced to the fields the converter reads.

SHA256SUMS carries the checksums.

The raw sample exists so the example notebook can run its converter rather than only display it. Converting the sample reproduces the shipped table for that trial exactly, and the notebook asserts this before going on.

Contents

group	trials	frames each	individuals
10-fish	0066, 0105, 0126	~24,600	10
30-fish	0084, 0115, 0120	~24,580	30
70-fish	0103, 0107, 0124	~24,570	70
150-fish	one trial	17,999	151

The last row is not a typo: the source directory is named 150-fish and the file reports 151 tracks. Both are preserved rather than one being corrected to match the other.

Columns: frame, time, id, group, sequence, X, Y, ANGLE, body_length. Positions are video pixels. ANGLE is the tracker's own measured body-axis heading, not an inference from displacement — which is why the schema is schooltracker_v1 (mosaic_v1 plus ANGLE) rather than plain mosaic_v1.

Use

import tarfile
from huggingface_hub import hf_hub_download
from mosaic.core.dataset import Dataset

path = hf_hub_download("EcodylicScience/mosaic-example-shiners",
                       "shiners-tracks.tar.gz", repo_type="dataset")
with tarfile.open(path) as tar:
    tar.extractall("data")

ds = Dataset("data/shiners-tracks/dataset.yaml").load()
tracks = ds.load_tracks("10-fish", "0066")

huggingface_hub >= 1.2.0 is worth pinning: older clients retry a rate-limit response with a 25-second backoff against a 5-minute window, so they fail where a current client waits.

Provenance and changes

Derived from the Dryad record accompanying Davidson et al. (2021). CC0 1.0, so this derivative carries the same terms.

Source: doi:10.5061/dryad.sbcc2fr2h (32 GB across 11 zips; about 45 GB of _fov.h5 unpacked).

What was changed:

• The _fov.h5 pose arrays were converted to mosaic schooltracker_v1 parquet tables. Column names and layout differ from the original release. Positions and headings are unaltered — x, y and the heading vector are carried through verbatim, with ANGLE = arctan2(heading_y, heading_x).
• Each trial's segment files were joined into one table: frame numbers offset by the preceding segments' lengths, and track identities re-linked across joins by linear-sum assignment on the last and first frames. The converter's docstring gives the margins.
• Fields not converted: the 256-ray visual field (fov_*, the bulk of the 45 GB), the body-local midline and shape descriptors, the eye positions, and the all-zero stimulus-object fields.
• The raw sample additionally has every unread field removed, which is why one trial is 8.9 MB rather than 932 MB. Kept arrays are byte-identical to the originals.

Not included: video, and the visual-field arrays. Both are in the Dryad record.

Citation

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