Evaluation

T2 — Spatial-temporal multiscale prediction. 3D MERFISH (500-gene panel) · predicts expression + 3D coordinates.

Task

Participants will predict, for an unobserved stage, both the gene expression and the 3D position of every cell. The two are scored as separate questions — tissue geometry carries a full quarter of the score on Task 2 — so matching every expression marginal while placing cells wrongly does not pass.

Each profiled embryo is expensive, so a developmental window is covered by a handful of time points rather than a dense series, and each embryo is imaged in its own arbitrary frame with no registration to any other. Every spatial metric here is therefore invariant to translation and rotation: a submission is never asked to register itself to an atlas.

The task runs at two organ scopes, each with its own ladder, and each holds stages out from inside the observed range as well as beyond it. Recovering a stage that sits between two training stages is imputation; predicting one past the last observation is extrapolation. They are different problems, and a model is asked for both. The heart setting follows heart-tube formation and looping; the embryo setting spans gastrulation and is the harder of the two.

Four embryonic heart forms in a row, each built from stacked contour slices: a straight tube at E8.25, a C-shaped bend at E9.25, an S-shaped loop at E9.5, and an empty violet outline at the held-out stage. — A whole stage is held out, not slices from inside an embryo. A submission carries both channels — what each cell expresses and where it sits — scored as separate questions.

A whole stage is held out, not slices from inside an embryo. A submission carries both channels — what each cell expresses and where it sits — scored as separate questions.

Splits

Validation and test ground truth are both withheld. A validation submission returns a leaderboard score, not the answers — those are released only when the final test set is.

Train (heart): E8.25 · E9.25 · E9.5; Heart-scope MERFISH. E8.5 and E8.75 sit between E8.25 and E9.25 and are held out.
Validation (heart): E8.5 · E10.5; One imputation target inside the observed range, one extrapolation target beyond it. Scored through the leaderboard; the answers are not distributed.
Test (heart): E8.75 · E12.5; The hidden counterparts of the same two questions. Held until the competition closes.
Train (embryo): E6.75 · E7.25 · E8.0; Whole-embryo scope, spanning gastrulation — the harder of the two settings.
Validation (embryo): E7.5; Sits between E7.25 and E8.0, so the embryo setting is imputation throughout. Scored through the leaderboard.
Test (embryo): E7.75; Its hidden counterpart, also bracketed by training stages.

Getting the marginals right is not enough — tissue geometry carries a quarter of the score on its own. And the held-out stages sit both inside the observed range and beyond it, so a model has to interpolate and extrapolate. Full task page →