One embryo resource, two modalities

Embryo collections across eleven stages (A), single-cell measurement (B), 3D MERFISH from serial sections (C), and the conditional knock-outs (D).

Download

The training stages are released to registered participants. Validation and test targets come back as a score rather than as answers, until the final phase releases the validation answers for every task.

To look at these stages before downloading them — cells in 3D, coloured by type, with gene expression — they are in the atlas: browse the challenge training data ↗

Modalities

Single-cell

Task 1

Single-cell RNA

Real dissociated cells profiled across the whole transcriptome, 32,285 genes rather than a panel. Cell-type labels ship with the training stages. This is what Task 1 predicts.

Spatial

Tasks 2 and 3

3D MERFISH — 500-gene panel

A whole heart or whole embryo is sliced continuously into serial 2D spatial-transcriptomic sections, which are then reassembled into a 3D volume. Every cell therefore carries both a 3D position and measured RNA, across several developmental stages, with cell-type labels. Coordinates are per-embryo local and are not registered across time points. The conditional knock-outs — Mab21l2, Gata4 and β-catenin, each with a matched wild type — are profiled the same way.

Where the data comes from

The 3D MERFISH resource and the conditional knock-out embryos were generated by Qingquan Zhang and Neil Chi at UC San Diego. The benchmark is built on that resource; the tasks, splits and scoring are the competition's.

Competition datasets are provided for research and educational purposes. Any use, reuse, publication, presentation, or redistribution of the data outside the Challenge must appropriately acknowledge the Virtual Embryo Challenge and credit Dr. Neil Chi’s group at the University of California, San Diego (UCSD), which generated the dataset. As the dataset has not yet been published, any use of the data in a publication or public presentation must receive prior approval from Dr. Neil Chi and the data-generating team. Any publication using the dataset must also appropriately credit Dr. Qingquan Zhang and Dr. Neil Chi.

Access and reproducibility

Training data is released for method development. Validation and test ground truth are withheld while they can still affect the board: a validation submission comes back as a leaderboard score, not the answers. At the start of the final phase the validation answers are released for every task — ranking has moved to the hidden test split by then — and the test leaderboard opens. Task 1 additionally permits training on external public single-cell data; only the evaluation stages are fixed, provided any external source is disclosed with the submission.

You may train on external data, public or your own, and for Task 1 this is expressly encouraged. What you may not use is measured data from a held-out stage or genotype, by any route — not directly, not through a model pre-trained on it, and not through a public dataset that contains it. Those are: E10.5 and E12.5 for Task 1; E7.5 and E7.75 in the embryo setting and E8.5, E10.5 and E12.5 in the heart setting for Task 2; and the Gata4 and β-catenin knockouts at E8.75 for Task 3. Nearness counts: external data is treated as a held-out stage when it sits closer to that stage than to the nearest stage we released for the same task, the midpoint being the boundary — holding out E9.5 and training on an external E9.45 embryo is using the answer under a different name, and so is a dataset labelled by somite count or Theiler stage that lands in the same window. Beyond the last released stage, as the extrapolation targets are, everything from the midpoint onwards counts. For the extrapolation targets the window is stated outright rather than derived: no external data from any time point between E9.5 and E13.5 may be used, and E10.5 and E12.5 — the validation and test targets themselves — are excluded absolutely; time points outside E9.5–E13.5 may be used provided the source and its stages are stated explicitly with the submission. For interpolation targets, external data too close to a held-out stage is also treated as held out: in Task 2 that means heart data from E8.25 to E8.75 and embryo data from E7.5 to E7.75 may not be used — the midpoint-derived protected windows around the held-out interpolation stages. The same applies to genotype: another allele of the same gene at a comparable stage, or a perturbation that phenocopies the held-out one, is the held-out condition. A general-purpose resource that spans one of those windows is not banned outright — remove the cells inside it before training and say so in the method summary. Using it with them left in is using the held-out data. Every external source must be disclosed with the submission; an undisclosed one is a violation whether or not it changed the result, because the disclosure is what makes this checkable.

Each task's loader in the starter kit reads a documented path list, and DATA_SOURCES.md records which file every task reads, its verified size, and its status — including two dependencies of the richer reference baselines that are not yet on shared storage. The floor and the simple baseline need neither.

A related resource

This site also hosts the Virtual Embryo atlas. It is not the benchmark — the challenge is scored against the releases listed above — but it covers the same organism over the same window, and it is browsable without downloading anything. Useful for orienting yourself in mouse development, and for Task 1, where external public single-cell data may be trained on as long as it is disclosed with the submission.

With one limit that applies to every external source, this atlas included: no measured data from a held-out stage or condition may be used — not for training, not for fine-tuning, not transferred in under another name. The atlas spans the same window as the benchmark, so some of what it contains sits at target time points; using it there is using the answer, however it is routed. The held-out stages are named for each task above, so what is off limits is knowable before you start.