EmbryoTempoFormer release bundle (FULL processed + checkpoints + splits) for S‑BIAD531

DOI: 10.5281/zenodo.18318139

This archive provides a reproducibility bundle for the EmbryoTempoFormer (ETF) pipeline for zebrafish brightfield time-lapse microscopy based on BioImage Archive accession S-BIAD531.

Contents- processed_28C5/: preprocessed uint8 NumPy arrays (*.npy), one per embryo, shape [T,H,W] = [192,384,384], for 28.5°C- processed_25C/: preprocessed uint8 NumPy arrays (*.npy), same format, for 25°C- checkpoints/: four model checkpoints (cnn_single, meanpool, nocons, full)- splits/: JSON split files (28C5.json, 25C.json) listing embryo IDs for train/val/test- MANIFEST.json: file list with SHA256 checksums and file sizes- SHA256SUMS.txt: checksum file for command-line verification

PurposeThis bundle enables fast, end-to-end reproduction of the quantitative results and figures reported in the accompanying code repository, without re-running preprocessing or training.

Recommended reproduction steps (for reviewers)1) Download and extract the archive, which creates:   embryo-tempoformer_release_v1/2) Clone the code repository and configure .env paths to point to the extracted folder:   - processed_28C5/, processed_25C/, splits/, checkpoints/3) Run:   bash scripts/reproduce_all.shThis produces aggregated CSV/JSON summaries, bootstrap confidence intervals, and publication-ready figures under runs/paper_eval_*/.

Integrity checkAfter extraction:  sha256sum -c SHA256SUMS.txt

Data provenanceRaw imaging data are available from the BioImage Archive S-BIAD531 record:https://www.ebi.ac.uk/bioimage-archive/galleries/S-BIAD531.htmlThe processed arrays in this archive are derived from the raw data via percentile intensity clipping, bilinear resizing to 384×384, and padding/trimming to 192 frames.