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Couldn't infer the same data file format for all splits. Got {NamedSplit('train'): (None, {}), NamedSplit('validation'): (None, {}), NamedSplit('test'): ('hdf5', {})}
Error code: FileFormatMismatchBetweenSplitsError
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st-data-distil processed subcellular datasets
Processed train/val/test splits used by st_data_distil / GSPNet-style gene spatial-pattern work.
This repo is a processed redistribution of published datasets. Please cite the original papers and respect their licenses/terms. Private by default.
Contents
| Folder | Dataset | Technology | Species | Tissue / cell line |
|---|---|---|---|---|
NIH3T3/ |
seqFISH+ NIH/3T3 | seqFISH+ | Mouse | NIH/3T3 fibroblasts |
U2OS/ |
Bento MERFISH U2-OS | MERFISH | Human | U2-OS |
CosMx_Lung/ |
CosMx Lung5 Rep1 | CosMx SMI | Human | Lung |
Typical files: *_train.h5ad, *_val.h5ad, *_test.h5ad. CosMx also has *_pattern.h5ad (pattern labels), molecule *_dataframe.pkl, and a full-FOV cosmx_spatial_adata_with_boundaries.h5ad.
Sources (cite these)
- NIH3T3 / seqFISH+: Eng et al., Nature 2019.
- U2OS / MERFISH: Bento toolkit paper (Mah et al., Genome Biology 2024) and the underlying MERFISH U2-OS experiment.
- CosMx Lung5 Rep1: NanoString CosMx SMI lung dataset (“High-plex subcellular imaging”).
Load
import anndata as ad
adata = ad.read_h5ad("NIH3T3/seqfish+_train.h5ad")
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