dataset large_stringlengths 16 35 | cells int64 11.5k 2.4M | rna_events int64 1.91M 1.1B | genes int64 298 5.01k | unit_shards int64 2 28 | size_bytes int64 19.3M 9.94B | population_format large_stringclasses 1
value | path large_stringlengths 25 44 |
|---|---|---|---|---|---|---|---|
dss_colitis_merfish | 1,439,542 | 119,553,365 | 940 | 17 | 1,349,393,560 | cell_major_rna_csr_numpy_parquet_v3 | datasets/dss_colitis_merfish |
gse246584_atm_radiation_xenium | 790,166 | 147,722,071 | 298 | 4 | 1,415,821,380 | cell_major_rna_csr_numpy_parquet_v3 | datasets/gse246584_atm_radiation_xenium |
gse269719_kidney_iri_xenium | 1,374,915 | 168,519,194 | 300 | 6 | 1,613,306,511 | cell_major_rna_csr_numpy_parquet_v3 | datasets/gse269719_kidney_iri_xenium |
gse280376_cardiac_repair_xenium | 225,023 | 61,134,068 | 475 | 7 | 541,108,205 | cell_major_rna_csr_numpy_parquet_v3 | datasets/gse280376_cardiac_repair_xenium |
gse285341_ddx54_pd1_xenium | 1,155,233 | 494,265,984 | 5,006 | 4 | 5,370,118,948 | cell_major_rna_csr_numpy_parquet_v3 | datasets/gse285341_ddx54_pd1_xenium |
gse291460_spinal_ko_xenium | 122,645 | 36,073,815 | 347 | 8 | 340,366,320 | cell_major_rna_csr_numpy_parquet_v3 | datasets/gse291460_spinal_ko_xenium |
gse295862_adipose_weightloss_xenium | 13,972 | 1,907,755 | 477 | 4 | 19,323,287 | cell_major_rna_csr_numpy_parquet_v3 | datasets/gse295862_adipose_weightloss_xenium |
gse296517_breast_fus_cosmx | 880,565 | 102,102,171 | 1,000 | 2 | 1,101,850,507 | cell_major_rna_csr_numpy_parquet_v3 | datasets/gse296517_breast_fus_cosmx |
gse296577_gbm_ohsv_xenium | 2,401,940 | 520,974,197 | 480 | 8 | 4,954,316,263 | cell_major_rna_csr_numpy_parquet_v3 | datasets/gse296577_gbm_ohsv_xenium |
gse325253_lung_drug_xenium | 1,561,700 | 681,015,170 | 5,006 | 2 | 7,440,009,880 | cell_major_rna_csr_numpy_parquet_v3 | datasets/gse325253_lung_drug_xenium |
gut_microbiota_merfish | 2,057,563 | 189,197,264 | 1,815 | 28 | 1,940,872,101 | cell_major_rna_csr_numpy_parquet_v3 | datasets/gut_microbiota_merfish |
merfish_sickness | 1,765,443 | 1,101,298,121 | 941 | 16 | 9,939,052,479 | cell_major_rna_csr_numpy_parquet_v3 | datasets/merfish_sickness |
perturbfish_astrocytes | 11,454 | 10,670,839 | 485 | 3 | 96,425,798 | cell_major_rna_csr_numpy_parquet_v3 | datasets/perturbfish_astrocytes |
uc_vedolizumab_cosmx | 80,562 | 19,552,710 | 1,000 | 7 | 203,967,001 | cell_major_rna_csr_numpy_parquet_v3 | datasets/uc_vedolizumab_cosmx |
SubcellPert: Benchmarking Subcellular Perturbation Prediction
SubcellPert benchmarks perturbation-response prediction across 14 imaging datasets and eight baselines, extending virtual cell evaluation from gene counts to intracellular RNA organization.
Project page · Paper · Code
Dataset overview
This snapshot contains 14 datasets, 13,880,723 cells, and 3,653,986,724 retained RNA events, with frozen benchmark splits and intervention descriptors. Each physical dataset is counted once. Seeds, baselines, and oracle/joint settings reuse the observations.
| Dataset | Cells | RNA events | Genes |
|---|---|---|---|
| DSS-Colitis | 1,439,542 | 119,553,365 | 940 |
| ATM-RT | 790,166 | 147,722,071 | 298 |
| Kidney-IRI | 1,374,915 | 168,519,194 | 300 |
| Cardiac-MI | 225,023 | 61,134,068 | 475 |
| Ddx54-PD1 | 1,155,233 | 494,265,984 | 5,006 |
| Spinal-KO | 122,645 | 36,073,815 | 347 |
| Adipose | 13,972 | 1,907,755 | 477 |
| Breast-FUS | 880,565 | 102,102,171 | 1,000 |
| GBM-oHSV | 2,401,940 | 520,974,197 | 480 |
| Lung-Drug | 1,561,700 | 681,015,170 | 5,006 |
| Gut-Microbiota | 2,057,563 | 189,197,264 | 1,815 |
| Sickness | 1,765,443 | 1,101,298,121 | 941 |
| PF-Astro | 11,454 | 10,670,839 | 485 |
| UC-VDZ | 80,562 | 19,552,710 | 1,000 |
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