SpatialBench canonical data v1

Xenium QC eval data for the SpatialBench canonical task xenium_qc_filter_min_umi_counts. Source: latch://147398958.node.

SpatialBench canonical data v3 (batch 3)

Batch 3 data assets for the remaining 4 canonical spatialbench tasks (excluding the 2.1 GB seeker ovary which exceeds GH's 2 GB per-asset limit and will go in a future v4 via LFS or split).

• vizgen_mouse_brain_aging_raw.h5ad (434 MB) — merfish normalization (log z-score gad2 mean)
• vizgen_mouse_brain_aging.h5ad (1.0 GB) — merfish clustering (astro2 vs astro)
• vizgen_mouse_brain_aging_leiden_no_celltype.h5ad (1.1 GB) — merfish cell-typing (astrocyte aging markers P/R)
• multimodal_spatial_xenium_mouse_kidney_no_domain_annotation.h5ad (1.9 GB) — xenium kidney (CN3/PTS3 neighborhood dynamics, MCQ)

SpatialBench canonical data v2 (batch 2)

Batch 2 of spatialbench canonical task data for Taiga experiments.

• ovary_1hr_hvg.h5ad (40MB) — seeker_3x3_ovary_1hr_pc1_cell_populations (MCQ)
• sp_query_clean_for_eval.h5ad (83MB) — bone_visium_c2l_niche_bone_formation_markers (marker P/R)
• xenium_mouse_kidney_subset_PT_day2_no_celltype.h5ad (109MB) — xenium classify_pt_distribution_advanced (distribution)
• GSM8677818_human_bone_qc_rawcounts.h5ad (59MB) — visium_spatial_niches_bone_meslin (jaccard, file 1/2)
• sp_query.h5ad (64MB) — visium_spatial_niches_bone_meslin (jaccard, file 2/2)

scBench canonical data v1 (4T1 tumor scRNA-seq)

Data for scBench canonical 7-task benchmark on mouse 4T1 mammary tumor scRNA-seq (Chromium 10x platform).

• 4T1_viable_raw_counts.h5ad (1.0 GB) — QC task
• 4T1_viable_filtered.h5ad (1.0 GB) — normalization task
• 4T1_viable_normalized.h5ad (1.5 GB) — HVG + cell-typing compartments tasks
• 4T1_cleaned_celltypes_only.h5ad (1.5 GB) — clustering + DE (contractile CAF) tasks
• 4T1_Thy1.1_CAFs.h5ad (279 MB) — trajectory analysis task

Source: latchbio/scbench. Public Apache-2.0 data.