mantispy.ds.aconcagua

mantispy.ds.aconcagua(cache_dir=None)

Aconcagua, a genome-scale optical pooled CRISPR screen of essential genes in HeLa cells.

One row per guide per well: the median profile of a guide’s cells in a well, after a per plate-and-well robust normalization against the well’s non-targeting controls, over a subset of the screen built for the optical-pooled-screens case study. The cells were segmented and measured with brieflow’s cp_emulator in four channels (DNA, alpha-tubulin, gamma-H2AX and F-actin); the brieflow feature names are mapped to mantispy’s CellProfiler-style grammar. The subset keeps all 250 non-targeting guides, four annotated positive controls (H2AX, ECT2, TUBB, CFL1), 50 strong and 50 weak known hits, and 396 random library genes, across eight plates and 46 wells.

Mitotic cells are pooled at their natural share rather than capped, so a profile mixes interphase and mitotic cells as the screen saw them, and each row records its Metadata_MitoticFraction. The file is staged on scverse-exampledata, so the loader fetches a single h5ad rather than rebuilding it from the raw per-cell table.

Parameters:

cache_dir (str | Path | None (default: None)) – Where to keep the download. Defaults to mantispy.settings.cache_dir.

Return type:

AnnData

Returns:

Guide-by-well profiles read with mantispy.io.read(), carrying Metadata_Plate, Metadata_Well, Metadata_Guide, Metadata_Gene, Metadata_Perturbation (the gene, or "nontargeting"), Metadata_Perturbation_Type ("crispr"), Metadata_Control and Metadata_Control_Type (negcon/poscon/treatment), Metadata_Tier (control/strong/weak/random), Metadata_CellCount and Metadata_MitoticFraction.

References

Di Bernardo and others [2026], this screen; [Funk et al., 2022], the screen it extends. The per-cell measurements are from brieflow; the subset is available through the CZ Biohub OPS Explorer.