mantispy.ds.bbbc021

mantispy.ds.bbbc021(cache_dir=None)

BBBC021, MCF-7 cells treated with small molecules, the standard mechanism-of-action benchmark.

Well-level CellProfiler profiles (cpg0010-caie-drugresponse), joined to the compound, concentration and mechanism of action the Broad Bioimage Benchmark Collection publishes with the image set. The image set covers 113 compounds. This returns the annotated subset the benchmark uses: 38 compounds plus DMSO, 103 treatments (a compound at a concentration) across 12 mechanisms. Downloads about 22 MB, half of it the Image.csv of each well, which is where the cell counts are.

Every well carries a mechanism, DMSO included; select treatments with adata[~adata.obs["Metadata_Control"]].

Parameters:

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

Return type:

AnnData

Returns:

632 wells by 473 features at well resolution, with Metadata_Plate, Metadata_Well, Metadata_Compound, Metadata_Concentration, Metadata_MOA, Metadata_Perturbation (compound at concentration), Metadata_Control, and Metadata_CellCount over the Metadata_SiteCount fields, of four imaged, that contributed cells.

References

Caie et al. [2010], the image set. Ljosa et al. [2013], these profiles and the benchmark. Images courtesy of Peter Caie and David Westwood, available from the Broad Bioimage Benchmark Collection [Ljosa et al., 2012].