SPACe: an open-source, single-cell analysis of Cell Painting data.

Autor: Stossi F; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA. fstossi@gmail.com.; GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, USA. fstossi@gmail.com., Singh PK; GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, USA.; Center for Translational Cancer Research, Institute of Biosciences & Technology, Texas A&M University, Houston, TX, USA., Marini M; GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, USA.; Department of Mathematics, University of Houston, Houston, TX, USA., Safari K; GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, USA.; Center for Translational Cancer Research, Institute of Biosciences & Technology, Texas A&M University, Houston, TX, USA., Szafran AT; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.; GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, USA., Rivera Tostado A; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.; GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, USA., Candler CD; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA., Mancini MG; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.; GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, USA., Mosa EA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.; GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, USA., Bolt MJ; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.; GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, USA., Labate D; GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, USA.; Department of Mathematics, University of Houston, Houston, TX, USA., Mancini MA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA. mancini@bcm.edu.; GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, USA. mancini@bcm.edu.; Center for Translational Cancer Research, Institute of Biosciences & Technology, Texas A&M University, Houston, TX, USA. mancini@bcm.edu.
Jazyk: angličtina
Zdroj: Nature communications [Nat Commun] 2024 Nov 23; Vol. 15 (1), pp. 10170. Date of Electronic Publication: 2024 Nov 23.
DOI: 10.1038/s41467-024-54264-4
Abstrakt: Phenotypic profiling by high throughput microscopy, including Cell Painting, has become a leading tool for screening large sets of perturbations in cellular models. To efficiently analyze this big data, available open-source software requires computational resources usually not available to most laboratories. In addition, the cell-to-cell variation of responses within a population, while collected and analyzed, is usually averaged and unused. We introduce SPACe (Swift Phenotypic Analysis of Cells), an open-source platform for analysis of single-cell image-based morphological profiles produced by Cell Painting. We highlight several advantages of SPACe, including processing speed, accuracy in mechanism of action recognition, reproducibility across biological replicates, applicability to multiple models, sensitivity to variable cell-to-cell responses, and biological interpretability to explain image-based features. We illustrate SPACe in a defined screening campaign of cell metabolism small-molecule inhibitors tested in seven cell lines to highlight the importance of analyzing perturbations across models.
Competing Interests: Competing interests: The authors declare no competing interests.
(© 2024. The Author(s).)
Databáze: MEDLINE
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