{"entity": "researcher", "timestamp": "2026-08-20T20:49:06.760Z", "family": "Singh", "given": "Shantanu", "initials": "S", "orcid": "0000-0003-3150-3025", "affiliations": ["Broad Institute of MIT and Harvard, Cambridge, MA, USA."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fab52cf5bb64d62878524fc2da36dd1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fab52cf5bb64d62878524fc2da36dd1"}}, "publications": [{"entity": "publication", "iuid": "0824f2f7c1d844aca1638ef6b6910254", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0824f2f7c1d844aca1638ef6b6910254.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0824f2f7c1d844aca1638ef6b6910254"}}, "title": "Author Correction: Cell Painting: a decade of discovery and innovation in cellular imaging.", "authors": [{"family": "Seal", "given": "Srijit", "initials": "S", "orcid": "0000-0003-2790-8679", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf360510777949acaa72a940f13e17bf.json"}}, {"family": "Trapotsi", "given": "Maria-Anna", "initials": "MA", "orcid": "0000-0002-9177-4241", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f90a4eeefb14159b4397b84a116e152.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c192389f99d4801b91f3350e07dfb9e.json"}}, {"family": "Singh", "given": "Shantanu", "initials": "S", "orcid": "0000-0003-3150-3025", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fab52cf5bb64d62878524fc2da36dd1.json"}}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J"}, {"family": "Greene", "given": "Nigel", "initials": "N"}, {"family": "Bender", "given": "Andreas", "initials": "A", "orcid": "0000-0002-6683-7546", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fea25f8013a14bb587c85df858f74d55.json"}}, {"family": "Carpenter", "given": "Anne E", "initials": "AE", "orcid": "0000-0003-1555-8261", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9bda2a39a0ac4fd9a7d95298608afb74.json"}}], "type": "published erratum", "published": "2025-02-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "22", "issue": "2", "pages": "447", "issn-l": "1548-7091"}, "abstract": null, "doi": "10.1038/s41592-024-02578-y", "pmid": "39668211", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS2077445"}, {"db": "pmc", "key": "PMC12221059"}, {"db": "pii", "key": "10.1038/s41592-024-02578-y"}], "notes": [], "created": "2026-08-20T09:03:21.194Z", "modified": "2026-08-20T09:03:21.283Z"}, {"entity": "publication", "iuid": "c24b1b477e1647c890209b9b74a6ebce", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c24b1b477e1647c890209b9b74a6ebce.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c24b1b477e1647c890209b9b74a6ebce"}}, "title": "Cell Painting: a decade of discovery and innovation in cellular imaging.", "authors": [{"family": "Seal", "given": "Srijit", "initials": "S", "orcid": "0000-0003-2790-8679", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf360510777949acaa72a940f13e17bf.json"}}, {"family": "Trapotsi", "given": "Maria-Anna", "initials": "MA", "orcid": "0000-0002-9177-4241", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f90a4eeefb14159b4397b84a116e152.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c192389f99d4801b91f3350e07dfb9e.json"}}, {"family": "Singh", "given": "Shantanu", "initials": "S", "orcid": "0000-0003-3150-3025", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fab52cf5bb64d62878524fc2da36dd1.json"}}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J"}, {"family": "Greene", "given": "Nigel", "initials": "N"}, {"family": "Bender", "given": "Andreas", "initials": "A", "orcid": "0000-0002-6683-7546", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fea25f8013a14bb587c85df858f74d55.json"}}, {"family": "Carpenter", "given": "Anne E", "initials": "AE", "orcid": "0000-0003-1555-8261", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9bda2a39a0ac4fd9a7d95298608afb74.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "22", "issue": "2", "pages": "254-268", "issn-l": "1548-7091"}, "abstract": "Modern quantitative image analysis techniques have enabled high-throughput, high-content imaging experiments. Image-based profiling leverages the rich information in images to identify similarities or differences among biological samples, rather than measuring a few features, as in high-content screening. Here, we review a decade of advancements and applications of Cell Painting, a microscopy-based cell-labeling assay aiming to capture a cell's state, introduced in 2013 to optimize and standardize image-based profiling. Cell Painting's ability to capture cellular responses to various perturbations has expanded owing to improvements in the protocol, adaptations for different perturbations, and enhanced methodologies for feature extraction, quality control, and batch-effect correction. Cell Painting is a versatile tool that has been used in various applications, alone or with other -omics data, to decipher the mechanism of action of a compound, its toxicity profile, and other biological effects. Future advances will likely involve computational and experimental techniques, new publicly available datasets, and integration with other high-content data types.", "doi": "10.1038/s41592-024-02528-8", "pmid": "39639168", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS2049550"}, {"db": "pmc", "key": "PMC11810604"}, {"db": "pii", "key": "10.1038/s41592-024-02528-8"}], "notes": [], "created": "2026-08-20T09:03:19.249Z", "modified": "2026-08-20T09:03:19.420Z"}, {"entity": "publication", "iuid": "934f69a0412044b4b32374cc6cd1ae49", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/934f69a0412044b4b32374cc6cd1ae49.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/934f69a0412044b4b32374cc6cd1ae49"}}, "title": "A Decade in a Systematic Review: The Evolution and Impact of Cell Painting.", "authors": [{"family": "Seal", "given": "Srijit", "initials": "S", "orcid": "0000-0003-2790-8679", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf360510777949acaa72a940f13e17bf.json"}}, {"family": "Trapotsi", "given": "Maria-Anna", "initials": "MA", "orcid": "0000-0002-9177-4241", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f90a4eeefb14159b4397b84a116e152.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c192389f99d4801b91f3350e07dfb9e.json"}}, {"family": "Singh", "given": "Shantanu", "initials": "S", "orcid": "0000-0003-3150-3025", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fab52cf5bb64d62878524fc2da36dd1.json"}}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9c300823ae241eea419a01e4397fcc2.json"}}, {"family": "Greene", "given": "Nigel", "initials": "N", "orcid": "0000-0003-0433-4596", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e97367503f749bc934ddb3f10a84891.json"}}, {"family": "Bender", "given": "Andreas", "initials": "A", "orcid": "0000-0002-6683-7546", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fea25f8013a14bb587c85df858f74d55.json"}}, {"family": "Carpenter", "given": "Anne E", "initials": "AE", "orcid": "0000-0003-1555-8261", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9bda2a39a0ac4fd9a7d95298608afb74.json"}}], "type": "preprint", "published": "2024-05-07", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "High-content image-based assays have fueled significant discoveries in the life sciences in the past decade (2013-2023), including novel insights into disease etiology, mechanism of action, new therapeutics, and toxicology predictions. Here, we systematically review the substantial methodological advancements and applications of Cell Painting. Advancements include improvements in the Cell Painting protocol, assay adaptations for different types of perturbations and applications, and improved methodologies for feature extraction, quality control, and batch effect correction. Moreover, machine learning methods recently surpassed classical approaches in their ability to extract biologically useful information from Cell Painting images. Cell Painting data have been used alone or in combination with other - omics data to decipher the mechanism of action of a compound, its toxicity profile, and many other biological effects. Overall, key methodological advances have expanded Cell Painting's ability to capture cellular responses to various perturbations. Future advances will likely lie in advancing computational and experimental techniques, developing new publicly available datasets, and integrating them with other high-content data types.", "doi": "10.1101/2024.05.04.592531", "pmid": "38766203", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11100607"}, {"db": "pii", "key": "2024.05.04.592531"}], "notes": [], "created": "2026-08-20T10:54:50.205Z", "modified": "2026-08-20T10:54:50.323Z"}, {"entity": "publication", "iuid": "bc1a8965388d4dcab37b9050baee86f9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bc1a8965388d4dcab37b9050baee86f9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bc1a8965388d4dcab37b9050baee86f9"}}, "title": "From pixels to phenotypes: Integrating image-based profiling with cell health data as BioMorph features improves interpretability.", "authors": [{"family": "Seal", "given": "Srijit", "initials": "S", "orcid": "0000-0003-2790-8679", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf360510777949acaa72a940f13e17bf.json"}}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9c300823ae241eea419a01e4397fcc2.json"}}, {"family": "Singh", "given": "Shantanu", "initials": "S", "orcid": "0000-0003-3150-3025", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fab52cf5bb64d62878524fc2da36dd1.json"}}, {"family": "Carpenter", "given": "Anne E", "initials": "AE", "orcid": "0000-0003-1555-8261", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9bda2a39a0ac4fd9a7d95298608afb74.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c192389f99d4801b91f3350e07dfb9e.json"}}, {"family": "Bender", "given": "Andreas", "initials": "A", "orcid": "0000-0002-6683-7546", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fea25f8013a14bb587c85df858f74d55.json"}}], "type": "journal article", "published": "2024-03-01", "journal": {"title": "Mol. Biol. Cell", "issn": "1939-4586", "volume": "35", "issue": "3", "pages": "mr2", "issn-l": "1059-1524"}, "abstract": "Cell Painting assays generate morphological profiles that are versatile descriptors of biological systems and have been used to predict in vitro and in vivo drug effects. However, Cell Painting features extracted from classical software such as CellProfiler are based on statistical calculations and often not readily biologically interpretable. In this study, we propose a new feature space, which we call BioMorph, that maps these Cell Painting features with readouts from comprehensive Cell Health assays. We validated that the resulting BioMorph space effectively connected compounds not only with the morphological features associated with their bioactivity but with deeper insights into phenotypic characteristics and cellular processes associated with the given bioactivity. The BioMorph space revealed the mechanism of action for individual compounds, including dual-acting compounds such as emetine, an inhibitor of both protein synthesis and DNA replication. Overall, BioMorph space offers a biologically relevant way to interpret the cell morphological features derived using software such as CellProfiler and to generate hypotheses for experimental validation.", "doi": "10.1091/mbc.E23-08-0298", "pmid": "38170589", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10916876"}], "notes": [], "created": "2026-08-20T09:38:45.160Z", "modified": "2026-08-20T09:38:45.255Z"}]}