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This enables an unbiased characterization of the effects of small chemical compounds. We established and extensively validated a Cell Painting protocol to screen the compound libraries of the European initiative EU-OPENSCREEN (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.eu-openscreen.eu\" ext-link-type=\"uri\">www.eu-openscreen.eu<\/jats:ext-link>\n                    ) in order to find robust and reproducible links between the known target or the pathway mechanism of each compound to the phenotypic profile. In this chapter, we describe the Cell Painting procedure, image analysis, and the downstream data processing procedures.\n                  <\/jats:p>","DOI":"10.1007\/978-1-0716-4985-5_4","type":"book-chapter","created":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T23:44:02Z","timestamp":1767311042000},"page":"73-91","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Cell Painting Protocol to Characterize Morphological Profiles of Large Compound Collections Using the EU-OPENSCREEN Library"],"prefix":"10.1007","author":[{"given":"Christopher","family":"Wolff","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"Neuenschwander","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michelle","family":"M\u00fcller","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Astrid","family":"M\u00fchl","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jens Peter","family":"von Kries","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher","family":"Schmied","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Edgar","family":"Specker","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2026,1,2]]},"reference":[{"issue":"4","key":"4_CR1","doi-asserted-by":"publisher","first-page":"2347","DOI":"10.1021\/acs.jmedchem.2c01577","volume":"66","author":"DH O\u2019Donovan","year":"2023","unstructured":"O\u2019Donovan DH, De Fusco C, Kuhnke L, Reichel A (2023) Trends in molecular properties, bioavailability, and permeability across the Bayer compound collection. 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