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Although existing software tools, both open-source and from AFM manufacturers, can analyze cells individually, there is a growing need for fast and accessible codes to compile data from multiple cells into a single dataset. To address this, we present CellMAP, a user-friendly software tool that streamlines the batch-processing of AFM-derived topography and stiffness maps of living cells. Our analysis pipeline includes but is not limited to: flattening of the underlying substrate surface, filtering of outlier values, measurement of the cell surface and volume, and measurement of height and stiffness distributions. CellMAP can also generate a composite cell that reflects the height and stiffness properties of an entire cell population.<\/jats:p>","DOI":"10.1186\/s12859-025-06060-0","type":"journal-article","created":{"date-parts":[[2025,2,4]],"date-time":"2025-02-04T14:29:22Z","timestamp":1738679362000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["CellMAP: an open-source software tool to batch-process cell topography and stiffness maps collected with an atomic force microscope"],"prefix":"10.1186","volume":"26","author":[{"given":"Antoine","family":"Allard","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maxime","family":"Liboz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rapha\u00ebl","family":"Cr\u00e9pin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sid","family":"Labdi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olek","family":"Maciejak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michel","family":"Malo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cl\u00e9ment","family":"Campillo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guillaume","family":"Lamour","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,2,4]]},"reference":[{"issue":"2186","key":"6060_CR1","doi-asserted-by":"publisher","first-page":"20190604","DOI":"10.1098\/rsta.2019.0604","volume":"378","author":"I Casuso","year":"2020","unstructured":"Casuso I, Redondo-Morata L, Rico F. 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