CellMAP: an open-source software tool to batch-process cell topography and stiffness maps collected with an atomic force microscope
Abstract Atomic force microscopy (AFM) is the gold-standard technique to simultaneously map the morphology and viscoelastic properties of living cells. Although existing software tools, both open-source and from AFM manufacturers, can analyze cells individually, there is a growing need for fast and...
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| Format: | Article |
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BMC
2025-02-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-025-06060-0 |
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| author | Antoine Allard Maxime Liboz Raphaël Crépin Sid Labdi Olek Maciejak Michel Malo Clément Campillo Guillaume Lamour |
| author_facet | Antoine Allard Maxime Liboz Raphaël Crépin Sid Labdi Olek Maciejak Michel Malo Clément Campillo Guillaume Lamour |
| author_sort | Antoine Allard |
| collection | DOAJ |
| description | Abstract Atomic force microscopy (AFM) is the gold-standard technique to simultaneously map the morphology and viscoelastic properties of living cells. 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. |
| format | Article |
| id | doaj-art-0a7f1c07cd5247669926157189de170f |
| institution | Kabale University |
| issn | 1471-2105 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj-art-0a7f1c07cd5247669926157189de170f2025-02-09T12:56:55ZengBMCBMC Bioinformatics1471-21052025-02-0126111610.1186/s12859-025-06060-0CellMAP: an open-source software tool to batch-process cell topography and stiffness maps collected with an atomic force microscopeAntoine Allard0Maxime Liboz1Raphaël Crépin2Sid Labdi3Olek Maciejak4Michel Malo5Clément Campillo6Guillaume Lamour7LAMBE, CNRS, Université Paris-Saclay, Univ Evry, CY Cergy Paris UniversitéLAMBE, CNRS, Université Paris-Saclay, Univ Evry, CY Cergy Paris UniversitéLAMBE, CNRS, Université Paris-Saclay, Univ Evry, CY Cergy Paris UniversitéLAMBE, CNRS, Université Paris-Saclay, Univ Evry, CY Cergy Paris UniversitéLAMBE, CNRS, Université Paris-Saclay, Univ Evry, CY Cergy Paris UniversitéLAMBE, CNRS, Université Paris-Saclay, Univ Evry, CY Cergy Paris UniversitéLAMBE, CNRS, Université Paris-Saclay, Univ Evry, CY Cergy Paris UniversitéLAMBE, CNRS, Université Paris-Saclay, Univ Evry, CY Cergy Paris UniversitéAbstract Atomic force microscopy (AFM) is the gold-standard technique to simultaneously map the morphology and viscoelastic properties of living cells. 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.https://doi.org/10.1186/s12859-025-06060-0Cell mechanicsTopographyAtomic force microscopyMATLABGraphical user interfaceBatch processing |
| spellingShingle | Antoine Allard Maxime Liboz Raphaël Crépin Sid Labdi Olek Maciejak Michel Malo Clément Campillo Guillaume Lamour CellMAP: an open-source software tool to batch-process cell topography and stiffness maps collected with an atomic force microscope BMC Bioinformatics Cell mechanics Topography Atomic force microscopy MATLAB Graphical user interface Batch processing |
| title | CellMAP: an open-source software tool to batch-process cell topography and stiffness maps collected with an atomic force microscope |
| title_full | CellMAP: an open-source software tool to batch-process cell topography and stiffness maps collected with an atomic force microscope |
| title_fullStr | CellMAP: an open-source software tool to batch-process cell topography and stiffness maps collected with an atomic force microscope |
| title_full_unstemmed | CellMAP: an open-source software tool to batch-process cell topography and stiffness maps collected with an atomic force microscope |
| title_short | CellMAP: an open-source software tool to batch-process cell topography and stiffness maps collected with an atomic force microscope |
| title_sort | cellmap an open source software tool to batch process cell topography and stiffness maps collected with an atomic force microscope |
| topic | Cell mechanics Topography Atomic force microscopy MATLAB Graphical user interface Batch processing |
| url | https://doi.org/10.1186/s12859-025-06060-0 |
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