Extended methods for spatial cell classification with DBSCAN-CellX

• Verfasst von: Küchenhoff, Leonie [VerfasserIn]
• Verfasst von: Lukas, Pascal [VerfasserIn]
• Verfasst von: Metz Zumarán, Camila [VerfasserIn]
• Verfasst von: Rothhaar, Paul [VerfasserIn]
• Verfasst von: Ruggieri, Alessia [VerfasserIn]
• Verfasst von: Lohmann, Volker [VerfasserIn]
• Verfasst von: Höfer, Thomas [VerfasserIn]
• Verfasst von: Stanifer, Megan [VerfasserIn]
• Verfasst von: Boulant, Steeve [VerfasserIn]
• Verfasst von: Rastgou Talemi, Soheil [VerfasserIn]
• Verfasst von: Graw, Frederik [VerfasserIn]
• Titel: Extended methods for spatial cell classification with DBSCAN-CellX
• Verf.angabe: Leonie Küchenhoff, Pascal Lukas, Camila Metz-Zumaran, Paul Rothhaar, Alessia Ruggieri, Volker Lohmann, Thomas Höfer, Megan L. Stanifer, Steeve Boulant, Soheil Rastgou Talemi & Frederik Graw
• E-Jahr: 2023
• Jahr: 01 November 2023
• Umfang: 11 S.
• Fussnoten: Gesehen am 29.07.2024
• Titel Quelle: Enthalten in: Scientific reports
• Ort Quelle: [London] : Springer Nature, 2011
• Jahr Quelle: 2023
• Band/Heft Quelle: 13(2023), Artikel-ID 18868, Seite 1-11
• ISSN Quelle: 2045-2322
• DOI: doi:10.1038/s41598-023-45190-4
• Datenträger: Online-Ressource
• Sprache: eng
• K10plus-PPN: 189676035X

Abstract

Abstract - Local cell densities and positioning within cellular monolayers and stratified epithelia have important implications for cell interactions and the functionality of various biological processes. To analyze the relationship between cell localization and tissue physiology, density-based clustering algorithms, such as DBSCAN, allow for a detailed characterization of the spatial distribution and positioning of individual cells. However, these methods rely on predefined parameters that influence the outcome of the analysis. With varying cell densities in cell cultures or tissues impacting cell sizes and, thus, cellular proximities, these parameters need to be carefully chosen. In addition, standard DBSCAN approaches generally come short in appropriately identifying individual cell positions. We therefore developed three extensions to the standard DBSCAN-algorithm that provide: (i) an automated parameter identification to reliably identify cell clusters, (ii) an improved identification of cluster edges; and (iii) an improved characterization of the relative positioning of cells within clusters. We apply our novel methods, which are provided as a user-friendly OpenSource-software package (DBSCAN-CellX), to cellular monolayers of different cell lines. Thereby, we show the importance of the developed extensions for the appropriate analysis of cell culture experiments to determine the relationship between cell localization and tissue physiology.