Persistence diagrams as morphological signatures of cells : A method to measure and compare cells within a population

Title data

Bokor Bleile, Yossi ; Yadav, Pooja ; Koehl, Patrice ; Rehfeldt, Florian:
Persistence diagrams as morphological signatures of cells : A method to measure and compare cells within a population.
In: PLoS Computational Biology. Vol. 22 (2026) Issue 1 . - e1013890.
ISSN 1553-7358
DOI: https://doi.org/10.1371/journal.pcbi.1013890

Official URL:

Abstract in another language

Quantifying cell morphology is central to understanding cellular regulation, fate, and heterogeneity, yet conventional image-based analyses often struggle with diverse or irregular shapes. We present a computational framework that uses topological data analysis to characterise and compare single-cell morphologies from fluorescence microscopy. Each cell is represented by its contour together with the position of its nucleus, from which we construct a filtration based on a radial distance function and derive a persistence diagram encoding the shape’s topological evolution. The similarity between two cells is quantified using the 2-Wasserstein distance between their diagrams, yielding a shape distance we call the PH distance. We apply this method to two representative experimental systems—primary human mesenchymal stem cells (hMSCs) and HeLa cells—and show that PH distances enable the detection of outliers in those systems, the identification of sub-populations, and the quantification of shape heterogeneity. We benchmark PH against three established contour-based distances (aspect ratio, Fourier descriptors, and elastic shape analysis) and show that PH offers better separation between cell types and greater robustness when clustering heterogeneous populations. Together, these results demonstrate that persistent-homology-based signatures provide a principled and sensitive approach for analysing cell morphology in settings where traditional geometric or image-based descriptors are insufficient.

Further data

Item Type:	Article in a journal
Refereed:	Yes
Institutions of the University:	Faculties > Faculty of Mathematics, Physics und Computer Science > Department of Physics > Chair Experimental Physics I - Physics of Living Matter > Chair Experimental Physics I - Physics of Living Matter - Univ.-Prof. Dr. Matthias Weiss Faculties Faculties > Faculty of Mathematics, Physics und Computer Science Faculties > Faculty of Mathematics, Physics und Computer Science > Department of Physics Faculties > Faculty of Mathematics, Physics und Computer Science > Department of Physics > Chair Experimental Physics I - Physics of Living Matter
Result of work at the UBT:	Yes
DDC Subjects:	500 Science > 530 Physics 500 Science > 570 Life sciences, biology
Date Deposited:	16 Apr 2026 05:51
Last Modified:	17 Apr 2026 04:58
URI:	https://eref.uni-bayreuth.de/id/eprint/96797