pyHiM: a new open-source, multi-platform software package for spatial genomics based on multiplexed DNA-FISH imaging

• Published in: Genome Biology
• Main Authors: Xavier Devos, Jean-Bernard Fiche, Marion Bardou, Olivier Messina, Christophe Houbron, Julian Gurgo, Marie Schaeffer, Markus Götz, Thomas Walter, Florian Mueller, Marcelo Nollmann
• Format: Article
• Language: English
• Published: BMC 2024-02-01
• Subjects: Spatial genomics; 3D chromatin structure; Transcription; Imaging; Bioimage informatics
• Online Access: https://doi.org/10.1186/s13059-024-03178-x

Abstract Genome-wide ensemble sequencing methods improved our understanding of chromatin organization in eukaryotes but lack the ability to capture single-cell heterogeneity and spatial organization. To overcome these limitations, new imaging-based methods have emerged, giving rise to the field of spatial genomics. Here, we present pyHiM, a user-friendly python toolbox specifically designed for the analysis of multiplexed DNA-FISH data and the reconstruction of chromatin traces in individual cells. pyHiM employs a modular architecture, allowing independent execution of analysis steps and customization according to sample specificity and computing resources. pyHiM aims to facilitate the democratization and standardization of spatial genomics analysis.