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© Research
Publication : Genome biology

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

Team: Quantitative RNA imaging
Team: Photonic BioImaging (UTechS PBI)
Member: Florian Muller
Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Genome biology - 13 Feb 2024

Devos X, Fiche JB, Bardou M, Messina O, Houbron C, Gurgo J, Schaeffer M, Götz M, Walter T, Mueller F, Nollmann M

Link to Pubmed [PMID] – 38351149

Link to DOI – 10.1186/s13059-024-03178-x

Genome Biol 2024 Feb; 25(1): 47

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.