1. pyHiM: a new open-source, multi-platform software package for spatial genomics based on multiplexed DNA-FISH imaging
- Author
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Xavier Devos, Jean-Bernard Fiche, Marion Bardou, Olivier Messina, Christophe Houbron, Julian Gurgo, Marie Schaeffer, Markus Götz, Thomas Walter, Florian Mueller, and Marcelo Nollmann
- Subjects
Spatial genomics ,3D chromatin structure ,Transcription ,Imaging ,Bioimage informatics ,Biology (General) ,QH301-705.5 ,Genetics ,QH426-470 - Abstract
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.
- Published
- 2024
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