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

作     者：Devos, Xavier Fiche, Jean-Bernard Bardou, Marion Messina, Olivier Houbron, Christophe Gurgo, Julian Schaeffer, Marie Gotz, Markus Walter, Thomas Mueller, Florian Nollmann, Marcelo 

作者机构：Univ Montpellier Ctr Biol Struct CNRS INSERMU1054UMR 5048 F-34090 Montpellier France PSL Univ Ctr Computat Biol CBIO Mines Paris F-75006 Paris France Inst Curie F-75248 Paris France INSERM U900 F-75248 Paris France Univ Paris Cite Inst Pasteur Imaging & Modeling Unit Paris France 

出 版 物：《GENOME BIOLOGY》 (Genome Biol.)

年 卷 期：2024年第25卷第1期

页      面：1页

核心收录：

基　　金：HORIZON EUROPE European Research Council 

主　　题：Spatial genomics 3D chromatin structure Transcription Imaging Bioimage informatics 

摘      要：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.