DNA/RNA/IF-seqFISHの画像解析プロトコールがMethods Mol. Biol. (Computational Methods for 3D Genome Analysis, edited by Ryuichi Nakato) に公開されました！
https://link.springer.com/protocol/10.1007/978-1-0716-4136-1_24#DOI
Image Analysis Protocol for DNA/RNA/Immunofluorescence (IF)-seqFISH Data
Hiroaki Ohishi & Hiroshi Ochiai
Abstract
Imaging-based spatial multi-omics technologies facilitate the analysis of higher-order genomic structures, gene transcription, and the localization of proteins and posttranslational modifications (PTMs) at the single-allele level, thereby enabling detailed observations of biological phenomena, including transcription machinery within cells and tissues. This chapter details the principles of such technologies, with a focus on DNA/RNA/immunofluorescence (IF) sequential fluorescence in situ hybridization (seqFISH). A comprehensive step-by-step protocol for image analysis is provided, covering image preprocessing, spot detection, and data visualization. For practical application, complete Jupyter Notebook codes are made available on GitHub (https://github.com/Ochiai-Lab/seqFISH_analysis).