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 ).
Keyphrases
- single molecule
- nucleic acid
- circulating tumor
- high resolution
- electronic health record
- randomized controlled trial
- cell free
- induced apoptosis
- copy number
- big data
- transcription factor
- gene expression
- deep learning
- genome wide
- data analysis
- dna methylation
- mass spectrometry
- genome wide identification
- artificial intelligence
- energy transfer
- real time pcr
- fluorescence imaging