IRIS-py

IRIS-py decodes fluorescence imaging data from in situ RNA sequencing into nucleotide barcodes while recording quality scores and spatial coordinates.

Key Features:

• Accurate Barcode Calling: Translates image-based fluorescence signals into nucleotide barcodes for in situ RNA-seq data.
• Quality and Spatial Information Recording: Records quality scores and spatial coordinates for each decoded barcode.
• Modular Design: Provides a modular architecture to enable extension for new in situ RNA-seq protocols and processing modules.
• Companion Visualization (DAIBC): Provides an R Shiny application, DAIBC, for visualization of barcode calls and spatial expression data.

Scientific Applications:

• Developmental Biology: Maps spatial gene expression to study tissue patterning during development.
• Cancer Research: Profiles spatial distribution of transcripts in tumor tissues to investigate spatially resolved gene expression in cancer.
• Neuroscience: Analyzes spatial expression patterns in neural tissues to investigate region-specific gene activity.

Methodology:

Converts fluorescence signals captured during in situ sequencing into nucleotide sequences while preserving associated quality scores and spatial coordinates.