Optocoder

Optocoder decodes bead barcodes from microscopy images to quantify spatially resolved gene expression in spatial transcriptomics experiments.

Key Features:

• Image alignment: Precise alignment of microscopy images to ensure spatial correspondence across imaging rounds.
• Bead detection: Automated detection of beads within microscopy images for downstream barcode assignment.
• Fluorescence signal correction: Correction for confounding fluorescence artifacts, including crosstalk and phasing.
• Supervised machine learning matching: Supervised machine learning algorithms to match optically decoded barcodes to their sequenced counterparts.
• Benchmarking: Performance evaluation using datasets from an in-house spatial transcriptomics platform and Slide-Seq(V2).

Scientific Applications:

• Spatial transcriptomics quantification: Generation of spatially resolved gene expression measurements by decoding bead barcodes from microscopy.
• Integration of optical and sequencing data: Alignment of optically decoded barcodes with sequencing results to enable combined optical-sequencing analyses.
• Tissue spatial mapping: Creation of detailed representations of tissue gene expression in space for downstream biological interpretation.

Methodology:

Performs image alignment, bead detection, fluorescence signal correction for crosstalk and phasing, supervised machine learning-based matching of optically decoded barcodes to sequenced counterparts, and benchmarking on in-house and Slide-Seq(V2) datasets.