ISTDECO

ISTDECO decodes barcoded fluorescent spot patterns in In Situ Transcriptomics (IST) image series to localize mRNA expression within tissue samples.

Key Features:

• Integrated spectral and spatial deconvolution: Combines spectral deconvolution across color channels and spatial deconvolution across imaging rounds into a unified algorithmic framework for decoding barcoded signals.
• Simultaneous localization and decoding: Performs spot localization and barcode decoding concurrently rather than as separate sequential steps.
• Multiplexed image processing: Processes multiplexed image series where fluorescent spots form barcoded patterns across imaging rounds and color channels that indicate mRNA presence.
• Robustness to noise and crowding: Reduces sensitivity to low signal-to-noise ratios and high spot-density/optical crowding to improve decoding accuracy.
• Validation on multiple datasets: Evaluated on simulated data and two real In Situ Transcriptomics datasets with state-of-the-art decoding performance.
• GPU acceleration: Implements GPU acceleration to accelerate processing times.

Scientific Applications:

• Gene expression localization: Localizing gene expression and mRNA signals directly within tissue samples in IST experiments.
• High-density transcriptomic imaging: Decoding barcoded mRNA in high spot-density or low signal-to-noise IST datasets.
• Spatial transcriptomics: Supporting analyses of cellular function and organization at the molecular level within tissue context.

Methodology:

Combines spectral and spatial deconvolution in a single algorithm that performs simultaneous spot localization and barcode decoding and uses GPU acceleration for computation.