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Baysor C++ Branch

Baysor segments imaging-based spatial transcriptomics data using spatial position, local gene composition, and optional prior segmentation inputs.

This cpp branch is the native C++ implementation of the main Baysor workflow. It is built with CMake and currently exposes three CLI subcommands:

run
preview
segfree

What Is Implemented

baysor run
baysor preview
baysor segfree
CSV / Parquet transcript-table input
image-mask and polygon prior segmentation
Xenium-aware input resolution through experiment.xenium
legacy and parquet output styles
HTML plotting / diagnostic outputs from run

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