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Dataset Preview

preview generates an HTML overview of a dataset without running full segmentation.

CLI shape:

./build/baysor preview [OPTIONS] coordinates

Typical Use

./build/baysor preview \
  -c configs/xenium.toml \
  -o preview.html \
  data/transcripts.parquet

or for Xenium-style columns:

./build/baysor preview \
  -c configs/xenium.toml \
  data/transcripts.parquet

What It Computes

The preview pipeline currently does the following:

  • loads molecules
  • estimates a molecule-confidence / noise model
  • computes neighborhood-composition colors
  • estimates a gene-structure embedding
  • writes an HTML summary report

Common Options

  • -c,--config
  • -x,--x-column
  • -y,--y-column
  • -z,--z-column
  • -g,--gene-column
  • --qv-column
  • --min-qv
  • --x-min, --x-max
  • --y-min, --y-max
  • --z-min, --z-max
  • -o,--output
  • --force-2d

Output

The default output is:

preview.html

Notes

  • preview accepts a transcript table directly.
  • for Xenium datasets, it also accepts experiment.xenium and resolves the underlying transcript table automatically.
  • this is useful for quick sanity checks before a full segmentation run.