Reference

Look-up material for when you know what you want to do and need the exact name, option, column or default. The command-line page is generated from SMINT's own argument parsers and the API pages from its docstrings, so they match the installed code.

• Command line

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  Every option of smint-alignment, smint-register, run_segmentation.py, the distributed segmentation entry point and smint-viewer, with defaults and a worked example per command.

  Command line

• Data formats

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  Every file SMINT reads or writes: centroid, matrix and annotation CSVs, landmark files, transforms, job_spec.json / status.json, and the segmentation and registration outputs, with example rows.

  Data formats

• Configuration

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  Every YAML key the segmentation pipelines read, with type, default and effect, and a complete example configuration.

  Configuration

• Alignment API

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  Pre-registration, same-section centroid registration and refinement, and STalign LDDMM for sequential sections.

  smint.alignment

• Segmentation API

  ---

  Distributed and single-process segmentation, stitching and cell / nucleus reconciliation, and the Cellpose 3 / 4 compatibility layer.

  smint.segmentation

• Jobs API

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  Run registrations out of process, locally or on SLURM, and follow them through status.json.

  smint.alignment.jobs

Which page answers my question?

Question	Go to
What does --snap-radius do, and what is its default?	Command line
Which columns must my input CSV have?	Data formats → Inputs
Which coordinate columns will SMINT pick?	Data formats → Coordinate columns
What does registration_status = assigned mean?	Data formats → Registration outputs
How do I read status.json after a run?	Data formats → Registration jobs
How do I set the tile overlap or run on SLURM GPUs?	Configuration → distributed
What does register_centroids return?	Alignment API
How do I submit a registration from Python?	Jobs API