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fix(io): read Vizgen MERSCOPE datasets#60

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bugfix/read-merscope
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fix(io): read Vizgen MERSCOPE datasets#60
EliHei2 wants to merge 1 commit into
mainfrom
bugfix/read-merscope

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@EliHei2

@EliHei2 EliHei2 commented Jun 1, 2026

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Implement MerscopePreprocessor (was NotImplementedError on main): resolve the detected_transcripts.csv / transcripts.parquet source, map cell/nucleus assignment columns to the standard schema, inline the BLANK feature filter, and load cell/nucleus boundary parquets (mirroring one onto the other when only one is present). Bundles the small column/boundary helpers it needs, so it is self-contained and independent of the platform-detection feature.

What to review:

  • src/segger/io/preprocessor.py: the helper functions + the new MerscopePreprocessor class.
  • src/segger/io/fields.py: Merscope fallback_filename + boundary-id fields.
  • Minimal: no qv/z or synthetic boundaries.

Base: main (does not depend on feat/io-platform-detection).

Implement MerscopePreprocessor (was NotImplementedError on main): resolve the
detected_transcripts.csv / transcripts.parquet source, map cell/nucleus
assignment columns to the standard schema, inline the BLANK feature filter, and
load cell/nucleus boundary parquets (mirroring one onto the other when only one
is present). Bundles the small column/boundary helpers it needs, so it is
self-contained and independent of the platform-detection feature.

What to review:
- src/segger/io/preprocessor.py: the helper functions + the new
  MerscopePreprocessor class.
- src/segger/io/fields.py: Merscope fallback_filename + boundary-id fields.
- Minimal: no qv/z or synthetic boundaries.

Base: main (does not depend on feat/io-platform-detection).
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