instrument-data-to-allotrope

Convert raw instrument data to Allotrope Simple Model (ASM) JSON by using auto-detection to route files to native allotropy parsers, outputting full ASM JSON alongside flattened CSV for LIMS integration. This preserves provenance metadata including file hashes and software versions for auditability.

ASM JSON is the Allotrope Simple Model format used to standardize raw instrument exports for LIMS, ELN, or data lakes. You need it to enable seamless integration with downstream analytics while preserving provenance metadata for reproducibility and auditing across transformation pipelines.

Yes, this conversion process uses pandas to generate a flattened 2D CSV from raw instrument exports alongside the full ASM JSON output. The flattened CSV enables quick analysis while the ASM JSON handles structured LIMS or data lake ingestion.

The allotropy library supports auto-detection for common instrument exports and routes them to native parsers for high-fidelity ASM output. When a native parser is unavailable, a flexible fallback parser processes the file to ensure continuous data conversion.

Generate an exportable Python parser by running the converter on your instrument data, which produces both ASM JSON and exportable parser code for data engineers. This exported code allows teams to reproduce the conversion pipeline independently while maintaining provenance.

Auto-detection relies on native allotropy parsers for common instrument types like NanoDrop and plate readers, but unknown or highly customized export formats trigger a flexible fallback parser. This fallback may produce lower-fidelity ASM output compared to native parser routing.