Metadata column namespace (REMBI modules)#

PhenoTypic’s metadata columns are self-describing, per-topic headers of the form Metadata<Topic>_<Label> — for example MetadataGenetic_Strain, MetadataCulture_Time, MetadataImage_ImageName. Each metadata enum in phenotypic.schema owns one category prefix:

Enum

Category prefix

REMBI module

METADATA (framework)

MetadataImage

ImageData

STUDY_METADATA

MetadataStudy

Study

EXPERIMENT_METADATA

MetadataExperiment

Study

GENETIC_METADATA

MetadataGenetic

Biosample

SAMPLE_METADATA

MetadataSample

Biosample

CONDITION_METADATA

MetadataCondition

SpecimenPreparation

CULTURE_METADATA

MetadataCulture

SpecimenPreparation

PLATE_METADATA

MetadataPlate

SpecimenPreparation

ACQUISITION_METADATA

MetadataAcquisition

ImageAcquisition

All prefixes share the Metadata column family. Code recognizes any metadata column with phenotypic.sdk_.is_metadata_header() (which matches every Metadata<Topic>_ prefix and the generic Metadata_ fallback) rather than a bare "Metadata_" string literal. The REMBI module is a separate axis exposed by MeasurementInfo.rembi_module() and folded into the run’s deliverables/rembi.yaml manifest; the per-topic category prefix and the REMBI module are independent (the time straddler MetadataCulture_Time carries rembi_module=Biosample).

This is a recommended vocabulary, not a validator: arbitrary metadata columns are always accepted. A user-supplied label that is not in the vocabulary keeps a generic Metadata_<Label> header and routes to the REMBI Uncategorized module.

See also

To attach metadata to a run and emit the deliverables/rembi.yaml manifest, see the how-to guide Describe a run’s metadata with REMBI — it covers the --metadata sample CSV, the --study profile, and how columns fold into REMBI modules, with downloadable example files.

Column order (bio-semantic clusters)#

Measurement sheets order the metadata front-block by a bench-scientist narrative, not by REMBI module:

  1. Identity — MetadataSample_*, MetadataPlate_*

  2. Strain — MetadataGenetic_*

  3. Condition — MetadataCondition_*, MetadataCulture_*

  4. Design & provenance — MetadataExperiment_*, MetadataStudy_*, MetadataAcquisition_*

Unknown/uncategorized Metadata_* tags trail the four clusters. Within a category, columns follow the enum’s declaration order. The framework MetadataImage_* block is per-image provenance and is placed after the measurements, before the per-object Object_Label / Bbox_* / Grid_* info block. REMBI (by_module, the run manifest) remains a separate provenance axis and is unaffected by this ordering.

Migration note (namespace rename)#

Metadata columns are now per-REMBI-module prefixed (MetadataGenetic_Strain instead of the previous shared Metadata_Strain). The ad-hoc Metadata_ImageFile column was consolidated into MetadataImage_ImageName (plus MetadataImage_FileSuffix). This is a clean break:

  • Old output folders still open in the GUI: curation state auto-migrates on load (the legacy Metadata_ImageFile curation column is renamed on read), and old master_measurements.parquet archives still load (the legacy Metadata_ImageName column is recognized as the image-stem key).

  • Old metadata columns will not auto-map to their REMBI module (they read as Uncategorized). To refresh a pre-migration run’s measurement parquets to the new namespace, re-run with --mode recompile.