Metadata
========

Schema enums in the **Metadata** group. Each page documents an enum's
DataFrame column labels and descriptions.

.. toctree::
   :maxdepth: 1
   :caption: Metadata

   METADATA <metadata>
   ACQUISITION_METADATA <acquisition_metadata>
   CONDITION_METADATA <condition_metadata>
   EXPERIMENT_METADATA <experiment_metadata>
   GENETIC_METADATA <genetic_metadata>
   INCUBATION_METADATA <incubation_metadata>
   PLATE_METADATA <plate_metadata>
   SAMPLE_METADATA <sample_metadata>


Metadata Tag Overview
---------------------

.. list-table::
   :header-rows: 1

   * - Tag class
     - Includes
     - Use for
   * - :doc:`METADATA <metadata>`
     - Framework-populated image bookkeeping, including image names, UUIDs, file formats, image types, bit depth, and file suffixes.
     - Use when reading provenance emitted by PhenoTypic itself; these are not the biological metadata columns users normally supply.
   * - :doc:`ACQUISITION_METADATA <acquisition_metadata>`
     - Image acquisition details, including imaging date, instrument, experimenter, resolution, and exposure time.
     - Use when tracking imaging batches or diagnosing acquisition effects.
   * - :doc:`CONDITION_METADATA <condition_metadata>`
     - Media, nutrients, supplements, treatments, compounds, doses, and stress conditions applied to colonies.
     - Use when comparing phenotypes across growth environments or perturbations.
   * - :doc:`EXPERIMENT_METADATA <experiment_metadata>`
     - Experiment-level bookkeeping, including experiment IDs, projects, datasets, protocols, and notes.
     - Use when organizing outputs across projects, protocols, or datasets.
   * - :doc:`GENETIC_METADATA <genetic_metadata>`
     - Organism and genetic identity, including species, strain, genotype, background, alleles, plasmids, markers, mating type, and ploidy.
     - Use when grouping or filtering colonies by genetic background.
   * - :doc:`INCUBATION_METADATA <incubation_metadata>`
     - Temperature, elapsed time, time units, timepoints, day indices, generation, humidity, and atmosphere.
     - Use for time-course analyses and incubation-condition grouping.
   * - :doc:`PLATE_METADATA <plate_metadata>`
     - Assay plate and physical layout, including plate IDs, batches, array density, and incubator position.
     - Use when grouping measurements by plate, batch, or spatial assay layout.
   * - :doc:`SAMPLE_METADATA <sample_metadata>`
     - Sample identity and provenance, including sample IDs, replicates, clones, source plate/well, library IDs, barcodes, and controls.
     - Use for sample-level biological identity and for linking colonies back to source materials.