API & data formats
Available tools
Section titled “Available tools”For a scannable capability map (formats, embeddings, DR, clustering, properties, distances, and more), see Available tools.
API reference
Section titled “API reference”The pages under advanced/api/ are auto-generated
from Python docstrings on every docs build (docs/scripts/generate_api_docs.py).
Edit docstrings in phenome/ and rebuild — there is no hand-maintained copy.
| Document | Description |
|---|---|
| PhenoMe pipeline | Main orchestrator class for the complete workflow. |
| Vision model wrappers | ModelWrapper (base), DinoV2ModelWrapper. |
| Visualization | PCA, t-SNE, UMAP, centroid plots, distance distributions, correlations. |
| Distance computation | Computing distances to reference groups. |
| Property computation | Custom property extraction from images and masks. |
| Report generation | ReportConfig and standalone HTML report generation. |
| Interactive explorer | Widget-based dashboard for exploring embeddings in Jupyter. |
| Utilities | Device helpers, transforms, image I/O, checkpoints, file discovery. |
| Metadata classes | MetadataBase, DefaultMetadata, PathTemplateMetadata, DataFrameMetadata. |
| Plugins | Property and metadata registries, report sections. |
Function location guide
Section titled “Function location guide”The Function location guide is auto-generated
in the same build step from live phenome exports (docs/scripts/api_docs/function_index.py).
It lists top-level imports, PhenoMe methods, and submodule exports with tier badges (public /
advanced / internal) and deep links into the API pages above.
Getting started
Section titled “Getting started”For a walkthrough of the complete pipeline, installation, and a first analysis, see the Getting started guide. For an overview of the core concepts, see Core concepts.
Extending the pipeline
Section titled “Extending the pipeline”- Extending PhenoMe - overview of extension points.
- Experiment details - metadata extraction.
- Select properties - property presets, requirement types, factories.
- Plugins - plugin registry, custom presets.
Technical reference
Section titled “Technical reference”| Document | Description |
|---|---|
| HDF5 database protocol | Internal checkpoint and result file structure. |