Python API¶
This section documents the public Python API directly from the ALHENA docstrings.
Most workflows use three pages:
- Reading data for H&E images and nuclei;
- Encoder for tile and cell embeddings;
- Cell typer for reference-based cell annotation.
The returned TileEmbeddings, CellEmbeddings, and AnnotationResult objects are documented
under Types.
| Page | Open it when |
|---|---|
| Encoder | You compute tile or cell embeddings, or want the adapters underneath. |
| Cell typer | You annotate cells, from tiles and nuclei or from cells encoded earlier. |
| Reading data | Your images or nuclei sit in files or arrays, or you read saved results. |
| Preprocessing | You check what a resolution does to a tile. |
| Cells and pooling | You build the nucleus-to-token table, or pool yourself. |
| Retrieval | You run the lower-level reference-retrieval operator. |
| References | You load a prebuilt or custom reference and inspect its class support. |
| Building a reference | You build a custom reference from atlas embeddings and labels. |
| Scoring | You evaluate annotations against known labels. |
| SpatialData | Your data is in a SpatialData object, or you run sopa's patch pipeline. |
| Plotting | You draw overlays, tile regions, compositions, matrices or legends. |
| Types | You need the fields of a result: TileEmbeddings, CellEmbeddings, AnnotationResult. |
| Errors and warnings | You catch an ALHENA error, or filter its warnings. |
| Constants | You need a fixed quantity: resolution, k, tau, the axes. |
Each heading names the public module to import a symbol from. On the Errors and Constants
pages, it names the private module that defines the symbol, and the page says where to import
it from. A re-exported symbol reaches either way, so alhena.load_celltyper and
alhena.api.load_celltyper are one function.
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