annotate_cell_types
Annotate cell types in spatial transcriptomics data using reference methods like Tangram, scANVI, or marker-based approaches. Select method, reference dataset, and parameters to assign cell identities.
Instructions
Annotate cell types in spatial transcriptomics data.
Args:
data_id: Dataset ID
params: Annotation parameters (method, reference_data_id, cell_type_key, etc.)
Note: Reference methods (tangram, scanvi) require reference_data_id to be preprocessed first.Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| data_id | Yes | ||
| params | No |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| data_id | Yes | ||
| method | Yes | ||
| output_key | Yes | ||
| confidence_key | No | ||
| cell_types | Yes | ||
| counts | Yes | ||
| confidence_scores | No | ||
| tangram_mapping_score | No |