Reference

Inference

predict(raw, mask, channel_names, mpp, *, ...)	Run the cell-type prediction pipeline.
PredictionResult(cell_types, probabilities, ...)	Structured predict() output when return_probabilities=True.
DCTConfig([zarr_path])	Inference-time configuration for deepcell_types.predict.
preprocess_fov(raw, mask, *, native_mpp, ...)	Canonical preprocessing for a single FOV.
PreprocessedFov(raw, mask, centroids, ...[, ...])	Result of preprocess_fov.
make_preprocessor(config)	Return a preprocess hook for deepcell_types.predict from a config.
apply_config(raw, channel_names, config)	Apply a bounded op pipeline to raw (C,H,W) -> (C,H,W) float32.
DEFAULT_CONFIG	Built-in mutable sequence.

Abstention

ABSTENTION_LABEL

Sentinel cell-type name used for cells flagged as abstained.

Utilities

download_model(*[, version])	Download the deepcell-types model checkpoint for local use.
download_baseline_checkpoint(name)	Download a baseline-model checkpoint (and any companion files).
download_training_data(*[, extract])	Download the public training-data corpus for deepcell-types (v1.1).
list_model_versions()	Return the available pre-trained model versions, default first.
list_baseline_names()	Return the available baseline identifiers, sorted.
list_supported_markers(*[, zarr_path])	Return the canonical marker names in the active registry, sorted.
list_supported_cell_types(*[, zarr_path])	Return the cell-type names the packaged registry recognizes, sorted.
resolve_supported_marker(marker, *[, zarr_path])	Resolve a marker name or alias to its canonical registry name.