| Class | Module | Docs |
|---|---|---|
Cohort | bioptimus.data.cohort | bioptimus.data.cohort |
ModelOutput | bioptimus.data.cohort | bioptimus.data.cohort |
PatientRecord | bioptimus.data.cohort | bioptimus.data.cohort |
WSIRecord | bioptimus.data.cohort | bioptimus.data.cohort |
MultiModelData | bioptimus.data.multi_model.multi_model_dataset | bioptimus.data.multi_model.multi_model_dataset |
BulkRNAData | bioptimus.data.omics.bulkrna | bioptimus.data.omics.bulkrna |
TileSpec | bioptimus.data.tile_spec | bioptimus.data.tile_spec |
PytorchTileDataset | bioptimus.data.wsi.torch_dataset | bioptimus.data.wsi.torch_dataset |
SamplingMode | bioptimus.data.wsi.torch_dataset | bioptimus.data.wsi.torch_dataset |
WSIData | bioptimus.data.wsi.wsi_dataset | bioptimus.data.wsi.wsi_dataset |
WSIDataset | bioptimus.data.wsi.wsi_dataset | bioptimus.data.wsi.wsi_dataset |
MegaTileExtractor | bioptimus.extraction.wsi.megatile_extraction | bioptimus.extraction.wsi.megatile_extraction |
TileExtractor | bioptimus.extraction.wsi.tile_extraction | bioptimus.extraction.wsi.tile_extraction |
GridLayout | bioptimus.extraction.wsi.types | bioptimus.extraction.wsi.types |
MegaTileRegion | bioptimus.extraction.wsi.types | bioptimus.extraction.wsi.types |
MegaTileSpec | bioptimus.extraction.wsi.types | bioptimus.extraction.wsi.types |
Inference | bioptimus.inference.inference | bioptimus.inference.inference |
ModelRequest | bioptimus.inference.schemas | bioptimus.inference.schemas |
ModelResponse | bioptimus.inference.schemas | bioptimus.inference.schemas |
SageMakerRequest | bioptimus.inference.schemas | bioptimus.inference.schemas |
HDF5Writer | bioptimus.inference.writers | bioptimus.inference.writers |
NPZWriter | bioptimus.inference.writers | bioptimus.inference.writers |
OutputFormat | bioptimus.inference.writers | bioptimus.inference.writers |
PredictionWriter | bioptimus.inference.writers | bioptimus.inference.writers |
ZarrWriter | bioptimus.inference.writers | bioptimus.inference.writers |
WSI | bioptimus.io.wsi.factory | bioptimus.io.wsi.factory |
WSIReader | bioptimus.io.wsi.interface | bioptimus.io.wsi.interface |
WSIProps | bioptimus.io.wsi.metadata | bioptimus.io.wsi.metadata |
Level | bioptimus.io.wsi.types | bioptimus.io.wsi.types |
MPP | bioptimus.io.wsi.types | bioptimus.io.wsi.types |
Magnification | bioptimus.io.wsi.types | bioptimus.io.wsi.types |
MeasurementUnit | bioptimus.io.wsi.types | bioptimus.io.wsi.types |
Region | bioptimus.io.wsi.types | bioptimus.io.wsi.types |
RegionLocation | bioptimus.io.wsi.types | bioptimus.io.wsi.types |
RegionMaskSpec | bioptimus.io.wsi.types | bioptimus.io.wsi.types |
RegionShape | bioptimus.io.wsi.types | bioptimus.io.wsi.types |
RegionSpec | bioptimus.io.wsi.types | bioptimus.io.wsi.types |
WSIBounds | bioptimus.io.wsi.types | bioptimus.io.wsi.types |
WSIDims | bioptimus.io.wsi.types | bioptimus.io.wsi.types |
Backbone | bioptimus.models.backbones | bioptimus.models.backbones |
Client | bioptimus.models.clients | bioptimus.models.clients |
AWSClient | bioptimus.models.clients.aws | bioptimus.models.clients.aws |
HTTPClient | bioptimus.models.clients.http | bioptimus.models.clients.http |
EndpointPaths | bioptimus.models.config_loader | bioptimus.models.config_loader |
ModelConfig | bioptimus.models.config_loader | bioptimus.models.config_loader |
EndpointModel | bioptimus.models.endpoint_model | bioptimus.models.endpoint_model |
ModelSpec | bioptimus.models.types | bioptimus.models.types |
Models | bioptimus.models.types | bioptimus.models.types |
OmicsPipeline | bioptimus.preprocess.omics.base | bioptimus.preprocess.omics.base |
OmicsPreprocessor | bioptimus.preprocess.omics.base | bioptimus.preprocess.omics.base |
Expm1Transform | bioptimus.preprocess.omics.transforms | bioptimus.preprocess.omics.transforms |
Log1pTransform | bioptimus.preprocess.omics.transforms | bioptimus.preprocess.omics.transforms |
SubsetColumns | bioptimus.preprocess.omics.transforms | bioptimus.preprocess.omics.transforms |
TPMNormaliser | bioptimus.preprocess.omics.transforms | bioptimus.preprocess.omics.transforms |
ZScoreNormaliser | bioptimus.preprocess.omics.transforms | bioptimus.preprocess.omics.transforms |
TissueMaskModel | bioptimus.preprocess.wsi.models.base | bioptimus.preprocess.wsi.models.base |
BioptimusTissueMaskModel | bioptimus.preprocess.wsi.models.bioptimus_mask | bioptimus.preprocess.wsi.models.bioptimus_mask |
TissueMaskProvider | bioptimus.preprocess.wsi.provider.base | bioptimus.preprocess.wsi.provider.base |
PrecomputedTissueMask | bioptimus.preprocess.wsi.provider.precomputed | bioptimus.preprocess.wsi.provider.precomputed |
TiledTissueMask | bioptimus.preprocess.wsi.provider.tiled | bioptimus.preprocess.wsi.provider.tiled |
Overview
TYPES
60 public classes.