Getting Started
Examples
convert_pytorch_onnx
Inference
HaloAIInference
RemoteTestHoverNet
Preprocessing
.h5path
Datasets
Graphs
Machine Learning
API Reference
SlideData
SlideData.counts
SlideData.extract_region()
SlideData.generate_tiles()
SlideData.plot()
SlideData.run()
SlideData.shape
SlideData.write()
HESlide
VectraSlide
MultiparametricSlide
CODEXSlide
SlideType
SlideType.asdict()
Tile
Tile.plot()
Tile.shape
SlideDataset
SlideDataset.run()
SlideDataset.write()
Tiles
Tiles.add()
Tiles.keys
Tiles.remove()
Tiles.tile_shape
Tiles.update()
Masks
Masks.add()
Masks.keys
Masks.remove()
Masks.slice()
OpenSlideBackend
BioFormatsBackend
DICOMBackend
h5pathManager
h5pathManager.add_mask()
h5pathManager.add_tile()
h5pathManager.get_mask()
h5pathManager.get_slidetype()
h5pathManager.get_tile()
h5pathManager.remove_mask()
h5pathManager.remove_tile()
h5pathManager.slice_masks()
h5pathManager.update_mask()
Pipeline
Pipeline.apply()
Pipeline.save()
MedianBlur
MedianBlur.F()
MedianBlur.apply()
GaussianBlur
GaussianBlur.F()
GaussianBlur.apply()
BoxBlur
BoxBlur.F()
BoxBlur.apply()
BinaryThreshold
BinaryThreshold.F()
BinaryThreshold.apply()
MorphOpen
MorphOpen.F()
MorphOpen.apply()
MorphClose
MorphClose.F()
MorphClose.apply()
ForegroundDetection
ForegroundDetection.F()
ForegroundDetection.apply()
SuperpixelInterpolation
SuperpixelInterpolation.F()
SuperpixelInterpolation.apply()
StainNormalizationHE
StainNormalizationHE.F()
StainNormalizationHE.apply()
StainNormalizationHE.fit_to_reference()
NucleusDetectionHE
NucleusDetectionHE.F()
NucleusDetectionHE.apply()
TissueDetectionHE
TissueDetectionHE.F()
TissueDetectionHE.apply()
LabelArtifactTileHE
LabelArtifactTileHE.F()
LabelArtifactTileHE.apply()
LabelWhiteSpaceHE
LabelWhiteSpaceHE.F()
LabelWhiteSpaceHE.apply()
SegmentMIF
SegmentMIF.F()
SegmentMIF.apply()
SegmentMIFRemote
SegmentMIFRemote.F()
SegmentMIFRemote.apply()
QuantifyMIF
QuantifyMIF.F()
QuantifyMIF.apply()
CollapseRunsVectra
CollapseRunsVectra.F()
CollapseRunsVectra.apply()
CollapseRunsCODEX
CollapseRunsCODEX.F()
CollapseRunsCODEX.apply()
RescaleIntensity
RescaleIntensity.F()
RescaleIntensity.apply()
HistogramEqualization
HistogramEqualization.F()
HistogramEqualization.apply()
AdaptiveHistogramEqualization
AdaptiveHistogramEqualization.F()
AdaptiveHistogramEqualization.apply()
TileStitcher
TileStitcher.checkTIFF()
TileStitcher.format_jvm_options()
TileStitcher.is_bfconvert_available()
TileStitcher.parseRegion()
TileStitcher.parse_regions()
TileStitcher.run_bfconvert()
TileStitcher.run_image_stitching()
TileStitcher.setup_bfconvert()
TileStitcher.shutdown()
TileStitcher.toShort()
BaseGraphBuilder
BaseGraphBuilder.process()
BaseGraphBuilder.process_with_centroids()
KNNGraphBuilder
RAGGraphBuilder
MSTGraphBuilder
SuperpixelExtractor
SuperpixelExtractor.process()
SLICSuperpixelExtractor
MergedSuperpixelExtractor
MergedSuperpixelExtractor.process()
ColorMergedSuperpixelExtractor
GraphFeatureExtractor
GraphFeatureExtractor.get_stats()
GraphFeatureExtractor.process()
PanNukeDataModule
PanNukeDataModule.test_dataloader
PanNukeDataModule.train_dataloader
PanNukeDataModule.valid_dataloader
DeepFocusDataModule
DeepFocusDataModule.test_dataloader
DeepFocusDataModule.train_dataloader
DeepFocusDataModule.valid_dataloader
TileDataset
EntityDataset
HoVerNet
HoVerNet.forward()
HACTNet
HACTNet.forward()
GNNLayer
GNNLayer.forward()
compute_hv_map()
loss_hovernet()
remove_small_objs()
post_process_batch_hovernet()
PathMLLogger
PathMLLogger.disable()
PathMLLogger.enable()
readtupleh5()
writedataframeh5()
writedicth5()
writestringh5()
writetupleh5()
readcounts()
writecounts()
Graph()
HACTPairData()
get_full_instance_map()
build_assignment_matrix()
two_hop()
two_hop_no_sparse()
DeepPatchFeatureExtractor
DeepPatchFeatureExtractor.process()
pannuke_multiclass_mask_to_nucleus_mask()
_remove_modules()
center_crop_im_batch()
dice_loss()
dice_score()
get_sobel_kernels()
wrap_transform_multichannel()
scatter_sum()
broadcast()
get_degree_histogram()
get_class_weights()
upsample_array()
pil_to_rgb()
segmentation_lines()
plot_mask()
contour_centroid()
sort_points_clockwise()
pad_or_crop()
RGB_to_HSI()
RGB_to_OD()
RGB_to_HSV()
RGB_to_LAB()
RGB_to_GREY()
normalize_matrix_rows()
normalize_matrix_cols()
plot_segmentation()
InferenceBase
InferenceBase.F()
InferenceBase.apply()
InferenceBase.get_model_card()
InferenceBase.reshape()
InferenceBase.set_citation()
InferenceBase.set_model_input_notes()
InferenceBase.set_model_output_notes()
InferenceBase.set_model_type()
InferenceBase.set_name()
InferenceBase.set_notes()
InferenceBase.set_num_classes()
Inference.F()
Inference.apply()
Inference.inference()
HaloAIInference.F()
HaloAIInference.apply()
RemoteTestHoverNet.apply()
RemoteTestHoverNet.remove()
RemoteMesmer
RemoteMesmer.F()
RemoteMesmer.apply()
RemoteMesmer.inference()
RemoteMesmer.remove()
remove_initializer_from_input()
check_onnx_clean()
convert_pytorch_onnx()
Contributing
See https://github.com/Dana-Farber-AIOS/pathml/blob/master/README.md#Installation