latest
Getting Started
Overview
License
Installation
Preprocessing
Loading Images
Individual Images
Datasets of Images
Supported slide types
Supported file formats
Creating Preprocessing Pipelines
What is a Transform?
What is a Pipeline?
Creating custom Transforms
Running Preprocessing Pipelines
How it works
Preprocessing a single WSI
Preprocessing a dataset of WSI
Distributed processing
HDF5 Integration
Overview
How it Works
About HDF5
.h5path
File Format
Reading and Writing
Datasets
Datasets
DataModules
Using public datasets
References
Machine Learning
DataLoaders
Models
References
Examples
Loading Images: Quickstart
Aperio SVS
Generic tiled TIFF
Hamamatsu NDPI
Hamamatsu VMS
Leica SCN
MIRAX
Olympus VSI
Trestle TIFF
Ventana BIF
Zeiss ZVI
DICOM
Volumetric + time-series OME-TIFF
CODEX spatial proteomics
MERFISH spatial gene expression
Visium 10x spatial gene expression
H&E Stain Deconvolution and Color Normalization
References
Brightfield Imaging: Quickstart
Multiparametric Imaging: Quickstart
Defining a Multiparametric Pipeline
AnnData Integration and Spatial Single Cell Analysis
References
Multiparametric Imaging: CODEX
Reading the slides
Define and run the preprocessing pipeline
Extract and concatenate the resulting count matrices
Annotate the clusters based on the markers intensity
Identification of cellular neighborhoods
Training an ML Model (HoVer-Net)
Data augmentation
Load PanNuke dataset
Model Training
Training with multi-GPU
Main training loop
Evaluate Model
Examples
Conclusion
References
Session info
Preprocessing Transforms Gallery
Transforms that modify an image
Blurring Transforms
Superpixel Interpolation
Stain Normalization
Transforms that create a mask
Binary Threshold
Nucleus Detection
Transforms that modify a mask
Morphological Opening
Morphological Closing
Foreground Detection
Tissue Detection
API Reference
Core API
SlideData
Convenience SlideData Classes
HESlide
VectraSlide
MultiparametricSlide
CODEXSlide
Slide Types
Tile
SlideDataset
Tiles and Masks helper classes
Slide Backends
OpenslideBackend
BioFormatsBackend
DICOMBackend
OpenSlideBackend
BioFormatsBackend
DICOMBackend
h5pathManager
SlideData
counts
extract_region
generate_tiles
plot
run
shape
write
SlideType
asdict
Tile
plot
shape
SlideDataset
run
write
Tiles
add
keys
remove
tile_shape
update
Masks
add
keys
remove
slice
h5pathManager
add_mask
add_tile
get_mask
get_slidetype
get_tile
remove_mask
remove_tile
slice_masks
update_mask
Preprocessing API
Pipeline
Transforms
Pipeline
apply
save
MedianBlur
F
apply
GaussianBlur
F
apply
BoxBlur
F
apply
BinaryThreshold
F
apply
MorphOpen
F
apply
MorphClose
F
apply
ForegroundDetection
F
apply
SuperpixelInterpolation
F
apply
StainNormalizationHE
F
apply
fit_to_reference
NucleusDetectionHE
F
apply
TissueDetectionHE
F
apply
LabelArtifactTileHE
F
apply
LabelWhiteSpaceHE
F
apply
SegmentMIF
F
apply
QuantifyMIF
F
apply
CollapseRunsVectra
F
apply
CollapseRunsCODEX
F
apply
RescaleIntensity
F
apply
HistogramEqualization
F
apply
AdaptiveHistogramEqualization
F
apply
Datasets API
PanNuke
DeepFocus
PanNukeDataModule
test_dataloader
train_dataloader
valid_dataloader
DeepFocusDataModule
test_dataloader
train_dataloader
valid_dataloader
ML API
h5path Dataset
HoVer-Net
Helper functions
TileDataset
HoVerNet
forward
compute_hv_map
loss_hovernet
remove_small_objs
post_process_batch_hovernet
Utilities API
Logging Utils
Core Utils
Datasets Utils
ML Utils
Miscellaneous Utils
PathMLLogger
disable
enable
readtupleh5
writedataframeh5
writedicth5
writestringh5
writetupleh5
readcounts
writecounts
pannuke_multiclass_mask_to_nucleus_mask
center_crop_im_batch
dice_loss
dice_score
get_sobel_kernels
wrap_transform_multichannel
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
Contributing
Contributing
Submitting a bug report
Requesting a new feature
For developers
Coordinate system conventions
Setting up a local development environment
Running tests
Building documentation locally
Checking code coverage
How to contribute code, documentation, etc.
Versioning and Distributing
Code Quality
Documentation Standards
Testing Standards
Thank You!
PathML
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Index
View PathML on GitHub
Index
A
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B
|
C
|
D
|
E
|
F
|
G
|
H
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
A
AdaptiveHistogramEqualization (class in pathml.preprocessing)
add() (pathml.core.Masks method)
(pathml.core.Tiles method)
add_mask() (pathml.core.h5managers.h5pathManager method)
add_tile() (pathml.core.h5managers.h5pathManager method)
apply() (pathml.preprocessing.AdaptiveHistogramEqualization method)
(pathml.preprocessing.BinaryThreshold method)
(pathml.preprocessing.BoxBlur method)
(pathml.preprocessing.CollapseRunsCODEX method)
(pathml.preprocessing.CollapseRunsVectra method)
(pathml.preprocessing.ForegroundDetection method)
(pathml.preprocessing.GaussianBlur method)
(pathml.preprocessing.HistogramEqualization method)
(pathml.preprocessing.LabelArtifactTileHE method)
(pathml.preprocessing.LabelWhiteSpaceHE method)
(pathml.preprocessing.MedianBlur method)
(pathml.preprocessing.MorphClose method)
(pathml.preprocessing.MorphOpen method)
(pathml.preprocessing.NucleusDetectionHE method)
(pathml.preprocessing.Pipeline method)
(pathml.preprocessing.QuantifyMIF method)
(pathml.preprocessing.RescaleIntensity method)
(pathml.preprocessing.SegmentMIF method)
(pathml.preprocessing.StainNormalizationHE method)
(pathml.preprocessing.SuperpixelInterpolation method)
(pathml.preprocessing.TissueDetectionHE method)
asdict() (pathml.core.SlideType method)
B
BinaryThreshold (class in pathml.preprocessing)
BioFormatsBackend (class in pathml.core)
BoxBlur (class in pathml.preprocessing)
C
center_crop_im_batch() (in module pathml.ml.utils)
CODEXSlide (class in pathml.core)
CollapseRunsCODEX (class in pathml.preprocessing)
CollapseRunsVectra (class in pathml.preprocessing)
compute_hv_map() (in module pathml.ml.hovernet)
contour_centroid() (in module pathml.utils)
counts (pathml.core.SlideData property)
D
DeepFocusDataModule (class in pathml.datasets)
dice_loss() (in module pathml.ml.utils)
dice_score() (in module pathml.ml.utils)
DICOMBackend (class in pathml.core)
disable() (pathml.PathMLLogger static method)
E
enable() (pathml.PathMLLogger static method)
extract_region() (pathml.core.BioFormatsBackend method)
(pathml.core.DICOMBackend method)
(pathml.core.OpenSlideBackend method)
(pathml.core.SlideData method)
F
F() (pathml.preprocessing.AdaptiveHistogramEqualization method)
(pathml.preprocessing.BinaryThreshold method)
(pathml.preprocessing.BoxBlur method)
(pathml.preprocessing.CollapseRunsCODEX method)
(pathml.preprocessing.CollapseRunsVectra method)
(pathml.preprocessing.ForegroundDetection method)
(pathml.preprocessing.GaussianBlur method)
(pathml.preprocessing.HistogramEqualization method)
(pathml.preprocessing.LabelArtifactTileHE method)
(pathml.preprocessing.LabelWhiteSpaceHE method)
(pathml.preprocessing.MedianBlur method)
(pathml.preprocessing.MorphClose method)
(pathml.preprocessing.MorphOpen method)
(pathml.preprocessing.NucleusDetectionHE method)
(pathml.preprocessing.QuantifyMIF method)
(pathml.preprocessing.RescaleIntensity method)
(pathml.preprocessing.SegmentMIF method)
(pathml.preprocessing.StainNormalizationHE method)
(pathml.preprocessing.SuperpixelInterpolation method)
(pathml.preprocessing.TissueDetectionHE method)
fit_to_reference() (pathml.preprocessing.StainNormalizationHE method)
ForegroundDetection (class in pathml.preprocessing)
forward() (pathml.ml.HoVerNet method)
G
GaussianBlur (class in pathml.preprocessing)
generate_tiles() (pathml.core.BioFormatsBackend method)
(pathml.core.DICOMBackend method)
(pathml.core.OpenSlideBackend method)
(pathml.core.SlideData method)
get_bot() (pathml.core.DICOMBackend static method)
get_image_shape() (pathml.core.BioFormatsBackend method)
(pathml.core.DICOMBackend method)
(pathml.core.OpenSlideBackend method)
get_mask() (pathml.core.h5managers.h5pathManager method)
get_slidetype() (pathml.core.h5managers.h5pathManager method)
get_sobel_kernels() (in module pathml.ml.utils)
get_thumbnail() (pathml.core.BioFormatsBackend method)
(pathml.core.DICOMBackend method)
(pathml.core.OpenSlideBackend method)
get_tile() (pathml.core.h5managers.h5pathManager method)
H
h5pathManager (class in pathml.core.h5managers)
HESlide (class in pathml.core)
HistogramEqualization (class in pathml.preprocessing)
HoVerNet (class in pathml.ml)
K
keys (pathml.core.Masks property)
(pathml.core.Tiles property)
L
LabelArtifactTileHE (class in pathml.preprocessing)
LabelWhiteSpaceHE (class in pathml.preprocessing)
loss_hovernet() (in module pathml.ml.hovernet)
M
Masks (class in pathml.core)
MedianBlur (class in pathml.preprocessing)
MorphClose (class in pathml.preprocessing)
MorphOpen (class in pathml.preprocessing)
MultiparametricSlide (class in pathml.core)
N
normalize_matrix_cols() (in module pathml.utils)
normalize_matrix_rows() (in module pathml.utils)
NucleusDetectionHE (class in pathml.preprocessing)
O
OpenSlideBackend (class in pathml.core)
P
pad_or_crop() (in module pathml.utils)
pannuke_multiclass_mask_to_nucleus_mask() (in module pathml.datasets.utils)
PanNukeDataModule (class in pathml.datasets)
PathMLLogger (class in pathml)
pil_to_rgb() (in module pathml.utils)
Pipeline (class in pathml.preprocessing)
plot() (pathml.core.SlideData method)
(pathml.core.Tile method)
plot_mask() (in module pathml.utils)
plot_segmentation() (in module pathml.utils)
post_process_batch_hovernet() (in module pathml.ml.hovernet)
Q
QuantifyMIF (class in pathml.preprocessing)
R
readcounts() (in module pathml.core.utils)
readtupleh5() (in module pathml.core.utils)
remove() (pathml.core.Masks method)
(pathml.core.Tiles method)
remove_mask() (pathml.core.h5managers.h5pathManager method)
remove_small_objs() (in module pathml.ml.hovernet)
remove_tile() (pathml.core.h5managers.h5pathManager method)
RescaleIntensity (class in pathml.preprocessing)
RGB_to_GREY() (in module pathml.utils)
RGB_to_HSI() (in module pathml.utils)
RGB_to_HSV() (in module pathml.utils)
RGB_to_LAB() (in module pathml.utils)
RGB_to_OD() (in module pathml.utils)
run() (pathml.core.SlideData method)
(pathml.core.SlideDataset method)
S
save() (pathml.preprocessing.Pipeline method)
segmentation_lines() (in module pathml.utils)
SegmentMIF (class in pathml.preprocessing)
shape (pathml.core.SlideData property)
(pathml.core.Tile property)
slice() (pathml.core.Masks method)
slice_masks() (pathml.core.h5managers.h5pathManager method)
SlideData (class in pathml.core)
SlideDataset (class in pathml.core)
SlideType (class in pathml.core)
sort_points_clockwise() (in module pathml.utils)
StainNormalizationHE (class in pathml.preprocessing)
SuperpixelInterpolation (class in pathml.preprocessing)
T
test_dataloader (pathml.datasets.DeepFocusDataModule property)
(pathml.datasets.PanNukeDataModule property)
Tile (class in pathml.core)
tile_shape (pathml.core.Tiles property)
TileDataset (class in pathml.ml)
Tiles (class in pathml.core)
TissueDetectionHE (class in pathml.preprocessing)
train_dataloader (pathml.datasets.DeepFocusDataModule property)
(pathml.datasets.PanNukeDataModule property)
U
update() (pathml.core.Tiles method)
update_mask() (pathml.core.h5managers.h5pathManager method)
upsample_array() (in module pathml.utils)
V
valid_dataloader (pathml.datasets.DeepFocusDataModule property)
(pathml.datasets.PanNukeDataModule property)
VectraSlide (class in pathml.core)
W
wrap_transform_multichannel() (in module pathml.ml.utils)
write() (pathml.core.SlideData method)
(pathml.core.SlideDataset method)
writecounts() (in module pathml.core.utils)
writedataframeh5() (in module pathml.core.utils)
writedicth5() (in module pathml.core.utils)
writestringh5() (in module pathml.core.utils)
writetupleh5() (in module pathml.core.utils)
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