Index

Symbols

--backend wsinfer command line option --batch-size wsinfer-run command line option --config wsinfer-run command line option --execution-id wsinfer-tosbu command line option --log-level wsinfer command line option --make-color-text wsinfer-tosbu command line option --model wsinfer-run command line option --model-path wsinfer-run command line option --no-make-color-text wsinfer-tosbu command line option --no-speedup wsinfer-run command line option --num-processes wsinfer-tosbu command line option --num-workers wsinfer-run command line option --patch-overlap-ratio wsinfer-run command line option --patch-size-px wsinfer-patch command line option --patch-spacing-um-px wsinfer-patch command line option --qupath wsinfer-run command line option --results-dir wsinfer-patch command line option wsinfer-run command line option --seg-binary-threshold wsinfer-patch command line option wsinfer-run command line option --seg-closing-kernel-size wsinfer-patch command line option wsinfer-run command line option

--seg-median-filter-size wsinfer-patch command line option wsinfer-run command line option --seg-min-hole-size-um2 wsinfer-patch command line option wsinfer-run command line option --seg-min-object-size-um2 wsinfer-patch command line option wsinfer-run command line option --seg-thumbsize wsinfer-patch command line option wsinfer-run command line option --speedup wsinfer-run command line option --study-id wsinfer-tosbu command line option --version wsinfer command line option --wsi-dir wsinfer-patch command line option wsinfer-run command line option wsinfer-tosbu command line option -b wsinfer-run command line option -c wsinfer-run command line option -i wsinfer-patch command line option wsinfer-run command line option -m wsinfer-run command line option -n wsinfer-run command line option -o wsinfer-patch command line option wsinfer-run command line option -p wsinfer-run command line option

_

__getitem__() (wsinfer.modellib.data.WholeSlideImagePatches method)

__len__() (wsinfer.modellib.data.WholeSlideImagePatches method) __version__ (in module wsinfer)

A

add_image_and_geojson() (in module wsinfer.qupath)

B

BackendNotAvailable

C

CannotReadSpacing

CanReadRegion (class in wsinfer.wsi)

D

draw_contours_on_thumbnail() (in module wsinfer.patchlib)

DuplicateFilePrefixesFound

G

get_avg_mpp() (in module wsinfer.patchlib) (in module wsinfer.wsi) get_multipolygon_from_binary_arr() (in module wsinfer.patchlib) (in module wsinfer.patchlib.patch) get_patch_coordinates_within_polygon() (in module wsinfer.patchlib) (in module wsinfer.patchlib.patch)

get_pretrained_torch_module() (in module wsinfer.modellib.models) get_registered_model() (in module wsinfer.modellib.models) get_wsi_cls() (in module wsinfer.patchlib) (in module wsinfer.wsi)

H

HAS_OPENSLIDE (in module wsinfer.wsi)

HAS_PAQUO (in module wsinfer.qupath) HAS_TIFFSLIDE (in module wsinfer.wsi)

J

jit_compile() (in module wsinfer.modellib.models)

L

LocalModelTorchScript (class in wsinfer.modellib.models) logger (in module wsinfer.patchlib) (in module wsinfer.patchlib.patch) (in module wsinfer.wsi)

M

make_compose_from_transform_config() (in module wsinfer.modellib.transforms) make_geojson() (in module wsinfer.write_geojson) make_qupath_project() (in module wsinfer.qupath) MASKS_DIR (in module wsinfer.patchlib) module wsinfer wsinfer.errors wsinfer.modellib wsinfer.modellib.data wsinfer.modellib.models wsinfer.modellib.run_inference wsinfer.modellib.transforms wsinfer.patchlib wsinfer.patchlib.patch wsinfer.patchlib.segment wsinfer.qupath wsinfer.write_geojson wsinfer.wsi

N

NoBackendException

O

OUTPUT wsinfer-tosbu command line option

P

PatchDirectoryNotFound

PATCHES_DIR (in module wsinfer.patchlib)

R

read_region() (wsinfer.wsi.CanReadRegion method) RESULTS_DIR wsinfer-tosbu command line option

ResultsDirectoryNotFound run_inference() (in module wsinfer.modellib.run_inference)

S

save_hdf5() (in module wsinfer.patchlib) segment_and_patch_directory_of_slides() (in module wsinfer.patchlib) segment_and_patch_one_slide() (in module wsinfer.patchlib)

segment_tissue() (in module wsinfer.patchlib) (in module wsinfer.patchlib.segment) set_backend() (in module wsinfer.wsi)

T

temporary_recursion_limit() (in module wsinfer.patchlib.patch)

U

UnknownArchitectureError

W

WholeSlideImageDirectoryNotFound WholeSlideImagePatches (class in wsinfer.modellib.data) WholeSlideImagesNotFound worker_init() (wsinfer.modellib.data.WholeSlideImagePatches method) write_geojsons() (in module wsinfer.write_geojson) wsinfer module wsinfer command line option --backend --log-level --version wsinfer-patch command line option --patch-size-px --patch-spacing-um-px --results-dir --seg-binary-threshold --seg-closing-kernel-size --seg-median-filter-size --seg-min-hole-size-um2 --seg-min-object-size-um2 --seg-thumbsize --wsi-dir -i -o wsinfer-run command line option --batch-size --config --model --model-path --no-speedup --num-workers --patch-overlap-ratio --qupath --results-dir --seg-binary-threshold --seg-closing-kernel-size --seg-median-filter-size --seg-min-hole-size-um2 --seg-min-object-size-um2 --seg-thumbsize --speedup --wsi-dir -b -c -i -m -n -o -p

wsinfer-tosbu command line option --execution-id --make-color-text --no-make-color-text --num-processes --study-id --wsi-dir OUTPUT RESULTS_DIR wsinfer.errors module wsinfer.modellib module wsinfer.modellib.data module wsinfer.modellib.models module wsinfer.modellib.run_inference module wsinfer.modellib.transforms module wsinfer.patchlib module wsinfer.patchlib.patch module wsinfer.patchlib.segment module wsinfer.qupath module wsinfer.write_geojson module wsinfer.wsi module WsinferException