34 lines (34 with data), 10.2 kB

ÇĽ─'îdocutils.nodesöîdocumentöôö)üö}ö(î	rawsourceöîöîchildrenö]ö(hîcommentöôö)üö}ö(hî▒WSITools documentation master file, created by
sphinx-quickstart.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.öh]öhîTextöôöî▒WSITools documentation master file, created by
sphinx-quickstart.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.öůöüö}ö(hhîparentöhubaî
attributesö}ö(îidsö]öîclassesö]öînamesö]öîdupnamesö]öîbackrefsö]öî	xml:spaceöîpreserveöuîtagnameöh	hhh
hîsourceöîA/projects/shart/digital_pathology/scripts/wsitools/docs/index.rstöîlineöKubhîsectionöôö)üö}ö(hhh]ö(hîtitleöôö)üö}ö(hîWSITools documentation!öh]öhîWSITools documentation!öůöüö}ö(hh1hh/h
hh%Nh'Nubah}ö(h]öh]öh]öh]öh ]öuh$h-hh*h
hh%h&h'Kubhî	paragraphöôö)üö}ö(hî5Tools to aid Digital pathology deep learning projectsöh]öhî5Tools to aid Digital pathology deep learning projectsöůöüö}ö(hhAhh?h
hh%Nh'Nubah}ö(h]öh]öh]öh]öh ]öuh$h=h%h&h'K	hh*h
hubhîbullet_listöôö)üö}ö(hhh]ö(hî	list_itemöôö)üö}ö(hîFree software: MIT licenseöh]öh>)üö}ö(hhVh]öhîFree software: MIT licenseöůöüö}ö(hhVhhXubah}ö(h]öh]öh]öh]öh ]öuh$h=h%h&h'KhhTubah}ö(h]öh]öh]öh]öh ]öuh$hRhhOh
hh%h&h'NubhS)üö}ö(hîDDocumentation: https://wsitools.readthedocs.io/en/latest/index.html
öh]öh>)üö}ö(hîCDocumentation: https://wsitools.readthedocs.io/en/latest/index.htmlöh]ö(hîDocumentation: öůöüö}ö(hîDocumentation: öhhoubhî	referenceöôö)üö}ö(hî4https://wsitools.readthedocs.io/en/latest/index.htmlöh]öhî4https://wsitools.readthedocs.io/en/latest/index.htmlöůöüö}ö(hh|hhzubah}ö(h]öh]öh]öh]öh ]öîrefuriöh|uh$hxhhoubeh}ö(h]öh]öh]öh]öh ]öuh$h=h%h&h'Khhkubah}ö(h]öh]öh]öh]öh ]öuh$hRhhOh
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hh%h&h'Kubh>)üö}ö(hX(WSITools is a whole slide image processing toolkit. It provides efficient ways to extract patches from whole slide
images, and some other useful features for pathological image processing.
Currently, it supports four patch extraction scenarios:
..  1. Extract patches from WSIs
..  2. Extract patches from WSIs and their label (i.e. their directory name)
..   1. TODO: Incomplete
..  3. Extract patches from a fixed and a float WSI
..  4. Extract patches from a fixed and a float WSI in places that intersect annotation objects
..   1. TODO: Incompleteöh]öhX(WSITools is a whole slide image processing toolkit. It provides efficient ways to extract patches from whole slide
images, and some other useful features for pathological image processing.
Currently, it supports four patch extraction scenarios:
..  1. Extract patches from WSIs
..  2. Extract patches from WSIs and their label (i.e. their directory name)
..   1. TODO: Incomplete
..  3. Extract patches from a fixed and a float WSI
..  4. Extract patches from a fixed and a float WSI in places that intersect annotation objects
..   1. TODO: Incompleteöůöüö}ö(hh░hh«h
hh%Nh'Nubah}ö(h]öh]öh]öh]öh ]öuh$h=h%h&h'KhhŁh
hubeh}ö(h]öîfeaturesöah]öh]öîfeaturesöah]öh ]öuh$h(hh*h
hh%h&h'Kubh))üö}ö(hhh]ö(h.)üö}ö(hîAdditional Featuresöh]öhîAdditional Featuresöůöüö}ö(hh╔hhăh
hh%Nh'Nubah}ö(h]öh]öh]öh]öh ]öuh$h-hh─h
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)üö}ö(hî1. Detect tissue in a WSIöh]öhî1. Detect tissue in a WSIöůöüö}ö(hhhhŇubah}ö(h]öh]öh]öh]öh ]öh"h#uh$h	hh─h
hh%h&h'Kubh
)üö}ö(hîK2. Export and parsing annotation from [QuPath_] and [`Aperio Image Scope`_]öh]öhîK2. Export and parsing annotation from [QuPath_] and [`Aperio Image Scope`_]öůöüö}ö(hhhhŃubah}ö(h]öh]öh]öh]öh ]öh"h#uh$h	hh─h
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)üö}ö(hî,3. WSI registration for image pairs [Paper_]öh]öhî,3. WSI registration for image pairs [Paper_]öůöüö}ö(hhhh˝ubah}ö(h]öh]öh]öh]öh ]öh"h#uh$h	hh─h
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)üö}ö(hî34. Reconstruct WSI from the processed image patchesöh]öhî34. Reconstruct WSI from the processed image patchesöůöüö}ö(hhhh ubah}ö(h]öh]öh]öh]öh ]öh"h#uh$h	hh─h
hh%h&h'K ubhîtargetöôö)üö}ö(hî$.. _QuPath: https://qupath.github.ioöh]öh}ö(h]öîqupathöah]öh]öîqupathöah]öh ]öîrefuriöîhttps://qupath.github.ioöuh$j

h'K!hh─h
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)üö}ö(hîb.. _Aperio Image Scope: https://www.leicabiosystems.com/digital-pathology/manage/aperio-imagescopeöh]öh}ö(h]öîaperio-image-scopeöah]öh]öîaperio image scopeöah]öh ]öj
îJhttps://www.leicabiosystems.com/digital-pathology/manage/aperio-imagescopeöuh$j

h'K"hh─h
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)üö}ö(hîT.. _Paper: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0220074öh]öh}ö(h]öîpaperöah]öh]öîpaperöah]öh ]öj
îIhttps://journals.plos.org/plosone/article?id=10.1371/journal.pone.0220074öuh$j

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