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WSI reader#1548

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bhashemian merged 53 commits intoProject-MONAI:masterfrom
bhashemian:pathology_dataset
Mar 5, 2021
Merged

WSI reader#1548
bhashemian merged 53 commits intoProject-MONAI:masterfrom
bhashemian:pathology_dataset

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@bhashemian bhashemian commented Feb 4, 2021

Fixes #1504

Description

Training models for pathology use cases requires loading patches from Whole Slide Imaging (WSI) scans. These images are enormous in size and usually much larger than user's available RAM (#1504). This PR provide a solution by implementing whole slide image readers for CuImage and OpenSlide.

Types of changes

  • Non-breaking change (fix or new feature that would not break existing functionality).
  • Breaking change (fix or new feature that would cause existing functionality to change).
  • New tests added to cover the changes.
  • Integration tests passed locally by running ./runtests.sh --codeformat --coverage.
  • Quick tests passed locally by running ./runtests.sh --quick.
  • In-line docstrings updated.
  • Documentation updated, tested make html command in the docs/ folder.

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WSI image reader

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