histolab
Extracts tiles and preprocesses H&E whole slide images with the histolab Python library (OpenSlide), covering slide inspection, tissue masks (TissueMask, BiggestTissueBoxMask), RandomTiler, GridTiler and ScoreTiler extraction, image and morphological filters, and Macenko or Reinhard stain normalization. Use when building a tile dataset from WSI files for deep learning. Use when detecting tissue and excluding background or pen annotations. Use when previewing tile locations and exporting tile CSV reports. Use when normalizing stain variation across slides. Not for spatial proteomics, multiplexed imaging, or deep learning pipelines; use pathml for those.
- Version
- 1.3
- License
- Apache-2.0 license
- Compatibility
- Requires Python 3.8–3.11 (histolab 0.7.0), OpenSlide system libraries, and Linux or macOS. Sample data via histolab.data requires pooch.
Pinned to revision df088027ff23, so it is the text this page describes rather than whatever the author pushed since.
Files
- skills/histolab/SKILL.md
- skills/histolab/references/core_capabilities.md
- skills/histolab/references/filters_preprocessing.md
- skills/histolab/references/slide_management.md
- skills/histolab/references/tile_extraction.md
- skills/histolab/references/tissue_masks.md
- skills/histolab/references/typical_workflows.md
- skills/histolab/references/visualization.md
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