alterlab-histolab

# Histolab ## Overview Histolab is a Python library for processing whole slide images (WSI) in digital pathology. It automates tissue detection, extracts informative tiles from gigapixel images, and prepares datasets for deep learning pipelines. The library handles multiple WSI formats, implements sophisticated tissue segmentation, and provides flexible tile extraction strategies. ## When to Use This Skill Use histolab for lightweight WSI tile pipelines: tissue detection, building tile datasets for ML training, H&E stain handling, and quick tile-based analysis of histopathology slides. For advanced spatial proteomics, multiplexed imaging, or full deep-learning pathology pipelines, use `pathml` instead. ## Installation ```bash uv pip install "histolab==0.7.0" ``` histolab wraps the **OpenSlide** C library, which is not bundled with the pip package. On macOS install it with `brew install openslide`; without it, any `import histolab.slide` fails with `Couldn't locate OpenSlide dylib`. The examples below are pinned to histolab 0.7.0; the API differs in older releases. ## Core Workflow 1. **Load** the slide with `Slide(path, processed_path=...)` and inspect dimensions/levels. 2. **Detect tissue** with a mask (`TissueMask` or `BiggestTissueBoxMask`). 3. **Preview** tile locations with `tiler.locate_tiles(slide)` before committing. 4. **Extract** tiles with one of three tilers (Random/Grid/Score). Minimal example: ```python from histolab.slide import Slide from histolab.t...