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 `alterlab-pathml` instead. ### Does NOT Trigger | Scenario | Use Instead | |----------|-------------| | End-to-end computational pathology, nucleus segmentation, multiplexed imaging (CODEX/Vectra) | `alterlab-pathml` | | Training the downstream classifier on the extracted tiles | `alterlab-pytorch-lightning` | | DICOM whole-slide or radiology images rather than SVS/NDPI | `alterlab-pydicom`, `alterlab-imaging-data-commons` | | Spatial transcriptomics on tissue sections | `alterlab-squidpy-spatial` | | Managing/versioning the slide collection itself | `alterlab-omero`, `alterlab-lamindb` | ## Installation ```bash # histolab 0.7.0 needs Python >= 3.8, < 3.12 and numpy 1.x — give it its own env uv venv --python 3.11 .venv-histolab uv pip install --python .venv-histolab "histolab==0.7.0" ope...