histolab
Category: clinical-and-health · License: Apache-2.0 license · Version: 1.3
Tags: digital pathology, whole slide images, H&E, tile extraction, medical imaging
When to use it
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.Example requests
Ask your agent in plain language, for example:- “How do I pull 512x512 tiles out of an H&E slide and skip the blank glass?”
- “I have 40 TCGA-BRCA .svs files in ./slides/ and need a training set of 20x patches for a ResNet. Some slides have green pen marks around the tumor and tiles over those regions are polluting my set. I’m using RandomTiler with n_tiles=200 and seed=42, but the pen regions still show up. Also I need a CSV with the tile coordinates. How should I set this up?”
- “My slides come from three different labs and the eosin intensity varies a lot, which is hurting my classifier’s generalization. How can I make the colors consistent before I train?”
Install
/plugin marketplace add KalarisLabs/research-agent-skills and install the whole clinical-and-health category with /plugin install clinical-and-health@research-agent-skills.