histolab
Extracts and preprocesses whole-slide histology image tiles with Histolab
by k-dense-aiFree
Description
histolab is an agent skill for extracting and preprocessing image tiles from whole-slide histology images using Histolab. It covers inspecting slide metadata, identifying tissue with masks, extracting tiles by random, grid or score-based selection, and standardising H&E staining. Its masks and scores are image-processing heuristics. The skill is firm that they do not diagnose cancer, do not count individual cells, and do not establish image quality. The skill targets Histolab 0.7.0, the latest published release at the review date. That release has strict dependency limits, including Python below 3.12, older NumPy, scikit-image, SciPy and Pillow versions, and openslide-python 1.3.1, so the skill advises keeping this stack in its own environment, away from modern scientific setups. The release does not support Windows, and the skill asks you to install the native OpenSlide library for your system first, then create a dedicated environment. Python 3.10 was the version tested. Use it when you are preparing slide tiles for analysis, for example before training an image model. It is part of the k-dense-ai scientific agent skills repository on GitHub, which has about 49,600 stars.…
Highlights
- Slide metadata and tissue masks
- Random, grid and score-based tile extraction
- H&E stain standardisation
- Targets Histolab 0.7.0
- Needs a dedicated older environment
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histolab FAQ
What does it do?
Extracts and preprocesses image tiles from whole-slide histology images, including tissue masks and H&E standardisation.
Can it diagnose from the tiles?
No. The skill says its masks and scores are image-processing heuristics that do not diagnose cancer or count cells.
Does it work on Windows?
The skill says this Histolab release is not supported on Windows.
What environment does it need?
A dedicated environment, with Python below 3.12 and the pinned older dependencies. Python 3.10 was tested, and the native OpenSlide library must be installed first.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill histolab.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best histolab alternatives?
Popular alternatives to histolab include data-scraper-agent, django-celery and django-patterns. See all histolab alternatives