Extract and prepare WSI tiles for analysis.
digital pathology
Extract informative tiles from whole-slide images and prepare them for analysis.
When to use it
Use it for basic slide processing, tissue detection, tile extraction, and H&E stain normalization; use pathml for advanced spatial proteomics, multiplexed imaging, or deep learning pipelines.
Give it whole-slide image files; it returns previewed and extracted tiles in the configured processed output directory.
What you provide
This skill
OpenSlide system libraries
Installs OpenSlide libraries
histolab
Installs histolab
pooch
Installs pooch
TCGA sample slides
Downloads sample slides
Requires Python 3.8–3.11 for histolab 0.7.0.
OpenSlide system libraries must be installed before histolab.
Runs on Linux or macOS; Windows is not supported as of histolab 0.7.0.