PyHIST

PyHIST is a Histological Image Segmentation Tool: a lightweight semi-automatic command-line tool to extract tiles from histopathology whole image slides. It is intended to be an easy-to-use tool to preprocess histological image data for usage in machine learning tasks.

Features:

• Designed for Aperio's SVS/TIFF format (see experimental support for other formats).
• Mask generation over regions with tissue content (foreground)
• Generation of tiles based on the foreground
• Quick overview of selected tiles
• Several tile generation methods (graph-based, random sampling, Otsu and adaptive thresholding)
• Ability to downsample from the original image
• Log generation with information for all the tiles generated from an image