histomics_stream

Overview

The goal of this project is to create a whole-slide image file reader for machine learning with TensorFlow. This reader will allow users to extract pixel data from whole-slide image formats, and will support reading paradigms that are commonly used during training and inference.

Installation for Python

histomics_stream can be easily installed with Python wheels. If you do not want the installation to be to your current Python environment, you should first create and activate a Python virtual environment (venv) to work in. Then, run the following from the command line:

pip uninstall -y large_image tensorflow histomics_stream
pip install 'large_image[all]' --find-links https://girder.github.io/large_image_wheels
pip install histomics_stream

Launch python3, import the histomics_stream package, and use it

import histomics_stream as hs

This has been tested with tensorflow:2.6.2-gpu.

History

Through version 1.0.6, this project was known as tensorflow_reader.