Table of Contents

1. histopathTDA
   1. Installation
   2. Anaconda
      1. Linux
   3. Virtual Environment
   4. Data Access
      1. Configure a persistent network drive mount
   5. Data Description

histopathTDA

This is a python library for conducting histopathology using TDA methods.

Installation

Anaconda

Currently the library is setup to build within its provided Anaconda environment. Setup to install via pip is currently under construction. To install Anaconda3 on MacOS or Windows, visit the install page here for MacOS or here for Windows, and follow the directions. On Linux installation instructions are provided here.

Alternatively, if you use homebrew on MacOS, you can install with

brew install --cask anaconda

or if you use chocolatey on Windows, you can install with

choco install anaconda3

Virtual Environment

Once you have Anaconda installed, use it to create a virtual environment that includes python dependencies by running the following in your shell

conda env create -f environment.yml

Alternatively, if you have make installed on your system, you can run

make create_environment

Once the environment is created, we can activate it with

conda activate histopathTDA

You may need to run conda init if this is the first time activating an Anaconda virtual environment. Now, once you have the anaconda environment activated, we use pip to install the package to our environment.

pip install .