pathml 1.0.2

Tools for computational pathology

A toolkit for computational pathology and machine learning.

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Installation

There are several ways to install PathML:

1. pip install (recommended for users)
2. clone repo to local machine and install from source (recommended for developers/contributors)

Options (1) and (2) require that you first install all external dependencies:

• openslide
• JDK 8

We recommend using conda for environment management. Download Miniconda here

Note: these instructions are for Linux. Commands may be different for other platforms.

Installation option 1: pip install

Create conda environment

conda create --name pathml python=3.8
conda activate pathml

Install external dependencies (Linux) with Apt

sudo apt-get install openslide-tools g++ gcc libblas-dev liblapack-dev

Install external dependencies (MacOS) with Brew

brew install openslide

Install OpenJDK 8

conda install openjdk==8.0.152

Optionally install CUDA (instructions here)

Install PathML

pip install pathml

Installation option 2: clone repo and install from source

Clone repo

git clone https://github.com/Dana-Farber-AIOS/pathml.git
cd pathml

Create conda environment

conda env create -f environment.yml
conda activate pathml

Optionally install CUDA (instructions here)

Install PathML:

pip install -e .

CUDA

To use GPU acceleration for model training or other tasks, you must install CUDA. This guide should work, but for the most up-to-date instructions, refer to the official PyTorch installation instructions.

Check the version of CUDA:

nvidia-smi

Install correct version of cudatoolkit:

# update this command with your CUDA version number
conda install cudatoolkit=11.0

After installing PyTorch, optionally verify successful PyTorch installation with CUDA support:

python -c "import torch; print(torch.cuda.is_available())"

Using with Jupyter

Jupyter notebooks are a convenient way to work interactively. To use PathML in Jupyter notebooks:

Set JAVA_HOME environment variable

PathML relies on Java to enable support for reading a wide range of file formats. Before using PathML in Jupyter, you may need to manually set the JAVA_HOME environment variable specifying the path to Java. To do so:

1. Get the path to Java by running echo $JAVA_HOME in the terminal in your pathml conda environment (outside of Jupyter)
2. Set that path as the JAVA_HOME environment variable in Jupyter:

   import os
   os.environ["JAVA_HOME"] = "/opt/conda/envs/pathml" # change path as needed
   

Register PathML as an IPython kernel

conda activate pathml
conda install ipykernel
python -m ipykernel install --user --name=pathml

This makes PathML available as a kernel in jupyter lab or notebook.

Contributing

PathML is an open source project. Consider contributing to benefit the entire community!

There are many ways to contribute to PathML, including:

• Submitting bug reports
• Submitting feature requests
• Writing documentation and examples
• Fixing bugs
• Writing code for new features
• Sharing workflows
• Sharing trained model parameters
• Sharing PathML with colleagues, students, etc.

See contributing for more details.

License

The GNU GPL v2 version of PathML is made available via Open Source licensing. The user is free to use, modify, and distribute under the terms of the GNU General Public License version 2.

Commercial license options are available also.

Contact

Questions? Comments? Suggestions? Get in touch!

[e-mail]