EZ WSI DicomWeb

EZ WSI DicomWeb is a python library that provides the ability to effortlessly extract an image patch from a pathology DICOM whole slide image (WSI) stored in a cloud DICOM store. This functionality is useful for different pathology workflows, especially those leveraging AI. The library can also generate tissue patches from a slide in an efficient manner.

This Github repository contains all source code, documentation, and unit tests for EZ WSI DicomWeb. EZ WSI DicomWeb uses Bazel as a build and test tool.

Requirements

• Python 3.8+

Installing EZ WSI DicomWeb

1. Install necessary tools including Bazel, and pip (sudo apt-get install pip).

2. Install the gcloud CLI and login. Run the following commands from a shell. These will automatically accept the Google Cloud Platform TOS.

   foo@bar$ gcloud auth application-default login
   foo@bar$ gcloud auth login
   foo@bar$ gcloud config set project <your_project>

3. Install EZ WSI DicomWeb. There are three recommended options for installing EZ WSI DicomWeb. The first is preferred. The third option is best if you wish to make modifications the library locally.

• Option 1: Direct pip install.

  foo@bar$ pip install --no-deps ez-wsi-dicomweb
  foo@bar$ pip install ez-wsi-dicomweb

• Option 2: Direct pip install via Github.

  foo@bar$ pip3 install git+https://github.com/GoogleCloudPlatform/EZ-WSI-DICOMweb.git
  

• Option 3: Clone the repository and manually install. This option is useful if you would like to make local modifications to the library and test them out.

  1. Run the following commands to make an installation directory for EZ WSI DicomWeb:

     foo@bar$ export EZ_WSI=$HOME/ez_wsi_install_dir
     foo@bar$ mkdir $EZ_WSI
     foo@bar$ cd $EZ_WSI

  2. Clone EZ WSI DicomWeb into the directory you just created:

     foo@bar$ git clone https://github.com/GoogleCloudPlatform/EZ-WSI-DICOMweb.git $EZ_WSI

  3. Install EZ WSI using pip.

     foo@bar$ pip install .

Using EZ WSI DicomWeb

Check out the Jupyter Notebook code here.

Testing EZ WSI DicomWeb

You can execute unit tests using the following command:

foo@bar:ez_wsi_install_dir$ bazel test ez_wsi_dicomweb/ez_wsi_errors_test

Alternatively, you can run all of EZ WSI's unit tests by running

foo@bar:ez_wsi_install_dir$ bazel test //...

For more information on flags you can pass to Bazel, such as --test_output=all see here.

Contributing

See CONTRIBUTING.md for details.

License

See LICENSE for details.