This repository is designed to maintain software for the SUNYCell project. For information on this software, including the SUNYCell biomedical image data repository, please contact Scott Doyle.
(Tested on Windows 10 with miniconda installed.)
It is highly recommended to use a virtual environment to install this software.
To install this package into your current environment, from the repository directory, run:
pip install -e .
This will install the sunycell package into your current environment.
The main dependency of the software is histomicstk.
There are some other utilities required as well, like python-dotenv for loading your secrets / API keys.
More on this below.
Following the installation, you will need to re-install shapely as the pip version does not install properly on Windows -- on importing histomicstk modules, it will complain about geos_c.dll being missing.
All you need to do is the following:
pip uninstall shapely
conda install shapely
It's silly, but it works.
In order to access files on the SUNYCell DSA, you'll need to create a .env file somewhere in your project directory.
This is a plaintext file that contains your secrets; in particular, the *_URL and *_KEY environment variables for different API endpoints.
Make sure that if you are running the example notebooks locally, they can find these files, and that you do NOT add them to your GitHub account!
We will be expanding this section with demonstration / educational resources for different parts of the SUNYCell ecosystem.