Cytomine Utils

A package with utilities to interact with Cytomine's API.

Installation

You can install Cytomine Utils via [pip]:

$ pip install git+ssh://[email protected]/rendeirolab/cytomine_utils.git

The only dependency is cytomine-python-client>=2.4.0 which will be installed automatically.

Usage

Save your credentials into a file ~/.cytomine.auth.json:

{
        "host": "cytomine.int.cemm.at",
        "upload_host": "cytomine-upload.int.cemm.at",
        "public_key": "",
        "private_key": ""
}

Where the values of public_key and private_key can be retrieved from your account page on Cytomine.

Then to connect to the server, call the connect function once each session, and the API is now ready to interface with the server:

import cytomine_utils as cu

cu.connect()
prjs = cu.get_projects()

Documentation

The documentation for the original Cytomine API is available here: https://doc.uliege.cytomine.org/

The API is fully documented and can be seen here: https://cytomine-utils.readthedocs.io/en/latest/

You can also build it locally:

$ make docs
$ browser docs/build/html/index.html

It requires the installation of dependencies like sphinx and its extensions:

pip install .[doc]  # OR
pip install -r docs/requirements.txt