Bigpicture Cytomine Python client

Cytomine-python-client is an open-source Cytomine client written in Python. This client is a Python wrapper around Cytomine REST API gateway.

Overview

The main access point to Cytomine data is its REST API. This client is a Python package that can be imported in an application and allows to import/export data from Cytomine-Core and Cytomine-IMS using RESTful web services e.g. to generate annotation (spatial) statistics, create regions of interest (e.g. tumor masks), add metadata to images/annotations, apply algorithms on image tiles, ...

See documentation for more details.

Requirements

• Python 3.5+

Install

The client can be installed from the github repository using pip:

pip install 'cytomine-python-client @ git+https://github.com/Cytomine-ULiege/bigpicture-cytomine-python-client.git'

Usage

See detailed usage documentation.

Basic example

Three parameters are required to connect:

• HOST: The full URL of Cytomine core (e.g. “http://demo.cytomine.be”).
• PUBLIC_KEY: Your cytomine public key.
• PRIVATE_KEY: Your cytomine private key.

First, the connection object has to be initialized.

from cytomine import Cytomine

host = "demo.cytomine.be"
public_key = "XXX" # check your own keys from your account page in the web interface
private_key = "XXX"

cytomine = Cytomine.connect(host, public_key, private_key)

The next sample code should print “Hello {username}” where {username} is replaced by your Cytomine username and print the list of available projects.

from cytomine.models import ProjectCollection

print(f"Hello {cytomine.current_user}")
projects = ProjectCollection().fetch()
print(projects)
for project in projects:
    print(project)

Other examples

• Scripts in examples directory
• Documentation by examples

References

When using our software, we kindly ask you to cite our website url and related publications in all your work (publications, studies, oral presentations,...). In particular, we recommend to cite (Marée et al., Bioinformatics 2016) paper, and to use our logo when appropriate. See our license files for additional details.

• URL: http://www.cytomine.org/
• Logo: Available here
• Scientific paper: Raphaël Marée, Loïc Rollus, Benjamin Stévens, Renaud Hoyoux, Gilles Louppe, Rémy Vandaele, Jean-Michel Begon, Philipp Kainz, Pierre Geurts and Louis Wehenkel. Collaborative analysis of multi-gigapixel imaging data using Cytomine, Bioinformatics, DOI: 10.1093/bioinformatics/btw013, 2016.

License

Apache 2.0