Cytomine-python-client is an open-source Cytomine client written in Python. This client is a Python wrapper around Cytomine REST API gateway.
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.
- Python 2.7 | 3.5+
To install official release of Cytomine-python-client, see @cytomine. Follow this guide to install forked version by ULiege.
To retrieve package using pip:
pip install --extra-index-url=https://packagecloud.io/cytomine-uliege/Cytomine-python-client/pypi/simple cytomine-python-clientor, to add the extra index permanently to your pip configuration:
curl -s https://packagecloud.io/install/repositories/cytomine-uliege/Cytomine-python-client/script.python.sh | bash
pip install cytomine-python-clientSee package repository for details.
To download and install manually the package in a Python env, run (here for version 2.7.3):
wget https://github.com/Cytomine-ULiege/Cytomine-python-client/releases/download/v2.7.3/Cytomine-Python-Client-2.7.3.zip
unzip Cytomine-Python-Client-2.7.3.zip
cd Cytomine-Python-Client-2.7.3
pip install .To ease developpement of new Cytomine software, the Cytomine-python-client package is available in Docker containers:
- cytomineuliege/software-python3-base provides a Python 3.5 environment with client already installed.
- cytomineuliege/software-python2-base provides a Python 2.7 environment with client already installed.
These Docker images are tagged with the Python client version number. Two image variants are given for each client version:
cytomineuliege/software-pythonX-base:<version>is the defacto image. If you are unsure about what your needs are, you probably want to use this one.cytomineuliege/software-pythonX-base:<version>-slimis an image that does not contain all the common package contained in the default tag and only contains the minimal packages needed to run Python. If you are working in an environment where only the python image will be deployed and you have space constraints, we recommend to use this one.
See official python Docker image for more details.
See detailed usage documentation.
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("Hello {}".format(cytomine.current_user))
projects = ProjectCollection().fetch()
print(projects)
for project in projects:
print(project)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.
Apache 2.0