Introduction

Cytomine is an open-source RESTful web platform composed of multiple services encapsulated in Docker containers.

Leveraging Docker power, you can install the whole Cytomine platform on a personal laptop (without collaborative tools), on a virtual machine or a dedicated server in your lab or at large scale, by hosting containers on different machines to increase performance and stability (horizontal scaling).

Cytomine Bootstrap

Cytomine-bootstrap is the Cytomine installer. Using a single command, the installer runs all required services as Docker containers. The services managed by Cytomine-bootstrap are given in the next figure.

To interact with Cytomine (that is what Cytomine-bootstrap launched), you can use a regular browser and access the graphical user interface (GUI). As a RESTful application, it is possible to interact external clients in different languages (Python, Javascript, Java).

Cytomine containers

Name	Required	Goal
Nginx	Yes	Main HTTP(S) proxy dispatching incoming requests.
Core	Yes	Main Cytomine server. Provide the REST API.
Postgres	Yes	Main database. Store most of data.
MongoDB	Yes	Secondary database. Store activity data.
IMS	Yes	Main image server.
IIP	Yes	Fast image extractor.
Memcached	Yes	Fast cache for images.
Bioformat	No	Support for additional image formats.
Software router	No	Manage algorithms and their execution. Required to use algorithms.
RabbitMQ	No	Communication between Core and Software router. Required to use algorithms.
Slurm	No	Execution server for algorithms. Required to use algorithms.
Web UI	No	Web graphical user interface. Required to use a GUI.