Learn how to exploit the full potential of the Cytomine software

In this section, we will explore the various features of this new ergonomic version of Cytomine, the solution for your projects in research, education or diagnostics.

Getting started

If you don't know Cytomine yet, follow first the Getting Started page to have a guided tour.

Cytomine concepts

The different Cytomine concepts and their features are deeply described in this guide.

The Roles of the users define their platform and project related permissions.

A Project is a secure working space to share images with other selected users.

The Storage and Upload page will explain how to upload and manage your uploaded files into Cytomine.

The Image viewer will allow you to browse gigapixel images and compare them in a collaborative way within a project.

Images can be multidimensional (2D+C+Z+T) and multispectral (such as in hyperspectral imagery, imaging mass spectrometry,...) using OME-Zarr (under development, to be documented).

With the concept of Annotations, we will be able to draw, save Regions Of Interest inside the images of a project and associate semantic values to them.

Images and annotations can be grouped into ImageGroups and AnnotationLinks, respectively, to handle multimodal datasets where a sample is described by multiple images.

The Cytomine platform allows the integration of external routine (workflows/algorithms/scripts) for data aggregation, Computer Vision, Machine/Deep Learning and other analyses. The Analysis page explicits how to launch such procedures in your project from the graphical user interface.

The Administrator Panel allows the administrator of a Cytomine instance to modify some global configurations and to have some global metrics.