Upgrade your Cytomine instance

On this page, you will learn how to upgrade an already installed Cytomine instance to a newer version.

If you experiment any issue, please describe your problem precisely in our ticket system on Github.


  • The hardware and system requirements are described on the installation page.
  • A Cytomine instance is installed and running.
  • In the following steps, we will use the command line. It is recommanded to know how to use it

Important note

The stability of the Cytomine upgrade has been tested from the previous major version.
If you want to upgrade for more than one major version, please consider to repeat this operation for each version.
Example : If you have the 1.2.1 version and you want to upgrade to the 3.0.0, follow this procedure to upgrade first to the 2.0.0 version then from the 2.0.0 to the 3.0.0.

Step 1 - Backup your data

It is always recommended to do a backup before an upgrade. Please consult our backup documentation.


Step 2 - Retrieve Cytomine-bootstrap

As an installation, we retrieve the Cytomine-bootstrap installation procedure.
Firstly, clone your current bootstrap folder.

cp -r Cytomine-bootstrap Cytomine-bootstrap-BU

Then download a new bootstrap by following the step 1 of our installation guide.


Step 3 - Configure Cytomine installation

Now, it is required to edit the Cytomine file configuration.sh in the Cytomine-bootstrap/ directory. So edit the Cytomine-bootstrap/configuration.sh file with the values of the Cytomine-bootstrap-BU/configuration.sh file.

In some upgrade the content of the configuration file changed. Please read the CHANGELOG to help you if you encounter some new values. This page will also explain the variables used to configure your installation.

Then run the init script of the Cytomine-bootstrap directory

bash init.sh


Step 4 - Deploy Cytomine

Then, you can deploy Cytomine by launching the following command in the Cytomine-bootstrap directory (the installation of Cytomine can take up to 1 hour depending on network and server speed):

sudo sh restart.sh

You can now discover your new Cytomine by connecting with your usual username.

Follow the User Guide to learn how to use the Cytomine platform.