Community Edition v3.2.3

Release of Cytomine-bootstrap (Version 3.2.3) of the Cytomine Community Edition platform.

DISCLAIMER :

• This v3.2.3 has mostly been developed to prepare the big refactoring that have lead to Community Edition 2023.1.
• This v3.2.3 is therefore not dedicated to be used in production.
• For production instances which need AI please prefer to install v3.1.0.
• For production instances starting from scratch, and which do not need AI apps, please consider to install Community Edition 2023.1.

User guide

You can find an user guide on our official documentation

More information on Cytomine website and on our online documentation.

Credits

The 3.2.0 version is a huge collaborative work of all our team and our contributors, and mainly the Cytomine team of the University of Liège.

List of modifications :

• Feature : Modification in the database structure in Core to allow management of multidimensional WSI.
• Feature : Modification of the IMS component to allow management of multidimensional WSI.
• Update of the Web UI related to these new features
• Update of the version of some components

Note :

As the ims component has changed (using ims-config.groovy instead of imageserverconfig.properties file for configuration). We recommand you to upgrade your Cytomine instance by fetching this version, filling all your configurations into the configuration files, running the init.sh file and run the restart.sh script of this repo.

Thanks to :

The Cytomine cooperative
The Cytomine research team at Montefiore Institut (ULiège University)

Version 3.1.0

Release of Cytomine-bootstrap (Version 3.1.0) of the Cytomine platform.

DISCLAIMER :

• For production instances which need AI please prefer to install this Legacy v3.1.0.
• For production instances starting from scratch, and which do not need AI apps, please consider to install Community Edition 2023.1.

User guide and information

You can find an user guide on our official documentation

Please see here to know how to install Cytomine with Docker.

More information on Cytomine website and on our online documentation.

List of modifications :

Various improvments in WebUI, Core and Software_router components. Check here, here and here

Thanks to :

The Cytomine cooperative
The Cytomine research team at Montefiore Institut (ULiège University)

Version 3.0.4

Release of Cytomine-bootstrap (Version 3.0.4) of the Cytomine platform.

You can find an user guide on our official documentation

Please see here to know how to install Cytomine with Docker.

More information on Cytomine website and on our online documentation.

List of modifications :

• Various bug fixes in WebUI and Core components. Check here and here
• Change default refresh rate for dockerhub/github repo
• Update and clean configuration file

Thanks to :
The Cytomine cooperative

Version 3.0.1

Release of Cytomine-bootstrap (Version 3.0.1) of the Cytomine platform.

You can find an user guide on our official documentation

Please see here to know how to install Cytomine with Docker.

More information on Cytomine website and on our online documentation.

List of modifications :
Various bug fixes in Core and IMS components.

Thanks to :
The Cytomine cooperative
The Cytomine research team at Montefiore Institut (ULiège University)

Version 3.0.0

Release of Cytomine-bootstrap (Version 3.0.0) of the Cytomine platform.

You can find an user guide on our official documentation

Please see here to know how to install Cytomine with Docker.

More information on Cytomine website and on our online documentation.

List of modifications :
Complete refactoring of the external algorithm management system. The new system based on containers technology greatly facilitate the integration and use of algorithms, inluding Artificial Intelligence algorithms, directly from the Cytomine graphical interface.

This 3.0.0 version is a huge collaborative work of all our team and our contributors, and mainly the Cytomine team of the University of Liège.

To add and execute algorithms, follow our documentation.

! Note that, by upgrading to the third version of Cytomine, the softwares plugged in your previous version will be no more runnable.

Thanks to :
The Cytomine cooperative
The Cytomine research team at Montefiore Institut (ULiège University)

Version 2.1.1

This version of Cytomine-bootstrap is compatible with the version 2.1.2 of Cytomine-Core and the version 1.1.2 of the Cytomine-Web-UI.

This minor release is made to set the current last version of V2 before releasing our next major release (V3).

You can find an user guide on our official documentation

When using our software, we kindly ask you to show our website URL and our logo in all your work (web site, publications, studies, oral presentations, manuals, ...). If you use Cytomine for scientific purpose, please cite Marée et al., Bioinformatics 2016 as reference paper. See our README file for additional details.

Please see here to know how to install Cytomine with Docker.

More information on Cytomine website and on our online documentation.

Thanks to :
The Cytomine society
The Cytomine research team at Montefiore Institut (ULiège University)

Version 2.1.0

This version of Cytomine-bootstrap is compatible with the version 2.1.1 of Cytomine-Core and the version 1.1.1 of the Cytomine-Web-UI.

You can find an user guide on our official documentation

When using our software, we kindly ask you to show our website URL and our logo in all your work (web site, publications, studies, oral presentations, manuals, ...). If you use Cytomine for scientific purpose, please cite Marée et al., Bioinformatics 2016 as reference paper. See our README file for additional details.

Please see here to know how to install Cytomine with Docker.

More information on Cytomine website and on our online documentation.

Thanks to :
The Cytomine society

Version 2.0.0

This version of Cytomine-bootstrap is compatible with the version 2.0.0 of Cytomine-Core and the first official version with the version 1.0.0 of the Cytomine-Web-UI.

You can find an user guide on our official documentation

When using our software, we kindly ask you to show our website URL and our logo in all your work (web site, publications, studies, oral presentations, manuals, ...). If you use Cytomine for scientific purpose, please cite Marée et al., Bioinformatics 2016 as reference paper. See our README file for additional details.

Please see here to know how to install Cytomine with Docker.

More information on Cytomine website and on our online documentation.

Thanks to :
The Cytomine society

Version 1.2.1

This version of Cytomine-bootstrap is compatible with the version 1.2.1 of Cytomine-IMS & Cytomine-Core.

When using our software, we recommend to cite (Marée et al., Bioinformatics 2016) paper when appropriate. See our license files for additional details.

Please see here to know how to install Cytomine with Docker.

More information on Cytomine website and on our online documentation.

Thanks to :
The Cytomine society

Version 1.2.0

This version of Cytomine-bootstrap is compatible with the version 1.2.0 of Cytomine-IMS & Cytomine-Core.

When using our software, we recommend to cite (Marée et al., Bioinformatics 2016) paper when appropriate. See our license files for additional details.

Please see here to know how to install Cytomine with Docker.

More information on Cytomine website and on our online documentation.

Changelog (upgrade guide from V1.1 to v1.2.0) :
New bootstrap architecture. The installation procedure has changed.

• Running the init.sh script after filling the configuration file is mandatory;
• Also, postgres has been updated, you need to backup databases, clean containers, delete postgres volumes then restart and restore data. You can do it by running the scripts in the utils folder.

Thanks to :
The Cytomine society