Version 3.0.0

Release of Cytomine-Core (Version 3.0.0) : module of the Cytomine platform.

Attached to this release, you will find the Core war file and the restapidoc.json documentation generated by the rest-api-doc Grails plugin.

Please see https://doc.cytomine.org/Admins 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 2.1.2

Release of Cytomine-Core (Version 2.1.2) : module of the Cytomine platform.

Attached to this release, you will find the Core war file and the restapidoc.json documentation generated by the rest-api-doc Grails plugin.

Please see https://doc.cytomine.org/Admins to know how to install Cytomine with Docker.

More information on Cytomine website and on our online documentation.

List of modifications :
Bug fix related to displayed deleted annotations
Improve user filtering
See the list of commits here

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

Version 2.1.1

Release of Cytomine-Core (Version 2.1.1) : module of the Cytomine platform.

Attached to this release, you will find the Core war file and the restapidoc.json documentation generated by the rest-api-doc Grails plugin.

Please see https://doc.cytomine.org/Admins to know how to install Cytomine with Docker.

More information on Cytomine website and on our online documentation.

List of modifications :
See the list of tickets here

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

Version 2.1.0

Release of Cytomine-Core (Version 2.1.0) : module of the Cytomine platform.

Attached to this release, you will find the Core war file and the restapidoc.json documentation generated by the rest-api-doc Grails plugin.

Please see https://doc.cytomine.org/Admins to know how to install Cytomine with Docker.

More information on Cytomine website and on our online documentation.

List of modifications :

• Add permission parameter into a project to allow contributors to download an image.
• Include back-end pagination for AbstractImage collections.
• Optimization for the online user requests

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

Version 2.0.0

Release of Cytomine-Core (Version 2.0.0) : module of the Cytomine platform.

Attached to this release, you will find the Core war file and the restapidoc.json documentation generated by the rest-api-doc Grails plugin.

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

More information on Cytomine website and on our online documentation.

List of modifications :

• Delete the embedded Front-end in BackboneJS. The new supported front-end is the Cytomine-Web-UI in VueJS ;
• Add the language of an user (used by the front-end) and its origin (who created it);
• Add feature of Tag-Domain Association. You can associate a named tag to a domain of Cytomine;
• Allow to have projects without an ontology;
• It is now possible to change the resolution and the magnification of an image instance;
• Upgrade email validator to accept new large set of top-level-domains;
• Implement a back-end search & pagination (The BDD requests are made with the max and offset and return exactly what is asked). Methods are in ModelService. The concerned domains are UploadedFile, Project, ImageInstance, Job, User;
• Add bounds function for setting filters for back-end searching;
• Add endpoint to check password validity of current User;
• Allow to target annotation when performing freehand correction;
• You need to explicitly allow Cytomine to share your position with other user of the project;
• Perimeter and area of existing annotations are now updated when updating image resolution;
• Remove [BLIND] from blinded name (front-end responsibility);
• Update the mailing template (when user forget username or password, when an annotation is shared) to use configurable values;
• Fix various redirection bugs when https is activated;
• URL loginWithoutLDAP/login moved to to loginWithoutSSO/login;
• You can now list all image instance accessible for an user;
• Fix multiples bugs (see https://github.com/cytomine/Cytomine-core/milestone/12);

Thanks to :
The Cytomine cooperative

Version 1.2.1

Release of Cytomine-Core (Version 1.2.1) : module of the Cytomine platform.

Attached to this release, you will find the Core war file and the restapidoc.json documentation generated by the rest-api-doc Grails plugin.

Please see http://doc.cytomine.be/pages/viewpage.action?pageId=10715266 to know how to install Cytomine with Docker.

More information on Cytomine website and on our online documentation.

List of modifications :

• fix multiples bugs (see https://github.com/cytomine/Cytomine-core/milestone/13)
• update Trumbowyg
• escape script balise into RTE
• Allow to return the last activity in imageList
• Allow to return the last activity and membersCount in projectList
• remove DICOM from supported formats list
• List the last consultations of an user into a project
• Fix snake_case to camelCase and subObject when doing direct SQL reque…
• export max number of point of an annotation into a config value
• add status conversion error for uploaded files
• fix resource access when https
• add default id sort when we list users
• improve uploadedFile conversion in bootstrap
• improve performance of UploadedFile by adding an index on ltree
• Allow insensitive username creation and connection
• fix pagination bug Project user list
• Fix : Incomplete data returned for userlayers
• Add rotation to user position
• Optimize online users request
• fix non unique ID bug for imageLayers
• update years in headers
• Allow LineString as annotation
• improve general configurations domain
• hide retrieval in front end if retrieval config is at false
• change versionning system
• add parameters & documentation for annotation crop feature

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

Version 1.2.0

Release of Cytomine-Core (Version 1.2.0) : module of the Cytomine platform.

Attached to this release, you will find the Core war file and the restapidoc.json documentation generated by the rest-api-doc Grails plugin.

Please see http://doc.cytomine.be/pages/viewpage.action?pageId=10715266 to know how to install Cytomine with Docker.

More information on Cytomine website and on our online documentation.

List of modifications :

• Refactoring of the UploadedFile domain to allow a tree of intermediate files (conversion, etc.).
• You can lock an user. This user will not be able to interact with Cytomine one locked.

Thanks to :
The Cytomine cooperative

Version 1.1

Release of Cytomine-Core (Version 1.1) : module of the Cytomine platform.

When using our software, we kindly ask you to cite our website url and related publications in all your work (publications, studies, oral presentations,...) using Cytomine. 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.

Attached to this release, you will find the Core war file and the restapidoc.json documentation generated by the rest-api-doc Grails plugin.

Please see http://doc.cytomine.be/pages/viewpage.action?pageId=10715266 to know how to install Cytomine with Docker.

More information on Cytomine website and on our online documentation.

List of modifications :

• New panel to manage users into a project : The User Configuration Panel.
  These panel contains an array of the project contributors with some connexion informations (Last connexion, Last viewed Image).
  Managers are in red, Online contributors are in blue.
  It also contains graphs with global user activities into the project.
• For each user, you will find a "Details" button that will open a new panel with specific connexion informations about the selected contributor : History, image consultation duration, frequency of connexions. CSV export are allowed.
• A new Admin zone (Dashboard) with stats(total & currently) & graphs.
• Improve performances (crops).
• Extend ProjectEditing Mode (Classic, Restricted (new) & Read Only) :
  • Classic : contributors can add, edit and modify annotations on all layers.
  • Restricted : Ex "Read Only" : contributors can add, edit and modify annotations on their own layer only.
  • Read Only : Is now a strict read only. contributors cannot add, delete or modify. Only visualization is allowed.
    "Read Only" projects will be considered as "Restricted" after the Cytomine upgrade.
• Allow authentication by LTI protocol.
• New mode on annotation layer Edit. Modes are now View, Edit & Follow.
• We can now share & comment an annotation made by a job.
• Can now lock user (only with http client for now).
• Librairy changes : Replace CKEditor by Trumbowyg and upgrade DataTables 1.9.4 -> 1.10.15.
• Allow jobs to upload images.
• Allow add multiple AlgoAnnotations with Terms into one single HTTP request.

Thanks to :
The Walloon Region for the Histoweb grant (2014 -- 2017)

Open Source release

Cytomine-Core

Version 1.0

Official 1.0 Open Source release of Cytomine-Core associated to the paper (Marée et al., Bioinformatics 2016) !

When using our software, you agree to cite our website url and related publications in all your work (publications, studies, oral presentations,...). In particular, you agree to cite our (Marée et al., Bioinformatics 2016) paper, and to use our logo when appropriate. See our license files for additional details.

• URL: http://www.cytomine.be/
• Logo: http://www.cytomine.be/logo/logo.png
• 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, 2016.

Attached to this release, you will find the Core war file and the restapidoc.json documentation generated by the rest-api-doc Grails plugin.

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

More information on Cytomine website and on our online documentation.

Open Source pre-release

Cytomine-Core

Version 0.99

This is the last version of Cytomine-Core before its official Open Source release.

Attached to this release, you will find the Core war file and the restapidoc.json documentation generated by the rest-api-doc Grails plugin.

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

More information on Cytomine website and on our online documentation.