WARNING

This API reference is under construction. Some endpoint specifications could be incorrect.

All interactions with the Cytomine server are performed through an HTTP API. It makes the link between the server side and a Cytomine client, such as the graphical web interface or a program using one of our API client libraries (for Python, Java and Javascript).

This API reference provides the specification for all endpoints available in Cytomine. The different endpoints are grouped into services in the left sidebar. For a more in-depth introduction, see Interact with Cytomine.

API endpoint conventions

For most of the services, a resource is created with a POST /api/resource.json request with a request body. The response provides the Cytomine identifier for that new resource.

To retrieve this resource, send a GET /api/resource/{id}.json request where {id} is the Cytomine resource identifier.

To update a resource, send a PUT /api/resource/{id}.json request with a request body where {id} is the Cytomine resource identifier.

The resource can be deleted with a DELETE /api/resource/{id}.json request where {id} is the Cytomine resource identifier.

It is possible to retrieve a list of resources with the same domain using a GET /api/resource.json request. These listing can often be filtered with path and/or query parameters.

API services

Service	Description
Image | Image instance	Manage images in a project
Image | Slice instance	Manage slices of an image in a project
Image | Image server	Manage image servers (IMS)
Image | Abstract image	Manage images in a storage
Image | Abstract slice	Manage slices of an image in a storage
Image | Companion file	Manage companion files of an image in a storage
Storage	Manage storages (virtual disk space)
Storage | Member	Manage storage members
Storage | Uploaded file	Manage uploaded files in a storage
Annotation	Manage annotations regardless its type
Annotation | User annot.	Manage annotations created by human users
Annotation | Algo annot.	Manage annotations created by jobs
Annotation | Reviewed annot.	Manage reviewed annotations validated by human users
Annotation | Annotation index	Manage annotation indexes
Annotation | Associated term	Manage terms associated to annotations
Annotation | Associated track	Manage tracks associated to annotations
Ontology	Manage ontologies
Ontology | Term	Manage terms in an ontology
Ontology | Relation	Manage relations
Ontology | Relation term	Manage relation between terms in ontology
Track	Manage tracks in an image
Analysis | Software	Manage software (also known as app or algorithm)
Analysis | Software parameter	Manage arguments taken by a software
Analysis | Job	Manage jobs, a software execution
Analysis | Job parameter	Manager parameter values for a job
Analysis | Job data	Manage file job results
Analysis | User job	Manage user jobs, a user created for a software execution
Analysis | Trusted source	Manage software trusted sources
Project	Manage projects
Project | Command	Manage command history on a project
Project | Member	Manage project members
Project | Default layer	Manage project default layers
Project | Representative user	Manage project representative users
Project | Associated software	Manage software installed in a project
User	Manage users
User | Role	Manage app-roles
User | Associated role	Manage app-roles associated to users
Activity | Annotation action	Manage actions performed on annotations
Activity | Image consultation	Manage consultation records on images
Activity | Project connection	Manage connection records on projects
Activity | User position	Manage user position records on images
Metadata | Property	Manage properties (key-pair value) metadata
Metadata | Attached file	Manage attached files metadata
Metadata | Rich-text description	Manage rich-text description metadata
Metadata | Tag	Manage tags metadata
Metadata | Tag association	Manage associations between a tag and a domain