Download OpenAPI specification:Download
| username required | string Valid username for authentication |
| password required | string Valid password for authentication |
List nodes that are located in a broken section.
Broken secrions of all stacks linked to the current project are tested if they contain any nodes. Stack orientatins are respected. Optionally, only particular skeletons can be checked.
| project_id required | string |
| skeleton_ids | string List of skeleton IDs to constrain tests on |
List annotations matching filtering criteria that are currently in use.
The result set is the intersection of annotations matching criteria (the criteria are conjunctive) unless stated otherwise.
| project_id required | string |
| annotations | string A list of (meta) annotations with which which resulting annotations should be annotated with. |
| annotates | string A list of entity IDs (like annotations and neurons) that should be annotated by the result set. |
| parallel_annotations | string A list of annotation that have to be used alongside the result set. |
| user_id | string Result annotations have to be used by this user. |
| neuron_id | string Result annotations will annotate this neuron. |
| skeleton_id | string Result annotations will annotate the neuron modeled by this skeleton. |
| ignored_annotations | string A list of annotation names that will be excluded from the result set. |
| if_modified_since | string Works only if |
List annotations matching filtering criteria that are currently in use.
The result set is the intersection of annotations matching criteria (the criteria are conjunctive) unless stated otherwise.
| project_id required | string |
| annotations | string A list of (meta) annotations with which which resulting annotations should be annotated with. |
| annotates | string A list of entity IDs (like annotations and neurons) that should be annotated by the result set. |
| parallel_annotations | string A list of annotation that have to be used alongside the result set. |
| user_id | string Result annotations have to be used by this user. |
| neuron_id | string Result annotations will annotate this neuron. |
| skeleton_id | string Result annotations will annotate the neuron modeled by this skeleton. |
| ignored_annotations | string A list of annotation names that will be excluded from the result set. |
| if_modified_since | string Works only if |
Add missing neuron name annotations.
To each passed in neuron, a list of neuron IDs and/or skelton IDs, the neuron name stored in the neuron's base name is added as annotation. Each neuron name annotation is meta-annotated with a "Name" annotation.
| project_id required | string |
| skeleton_ids | string A list of skeleton IDs to update |
| entity_ids | string A list of target entity IDs to update |
Get annotations and who used them for a set of skeletons.
This method focuses only on annotations linked to skeletons and is likely to be faster than the general query. Returns an object with two fields: "annotations", which is itself an object with annotation IDs as fields, giving access to the corresponding annotation names. And the field "skeletons" is also an object, mapping skeleton IDs to lists of annotation-annotator ID pairs. Also, as JSON separator a colon is used instead of a comma.
| project_id required | string |
| skeleton_ids | string A list of skeleton IDs which are annotated by the resulting annotations. |
Query annotations linked to a list of objects.
These objects can for instance be neurons, annotations or stack groups. From a database perspective, these objects are class instances.
Returned is an object with the fields "entities" and "annotations". The former is an object mapping an entity ID to a list of annotations. Each annotation is represented by an object containing its "id" and "uid", the user who annotated it. The latter maps annotation IDs to annotation names. For instance::
{ "entities": { "42": [{id: 1, uid: 12}, {id: 3, uid: 14}] }, "annotations": { 12: "example1", 14: "example2" } }
| project_id required | string |
| object_ids | string A list of object IDs for which annotations should be returned. |
Query entities based on various constraints
Entities are objects that can be referenced within CATMAID's semantic space, e.g. neurons, annotations or stack groups. This API allows to query them, mainly by annotations that have been used with them. Multiple annotation parameters can be used to combine different annotation sets with AND. Elements of one annotation parameter are combined with OR.
| project_id required | string |
| annotation_date_start | string The earliest YYYY-MM-DD date result elements have been annotated at. |
| annotation_date_end | string The latest YYYY-MM-DD date result elements have been annotated at. |
| name | string The name (or a part of it) of result elements. |
| annotated_by | string A result element was annotated by a user with this ID. |
| annotated_with | string A comma separated list of annotation IDs which all annotate the result elements. |
| not_annotated_with | string A comma separated list of annotation IDs which don't annotate the result elements. |
| sub_annotated_with | string A comma separated list of annotation IDs that are contained in either 'annotated_with' or 'not_annotated_with' that get expanded to also include their sub-annotations in the query (of which then at least one has to match inclusion or exclusion respectively). |
| with_annotations | string Indicate if annotations of result elements should be returned. |
| types | string Allowed result types. Multple types can be passed with multiple parameters. Defaults to 'neuron' and 'annotation'. |
| sort_by | string Indicates how results are sorted. |
| sort_dir | string Indicates sorting direction. |
| range_start | string The first result element index. |
| range_length | string The number of results |
| annotation_reference | string Whether annoation references are IDs or names, can be 'id' or 'name. |
Get a collection of connectors.
The connectors field of the returned object contains a list of all result
nodes, each represented as a list of the form:
[id, x, y, z, confidence, creator_id, editor_id, creation_time, edition_time]
Both edition time and creation time are returned as UTC epoch values. If
tags are requested, the tags field of the response object will contain a
mapping of connector IDs versus tag lists. If partners are requested, the
partners field of the response object will contain a mapping of connector
IDs versus lists of partner links. Each partner link is an array of the
following format:
[link_id, treenode_id, skeleton_id, relation_id, confidence]
If both skeleton_ids and relation_type are used, the linked skeletons
need to be linked by the specified relation. Without relation_type,
linked skeletons can have any relation and without skeleton_ids a
connector needs to have a least one link with the specified relation.
| project_id required | string Project of connectors |
| skeleton_ids | string Skeletons linked to connectors |
| tags | string Require a set of tags |
| relation_type | string Relation of linked skeletons to connector. |
| with_tags | string If connector tags should be fetched |
| with_partners | string If partner node and link information should be fetched |
Get a list of all connector nodes that intersect with the passed in bounding box.
| project_id required | string |
| limit | string Limit the number of returned nodes. |
| minx required | string Minimum world space X coordinate |
| miny required | string Minimum world space Y coordinate |
| minz required | string Minimum world space Z coordinate |
| maxx required | string Maximum world space X coordinate |
| maxy required | string Maximum world space Y coordinate |
| maxz required | string Maximum world space Z coordinate |
| with_locations required | string Whether to return the location of each connector. |
| with_links required | string Whether to return every individual link |
| skeleton_ids | string Skeletons linked to connectors |
Get a list of all connector nodes that intersect with the passed in bounding box.
| project_id required | string |
| limit | string Limit the number of returned nodes. |
| minx required | string Minimum world space X coordinate |
| miny required | string Minimum world space Y coordinate |
| minz required | string Minimum world space Z coordinate |
| maxx required | string Maximum world space X coordinate |
| maxy required | string Maximum world space Y coordinate |
| maxz required | string Maximum world space Z coordinate |
| with_locations required | string Whether to return the location of each connector. |
| with_links required | string Whether to return every individual link |
| skeleton_ids | string Skeletons linked to connectors |
Get connectors linked to a set of skeletons.
The result data set includes information about linked connectors on a given input set of skeletons. These links are further constrained by relation type, with currently support available for: postsynaptic_to, presynaptic_to, abutting, gapjunction_with, tightjunction_with, desmosome_with.
Returned is an object containing an array of links to connectors and a set of tags for all connectors found (if not disabled). The link array contains one array per connector link with the following content: [Linked skeleton ID, Connector ID, Connector X, Connector Y, Connector Z, Link confidence, Link creator ID, Linked treenode ID, Link edit time].
A POST handler is able to accept large lists of skeleton IDs.
| project_id required | string |
| skeleton_ids required | string Skeletons to list connectors for |
| relation_type required | string Relation of listed connector links |
| with_tags | string If connector tags should be fetched |