API Reference

Version:

Schemes:

Summary

Tag: api-token-auth

Operation	Description
POST /api-token-auth/	Generate an authorization token to use for API requests.

Tag: client

Operation	Description
GET /client/datastores/	List key-value store datastores used by the client.
POST /client/datastores/	Create a key-value store datastore for the client.
DELETE /client/datastores/{name}	Delete a key-value store datastore for the client.
GET /client/datastores/{name}/	List key-value data in a datastore for the client.
PUT /client/datastores/{name}/	Create or replace a key-value data entry for the client.

Tag: neurons

Operation	Description
GET /{project_id}/neurons/	List neurons matching filtering criteria.
POST /{project_id}/neurons/from-models	Retrieve neuron IDs modeled by particular entities, eg skeletons.
POST /{project_id}/neurons/{neuron_id}/rename	Rename a neuron.

Tag: nodes

Operation	Description
POST /{project_id}/nodes/	Retrieve all nodes intersecting a bounding box
POST /{project_id}/nodes/find-labels	List nodes with labels matching a query, ordered by distance.
POST /{project_id}/nodes/location	Get locations for a particular set of nodes in a project.

Tag: pointclouds

Operation	Description
GET /{project_id}/pointclouds/	List all available point clouds or optionally a sub set.
POST /{project_id}/pointclouds/	List all available point clouds or optionally a sub set.
PUT /{project_id}/pointclouds/	Create a new pointcloud by providing.
GET /{project_id}/pointclouds/{pointcloud_id}/	Return a point cloud.
DELETE /{project_id}/pointclouds/{pointcloud_id}/	Delete a point cloud.
GET /{project_id}/pointclouds/{pointcloud_id}/images/{image_id}/	Return a point cloud.

Tag: points

Operation	Description
GET /{project_id}/points/	List points, optionally constrained by various properties.
PUT /{project_id}/points/	Add a new point. Expect at least the location as parameters.
GET /{project_id}/points/{point_id}/	Return details on one particular point.
POST /{project_id}/points/{point_id}/	Update one particular point.
DELETE /{project_id}/points/{point_id}/	Delete one particular point.

Tag: samplers

Operation	Description
GET /{project_id}/samplers/	Get a collection of available samplers.
POST /{project_id}/samplers/add	Create a new sampler for a skeleton.
GET /{project_id}/samplers/connectors/	Get a list of connectors that already have a state associated with them.
GET /{project_id}/samplers/connectors/states/	Get a list of all available connectors states and their IDs.
GET /{project_id}/samplers/domains/intervals/states/	Get a list of all available interval states.
POST /{project_id}/samplers/domains/intervals/{interval_id}/connectors/{connector_id}/set-state	Set state of sampler connector
GET /{project_id}/samplers/domains/intervals/{interval_id}/details	Get details on a particular interval.
POST /{project_id}/samplers/domains/intervals/{interval_id}/set-state	Set state of an interval.
GET /{project_id}/samplers/domains/types/	Get a list of all available domain types.
GET /{project_id}/samplers/domains/{domain_id}/details	Get details on a particular domain.
GET /{project_id}/samplers/domains/{domain_id}/intervals/	Get a collection of available sampler domains intervals.
POST /{project_id}/samplers/domains/{domain_id}/intervals/add-all	Create all intervals in a particular domain.
GET /{project_id}/samplers/states/	Get a list of all available sampler states and their IDs.
GET /{project_id}/samplers/{sampler_id}/	Get details on a particular sampler.
POST /{project_id}/samplers/{sampler_id}/	Set fields of a particular sampler.
POST /{project_id}/samplers/{sampler_id}/delete	Delete a sampler if permissions allow it.
GET /{project_id}/samplers/{sampler_id}/domains/	Get a collection of available sampler domains.
POST /{project_id}/samplers/{sampler_id}/domains/add	Create a new domain for a sampler.
POST /{project_id}/samplers/{sampler_id}/domains/add-all	Create a new domain for a sampler.

Tag: similarity

Operation	Description
GET /{project_id}/similarity/configs/	List all available NBLAST configurations.
PUT /{project_id}/similarity/configs/	Create a new similarity/NBLAST configuration either by providing
GET /{project_id}/similarity/configs/{config_id}/	Delete a NBLAST configuration.
DELETE /{project_id}/similarity/configs/{config_id}/	Delete a NBLAST configuration.
GET /{project_id}/similarity/queries/	List all available NBLAST similarity tasks.
POST /{project_id}/similarity/queries/similarity	Compare two sets of objects (skeletons or point clouds) and return an
GET /{project_id}/similarity/queries/{similarity_id}/	Get a particular similarity query result.
DELETE /{project_id}/similarity/queries/{similarity_id}/	Delete a NBLAST similarity task.

Tag: skeleton

Operation	Description
POST /{project_id}/skeleton/connectivity_matrix	Return a sparse connectivity matrix representation for the given skeleton

Tag: skeletons

Operation	Description
GET /{project_id}/skeletons/	List skeletons matching filtering criteria.
POST /{project_id}/skeletons/cable-length	Get the cable length of a set of skeletons.
POST /{project_id}/skeletons/compact-detail	Get a compact treenode representation of a list of skeletons, optionally
POST /{project_id}/skeletons/confidence-compartment-subgraph	Get a synaptic graph between skeletons compartmentalized by confidence.
POST /{project_id}/skeletons/connectivity	Retrieve a list of down/up-stream partners of a set of skeletons.
GET /{project_id}/skeletons/connectivity-counts	Get the number of synapses per type for r a set of skeletons.
POST /{project_id}/skeletons/connectivity-counts	Get the number of synapses per type for r a set of skeletons.
POST /{project_id}/skeletons/connectivity_matrix/csv	Return a CSV file that represents the connectivity matrix of a set of row
POST /{project_id}/skeletons/import	Import a neuron modeled by a skeleton from an uploaded file.
GET /{project_id}/skeletons/in-bounding-box	Get a list of all skeletons that intersect with the passed in bounding
POST /{project_id}/skeletons/in-bounding-box	Get a list of all skeletons that intersect with the passed in bounding
GET /{project_id}/skeletons/node-labels	Return relationship between label IDs and skeleton IDs
POST /{project_id}/skeletons/node-labels	Return relationship between label IDs and skeleton IDs
POST /{project_id}/skeletons/review-status	Retrieve the review status for a collection of skeletons.
POST /{project_id}/skeletons/sampler-count	Get the number of samplers associated with each skeleton in the passed in
POST /{project_id}/skeletons/within-spatial-distance	Find skeletons within a given L-infinity distance of a treenode.
GET /{project_id}/skeletons/{skeleton_id}/cable-length	Get the cable length for a skeleton
GET /{project_id}/skeletons/{skeleton_id}/compact-detail	Get a compact treenode representation of a skeleton, optionally with the
POST /{project_id}/skeletons/{skeleton_id}/find-labels	List nodes in a skeleton with labels matching a query.
GET /{project_id}/skeletons/{skeleton_id}/neuroglancer	Export a morphology-only skeleton in neuroglancer's binary format.
GET /{project_id}/skeletons/{skeleton_id}/node-overview	Get information on a skeleton's treenodes, reviews and labels.
POST /{project_id}/skeletons/{skeleton_id}/open-leaves	List open leaf nodes in a skeleton.
POST /{project_id}/skeletons/{skeleton_id}/review	Export skeleton as a set of segments with per-node review information.
GET /{project_id}/skeletons/{skeleton_id}/root	Retrieve ID and location of the skeleton's root treenode.
GET /{project_id}/skeletons/{skeleton_id}/sampler-count	Get the number of samplers associated with this skeleton.

Tag: stats

Operation	Description
GET /{project_id}/stats/cable-length	Get the largest skeletons based on cable length.
GET /{project_id}/stats/editor	Get the total number of edited nodes per user.
GET /{project_id}/stats/nodecount	Get the total number of created nodes per user.
GET /{project_id}/stats/user-history	Get per user contribution statistics

Tag: transactions

Operation	Description
GET /{project_id}/transactions/	Get a collection of all available transactions in the passed in project.
GET /{project_id}/transactions/location	Try to associate a location in the passed in project for a particular

Tag: groups

Operation	Description
GET /groups/	List all available point clouds.

Tag: treenodes

Operation	Description
POST /{project_id}/treenodes/compact-detail	Retrieve node information in a compact form. A list of elements of the
GET /{project_id}/treenodes/{treenode_id}/compact-detail	Retrieve node information in a compact form. A list of the following form
POST /{project_id}/treenodes/{treenode_id}/confidence	Update confidence of edge between a node to either its parent or its
GET /{project_id}/treenodes/{treenode_id}/info	Retrieve skeleton and neuron information about this treenode.
GET /{project_id}/treenodes/{treenode_id}/suppressed-virtual/	List suppressed virtual nodes along the edge to this node.
POST /{project_id}/treenodes/{treenode_id}/suppressed-virtual/	Suppress a virtual treenode along the edge to this node.
DELETE /{project_id}/treenodes/{treenode_id}/suppressed-virtual/{suppressed_id}	Unsuppress a virtual treenode.

Tag: volumes

Operation	Description
GET /{project_id}/volumes/	Get a collection of all available volumes.
POST /{project_id}/volumes/add	Create a new volume
POST /{project_id}/volumes/entities/	Retrieve a mapping of volume IDs to entity (class instance) IDs.
POST /{project_id}/volumes/import	Import triangle mesh volumes from an uploaded files.
GET /{project_id}/volumes/skeleton-innervations	Test environment only contains two skeletons - based on that, sql query
POST /{project_id}/volumes/skeleton-innervations	Test environment only contains two skeletons - based on that, sql query
POST /{project_id}/volumes/{volume_id}/	Get detailed information on a spatial volume or set its properties..
DELETE /{project_id}/volumes/{volume_id}/	Get detailed information on a spatial volume or set its properties..
GET /{project_id}/volumes/{volume_id}/export\.(P{extension}\w+)	Export volume as a triangle mesh file.
GET /{project_id}/volumes/{volume_id}/intersect	Test if a point intersects with the bounding box of a given volume.

Tag: projects

Operation	Description
GET /projects/	List projects visible to the requesting user.
GET /projects/export	Detailed list of projects visible to the requesting user.

Tag: analytics

Operation	Description
POST /{project_id}/analytics/broken-section-nodes	List nodes that are located in a broken section.

Tag: annotations

Operation	Description
GET /{project_id}/annotations/	List annotations matching filtering criteria that are currently in use.
POST /{project_id}/annotations/	List annotations matching filtering criteria that are currently in use.
POST /{project_id}/annotations/forskeletons	Get annotations and who used them for a set of skeletons.
POST /{project_id}/annotations/query	Query annotations linked to a list of objects.
POST /{project_id}/annotations/query-targets	Query entities based on various constraints

Tag: connectors

Operation	Description
POST /{project_id}/connectors/	Get a collection of connectors.
GET /{project_id}/connectors/in-bounding-box	Get a list of all connector nodes that intersect with the passed in
POST /{project_id}/connectors/in-bounding-box	Get a list of all connector nodes that intersect with the passed in
GET /{project_id}/connectors/links/	Get connectors linked to a set of skeletons.
POST /{project_id}/connectors/links/	Get connectors linked to a set of skeletons.
GET /{project_id}/connectors/types/	Get a list of available connector types.
GET /{project_id}/connectors/user-info	Return information on a treenode connector edge.
GET /{project_id}/connectors/{connector_id}/	Get detailed information on a connector and its partners

Tag: interpolatable-sections

Operation	Description
GET /{project_id}/interpolatable-sections/	Get all section locations for all orientations.

Tag: labels

Operation	Description
GET /{project_id}/labels/	List all labels (front-end node tags) in use.
GET /{project_id}/labels/detail	List all labels (front-end node tags) in use alongside their IDs.
GET /{project_id}/labels/stats	Get usage statistics of node labels.
GET /{project_id}/labels/{node_type}/{node_id}/	List all labels (front-end node tags) attached to a particular node.

Tag: landmarks

Operation	Description
GET /{project_id}/landmarks/	List available landmarks, optionally only the ones in a set of landmark
PUT /{project_id}/landmarks/	Add a new landmark. Expect at least the name as parameter.
GET /{project_id}/landmarks/groups/	List available landmark groups.
PUT /{project_id}/landmarks/groups/	Add a new landmarkgroup. Expect at least the name as parameter.
POST /{project_id}/landmarks/groups/import	Import and link landmarks, landmark groups and locations.
PUT /{project_id}/landmarks/groups/links/	Link a location group to another landmark group. If the passed in
DELETE /{project_id}/landmarks/groups/links/{link_id}/	Delete the link between two landmark groups. Won't delete links that
POST /{project_id}/landmarks/groups/materialize	Create all passed in landmarks along with a set of groups in one go.
GET /{project_id}/landmarks/groups/{landmarkgroup_id}/	Get details on one particular landmarkgroup group, including its
POST /{project_id}/landmarks/groups/{landmarkgroup_id}/	Update an existing landmark group.
PUT /{project_id}/landmarks/groups/{landmarkgroup_id}/locations/{location_id}/	Link a location to a landmark group.
DELETE /{project_id}/landmarks/groups/{landmarkgroup_id}/locations/{location_id}/	Remove the link between a location and a landmark group.
GET /{project_id}/landmarks/groups/{landmarkgroup_id}/transitively-linked	Get a list of landmark groups that are transitively linked to the
GET /{project_id}/landmarks/{landmark_id}/	Get details on one particular landmark.
POST /{project_id}/landmarks/{landmark_id}/	Update an existing landmark.
DELETE /{project_id}/landmarks/{landmark_id}/	Delete one particular landmark.
DELETE /{project_id}/landmarks/{landmark_id}/groups/{group_id}/	Delete the link between a location and a landmark and a group and a
PUT /{project_id}/landmarks/{landmark_id}/locations/	Add a new location or use an existing one and link it to a landmark.
DELETE /{project_id}/landmarks/{landmark_id}/locations/{location_id}/	Delete the link between a location and a landmark. If the last link

Security

basic

Type: basic

Paths

Generate an authorization token to use for API requests.

POST /api-token-auth/

Tags: api-token-auth

Generate an authorization token to use for API requests.

Use your user credentials to generate an authorization token for querying the API. This token is tied to your account and shares your permissions. To use this token set the Authorization HTTP header to "Token " concatenated with the token string, e.g.:

Authorization: Token 9944b09199c62bcf9418ad846dd0e4bbdfc6ee4b

Requests using token authorization are not required to set cross-site request forgery (CSRF) token headers.

Requests using this token can do anything your account can do, so do not distribute this token or check it into source control.

201 Created

List key-value store datastores used by the client.

GET /client/datastores/

Tags: client

List key-value store datastores used by the client.

200 OK

Create a key-value store datastore for the client.

POST /client/datastores/

Tags: client

Create a key-value store datastore for the client.

The request user must not be anonymous and must have browse, annotate or administer permissions for at least one project.

application/x-www-form-urlencoded

name	String key for the datastore. This will be used in URLs so may only contain alphanumeric characters and hyphens.	formData	string

201 Created

Delete a key-value store datastore for the client.

DELETE /client/datastores/{name}

Tags: client

Delete a key-value store datastore for the client.

Must be a super user to perform.

name		path	string

204 No Content

List key-value data in a datastore for the client.

GET /client/datastores/{name}/

Tags: client

List key-value data in a datastore for the client.

Returns key-values belong to the request user or no user, optionally filtering for those pairs belong to a specific project or no project.

name	String key for the datastore with which this key-value entry is associated.	path	string
project_id	ID of a project to associate this data with, if any.	query	integer

200 OK

Create or replace a key-value data entry for the client.

PUT /client/datastores/{name}/

Tags: client

Create or replace a key-value data entry for the client.

Each entry is associated with a datastore, an optional project, an optional user, and a key. Creating a request that duplicates this quadruple will replace rather than create the value in the key-value pair.

Entries associated with neither a project nor user are considered global; those associated with a project but no user are project- default; those associated with a user but no project are user-default; and those associated with both a project and a user are user-project specific. When listing key-value data, all four of these values, if existing, will be returned.

application/x-www-form-urlencoded

name	String key for the datastore with which this key-value entry is associated.	path	string
project_id	ID of a project to associate this data with, if any.	formData	integer
ignore_user	Whether to associate this key-value entry with the instance rather than the request user. Only project administrators can do this for project-associated instance data, and only super users can do this for global data (instance data not associated with any project).	formData	boolean
key	A key for this entry.	formData	string
value	A value for this entry. Must be valid JSON.	formData	string

200 OK

List all available point clouds.

GET /groups/

Tags: groups

List all available point clouds.

application/x-www-form-urlencoded

member_id	Return only groups this user is member of.	formData	integer

200 OK

List projects visible to the requesting user.

GET /projects/

Tags: projects

List projects visible to the requesting user.

200 OK

Detailed list of projects visible to the requesting user.

GET /projects/export

Tags: projects

Detailed list of projects visible to the requesting user.

200 OK

List nodes that are located in a broken section.

POST /{project_id}/analytics/broken-section-nodes

Tags: analytics

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.

application/x-www-form-urlencoded

project_id		path	string
skeleton_ids	List of skeleton IDs to constrain tests on	formData	string[]

201 Created

List annotations matching filtering criteria that are currently in use.

GET /{project_id}/annotations/

Tags: annotations

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.

application/x-www-form-urlencoded

project_id		path	string
annotations	A list of (meta) annotations with which which resulting annotations should be annotated with.	formData	string[]
annotates	A list of entity IDs (like annotations and neurons) that should be annotated by the result set.	formData	string[]
parallel_annotations	A list of annotation that have to be used alongside the result set.	formData	string[]
user_id	Result annotations have to be used by this user.	formData	integer
neuron_id	Result annotations will annotate this neuron.	formData	integer
skeleton_id	Result annotations will annotate the neuron modeled by this skeleton.	formData	integer
ignored_annotations	A list of annotation names that will be excluded from the result set.	formData	string[]

200 OK

List annotations matching filtering criteria that are currently in use.

POST /{project_id}/annotations/

Tags: annotations

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.

application/x-www-form-urlencoded

project_id		path	string
annotations	A list of (meta) annotations with which which resulting annotations should be annotated with.	formData	string[]
annotates	A list of entity IDs (like annotations and neurons) that should be annotated by the result set.	formData	string[]
parallel_annotations	A list of annotation that have to be used alongside the result set.	formData	string[]
user_id	Result annotations have to be used by this user.	formData	integer
neuron_id	Result annotations will annotate this neuron.	formData	integer
skeleton_id	Result annotations will annotate the neuron modeled by this skeleton.	formData	integer
ignored_annotations	A list of annotation names that will be excluded from the result set.	formData	string[]

201 Created

Get annotations and who used them for a set of skeletons.

POST /{project_id}/annotations/forskeletons

Tags: annotations

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.

application/x-www-form-urlencoded

project_id		path	string
skeleton_ids	A list of skeleton IDs which are annotated by the resulting annotations.	formData	string[]

201 Created

Query annotations linked to a list of objects.

POST /{project_id}/annotations/query

Tags: 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" } }

application/x-www-form-urlencoded

project_id		path	string
object_ids	A list of object IDs for which annotations should be returned.	formData	string[]

201 Created

Query entities based on various constraints

POST /{project_id}/annotations/query-targets

Tags: annotations

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.

application/x-www-form-urlencoded

project_id		path	string
name	The name (or a part of it) of result elements.	formData	string
annotated_by	A result element was annotated by a user with this ID.	formData	integer
annotation_date_start	The earliest YYYY-MM-DD date result elements have been annotated at.	query	string
annotation_date_end	The latest YYYY-MM-DD date result elements have been annotated at.	query	string
annotated_with	A comma separated list of annotation IDs which all annotate the result elements.	formData	integer
not_annotated_with	A comma separated list of annotation IDs which don't annotate the result elements.	formData	integer
sub_annotated_with	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).	formData	integer
with_annotations	Indicate if annotations of result elements should be returned.	formData	boolean
types	Allowed result types. Multple types can be passed with multiple parameters. Defaults to 'neuron' and 'annotation'.	formData	string
sort_by	Indicates how results are sorted.	formData	string
sort_dir	Indicates sorting direction.	formData	string
range_start	The first result element index.	formData	integer
range_length	The number of results	formData	integer
annotation_reference	Whether annoation references are IDs or names, can be 'id' or 'name.	formData	string

201 Created

Get a collection of connectors.

POST /{project_id}/connectors/

Tags: connectors

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.

application/x-www-form-urlencoded

project_id	Project of connectors	path	integer
skeleton_ids	Skeletons linked to connectors	formData	string[]
tags	Require a set of tags	formData	string[]
relation_type	Relation of linked skeletons to connector.	formData	string
with_tags	If connector tags should be fetched	formData	boolean
with_partners	If partner node and link information should be fetched	formData	boolean

201 Created

Get a list of all connector nodes that intersect with the passed in

GET /{project_id}/connectors/in-bounding-box

Tags: connectors

Get a list of all connector nodes that intersect with the passed in bounding box.

application/x-www-form-urlencoded

project_id		path	string
limit	Limit the number of returned nodes.	formData	integer
minx	Minimum world space X coordinate	formData	float
miny	Minimum world space Y coordinate	formData	float
minz	Minimum world space Z coordinate	formData	float
maxx	Maximum world space X coordinate	formData	float
maxy	Maximum world space Y coordinate	formData	float
maxz	Maximum world space Z coordinate	formData	float
with_locations	Whether to return the location of each connector.	formData	float
with_links	Whether to return every individual link	formData	float
skeleton_ids	Skeletons linked to connectors	formData	string[]

200 OK

Get a list of all connector nodes that intersect with the passed in

POST /{project_id}/connectors/in-bounding-box

Tags: connectors

Get a list of all connector nodes that intersect with the passed in bounding box.

application/x-www-form-urlencoded

project_id		path	string
limit	Limit the number of returned nodes.	formData	integer
minx	Minimum world space X coordinate	formData	float
miny	Minimum world space Y coordinate	formData	float
minz	Minimum world space Z coordinate	formData	float
maxx	Maximum world space X coordinate	formData	float
maxy	Maximum world space Y coordinate	formData	float
maxz	Maximum world space Z coordinate	formData	float
with_locations	Whether to return the location of each connector.	formData	float
with_links	Whether to return every individual link	formData	float
skeleton_ids	Skeletons linked to connectors	formData	string[]

201 Created

Get connectors linked to a set of skeletons.

GET /{project_id}/connectors/links/

Tags: 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.

application/x-www-form-urlencoded

project_id		path	string
skeleton_ids	Skeletons to list connectors for	formData	string[]
relation_type	Relation of listed connector links	formData	string
with_tags	If connector tags should be fetched	formData	boolean

200 OK

Get connectors linked to a set of skeletons.

POST /{project_id}/connectors/links/

Tags: 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.

application/x-www-form-urlencoded

project_id		path	string
skeleton_ids	Skeletons to list connectors for	formData	string[]
relation_type	Relation of listed connector links	formData	string
with_tags	If connector tags should be fetched	formData	boolean

201 Created

Get a list of available connector types.

GET /{project_id}/connectors/types/

Tags: connectors

Get a list of available connector types.

Returns a list of all available connector link types in a project. Each list element consists of an object with the following fields: type, relation, relation_id.

project_id		path	string

200 OK

Return information on a treenode connector edge.

GET /{project_id}/connectors/user-info

Tags: connectors

Return information on a treenode connector edge.

Returns a JSON array with elements representing information on the matched links. They have the following form:

{ "user": ..., "creaetion_time": ..., "edition_time": ... }

Developer node: This function is called often (every connector mouseover) and should therefore be as fast as possible. Analogous to user_info for treenodes and connectors.

application/x-www-form-urlencoded

project_id	Project of connectors	formData	string[]
treenode_id	The treenode, the connector is linked to	formData	integer
connector_id	The connector, the treenode is linked to	formData	integer
relation_id	The relation ID of the link, can be used instead of relation_name	formData	integer
relation_name	The relation name of the link, can be used instead of relation_id	formData	string

200 OK

Get detailed information on a connector and its partners

GET /{project_id}/connectors/{connector_id}/

Tags: connectors

Get detailed information on a connector and its partners

project_id		path	string
connector_id		path	string

200 OK

Get all section locations for all orientations.

GET /{project_id}/interpolatable-sections/

Tags: interpolatable-sections

Get all section locations for all orientations.

project_id		path	string

200 OK

List all labels (front-end node tags) in use.

GET /{project_id}/labels/

Tags: labels

List all labels (front-end node tags) in use.

application/x-www-form-urlencoded

project_id	Project containing node of interest	formData	string

200 OK

List all labels (front-end node tags) in use alongside their IDs.

GET /{project_id}/labels/detail

Tags: labels

List all labels (front-end node tags) in use alongside their IDs.

application/x-www-form-urlencoded

project_id	Project containing node of interest	formData	string

200 OK

Get usage statistics of node labels.

GET /{project_id}/labels/stats

Tags: labels

Get usage statistics of node labels.

application/x-www-form-urlencoded

project_id	Project from which to get label stats	formData	string

200 OK

List all labels (front-end node tags) attached to a particular node.

GET /{project_id}/labels/{node_type}/{node_id}/

Tags: labels

List all labels (front-end node tags) attached to a particular node.

application/x-www-form-urlencoded

node_id	ID of node to list labels for	formData	string
node_type	Either 'connector', 'treenode' or 'location'	formData	string
project_id	Project containing node of interest	formData	string

200 OK

List available landmarks, optionally only the ones in a set of landmark

GET /{project_id}/landmarks/

Tags: landmarks

List available landmarks, optionally only the ones in a set of landmark groups.

application/x-www-form-urlencoded

project_id	Project of landmark	path	integer
with_locations	Whether to return linked locations	formData	string

200 OK

Add a new landmark. Expect at least the name as parameter.

PUT /{project_id}/landmarks/

Tags: landmarks

Add a new landmark. Expect at least the name as parameter.

application/x-www-form-urlencoded

project_id	Project of landmark	path	integer
name	Name of new landmark	formData	string

200 OK

List available landmark groups.

GET /{project_id}/landmarks/groups/

Tags: landmarks

List available landmark groups.

application/x-www-form-urlencoded

project_id	Project of landmark groups	path	integer
with_members	Whether to return group members	formData	boolean
with_locations	Whether to return linked locations	formData	string
with_names	Whether to return location with their landmark names	formData	string
with_links	Whether to return links to other groups	formData	string
with_relations	Whether to return a map of used relation IDs to their names	formData	string

200 OK

Add a new landmarkgroup. Expect at least the name as parameter.

PUT /{project_id}/landmarks/groups/

Tags: landmarks

Add a new landmarkgroup. Expect at least the name as parameter.

application/x-www-form-urlencoded

project_id	Project of landmark group	path	integer
name	Name of new landmark group	formData	string

200 OK

Import and link landmarks, landmark groups and locations.

POST /{project_id}/landmarks/groups/import

Tags: landmarks

Import and link landmarks, landmark groups and locations.

The passed in parameter is a list of two-element lists, each representing a group along with its linked landmark and locations. The group is represented by its name and the members are a list of four-element lists, containing the landmark name and the location. This results in the following format:

[[group_1_name, [[landmark_1_name, x, y, z], [landmark_2_name, x, y, z]]], ...]

Note that this parameter has to be transmitted as a JSON encoded string.

application/x-www-form-urlencoded

project_id	The project the landmark group is part of.	path	integer
data	The data to import.	formData	string
reuse_existing_groups	Whether existing groups should be reused.	formData	boolean
reuse_existing_landmarks	Whether existing landmarks should be reused.	formData	boolean
create_non_existing_groups	Whether non-existing groups should be created.	formData	boolean
create_non_existing_landmarks	Whether non-existing landmarks should be created.	formData	boolean

201 Created

Link a location group to another landmark group. If the passed in

PUT /{project_id}/landmarks/groups/links/

Tags: landmarks

Link a location group to another landmark group. If the passed in groups already are in relation to each other using the passed in relation, no new link is created. Instead, the existing link will be returned. A flag in the result indicates whether the returned object is new.

application/x-www-form-urlencoded

project_id	Project of landmark group	path	integer
group_1_id	The first landmark group, has role of subject.	formData	integer
relation_id	The relation between group 1 and 2, has role of predicate.	formData	integer
group_2_id	The first landmark group, has role of object.	formData	integer

200 OK

Delete the link between two landmark groups. Won't delete links that

DELETE /{project_id}/landmarks/groups/links/{link_id}/

Tags: landmarks

Delete the link between two landmark groups. Won't delete links that don't connect to landmark groups.

link_id	The link to delete	path	integer
project_id	Project of landmark group	path	integer

204 No Content

Create all passed in landmarks along with a set of groups in one go.

POST /{project_id}/landmarks/groups/materialize

Tags: landmarks

Create all passed in landmarks along with a set of groups in one go.

The format for the passed in landmarks is expected to be [name, x1, y1, z1, x2, y2, z2], representing a shared landmark at locations (x1, y1, z1) for group A and (x2, y2, z2) for group B.

The format for the optionally passed in links is: [group_name_1, relation_name, group_name_2] elements, representing a relation between two groups. Whether group A and B map to 1 and 2 or vice versa depends on the semantics of the relation.

application/x-www-form-urlencoded

project_id	The project to operate in.	path	integer
group_a_name	The name of landmark group A.	formData	string
group_b_name	The name of landmark group B.	formData	string
landmarks	A list of landmark definitions for group B.	formData	string
links	A list of link definitions between group A and B.	formData	string
reuse_existing_landmarks	If existing landmarks can be reused, no error will be thrown if a landmark with the same name exists alrady.	formData	string

201 Created

Get details on one particular landmarkgroup group, including its

GET /{project_id}/landmarks/groups/{landmarkgroup_id}/

Tags: landmarks

Get details on one particular landmarkgroup group, including its members.

application/x-www-form-urlencoded

landmarkgroup_id	The ID of the landmark group.	path	integer
project_id	The project the landmark group is part of.	path	integer
with_members	Whether to return group members	formData	boolean
with_locations	Whether to return linked locations	formData	string
with_names	Whether to return linked landmark names	formData	string

200 OK

Update an existing landmark group.

POST /{project_id}/landmarks/groups/{landmarkgroup_id}/

Tags: landmarks

Update an existing landmark group.

Currently, only the name and group members can be updated. Edit permissions are only needed when removing group members.

application/x-www-form-urlencoded

landmarkgroup_id		path	string
project_id	The project the landmark group is part of.	path	integer
landmark_id	The ID of the landmark group.	path	integer
name	The new name of the landmark group.	formData	string
members	The new members of the landmark group.	formData	string[]
append_members	Whether the existing members should be extended by the passed in members. No members will be removed.	formData	boolean

201 Created

Remove the link between a location and a landmark group.

DELETE /{project_id}/landmarks/groups/{landmarkgroup_id}/locations/{location_id}/

Tags: landmarks

Remove the link between a location and a landmark group.

landmarkgroup_id	The landmark group to link	path	integer
project_id	Project of landmark group	path	integer
location_id	Existing location ID	path	integer

204 No Content

Link a location to a landmark group.

PUT /{project_id}/landmarks/groups/{landmarkgroup_id}/locations/{location_id}/

Tags: landmarks

Link a location to a landmark group.

landmarkgroup_id	The landmark group to link	path	integer
project_id	Project of landmark group	path	integer
location_id	Existing location ID	path	integer

200 OK

Get a list of landmark groups that are transitively linked to the

GET /{project_id}/landmarks/groups/{landmarkgroup_id}/transitively-linked

Tags: landmarks

Get a list of landmark groups that are transitively linked to the input group with the passed in relation.

application/x-www-form-urlencoded

landmarkgroup_id	The starting landmark group	path	integer
project_id	Project of landmark groups	path	integer
relation_id	The relation a valid group link has to have	formData	integer
max_depth	(optional) Maximum number of hops from the source group. 0 to disable.	formData	integer

200 OK

Delete one particular landmark.

DELETE /{project_id}/landmarks/{landmark_id}/

Tags: landmarks

Delete one particular landmark.

landmark_id	The ID of the landmark.	path	integer
project_id	The project the landmark is part of.	path	integer

204 No Content

Get details on one particular landmark.

GET /{project_id}/landmarks/{landmark_id}/

Tags: landmarks

Get details on one particular landmark.

If locations are returned alongside the landmarks, they are all points that are linked to a particular landmark, regardless of which group the location is linked to.

application/x-www-form-urlencoded

landmark_id	The ID of the landmark.	path	integer
project_id	The project the landmark is part of.	path	integer
with_locations	Whether to return linked locations	formData	string

200 OK

Update an existing landmark.

POST /{project_id}/landmarks/{landmark_id}/

Tags: landmarks

Update an existing landmark.

Currently, only the name can be updated.

application/x-www-form-urlencoded

landmark_id	The ID of the landmark.	path	integer
project_id	The project the landmark is part of.	path	integer
name	The name of the landmark.	formData	string

201 Created

Delete the link between a location and a landmark and a group and a

DELETE /{project_id}/landmarks/{landmark_id}/groups/{group_id}/

Tags: landmarks

Delete the link between a location and a landmark and a group and a location, if and only if both exist. If the last link to a location is deleted, the location is removed as well.

group_id	The group to unlink from	path	integer
landmark_id	The landmark to unlink from	path	integer
project_id	Project of landmark group	path	integer
keep_points	Wheter only links should be deleted and points should be kept.	path	boolean

204 No Content

Add a new location or use an existing one and link it to a landmark.

PUT /{project_id}/landmarks/{landmark_id}/locations/

Tags: landmarks

Add a new location or use an existing one and link it to a landmark.

Either (x,y,z) or location_id have to be provided.

application/x-www-form-urlencoded

landmark_id	The landmark to link	path	integer
project_id	Project of landmark group	path	integer
location_id	Optional existing location ID	formData	integer
x	Optional new location X coodinate	formData	float
y	Optional new location Y coodinate	formData	float
z	Optional new location Z coodinate	formData	float

200 OK

Delete the link between a location and a landmark. If the last link

DELETE /{project_id}/landmarks/{landmark_id}/locations/{location_id}/

Tags: landmarks

Delete the link between a location and a landmark. If the last link to a location is deleted, the location is removed as well.

landmark_id	The landmark to unlink	path	integer
project_id	Project of landmark group	path	integer
location_id	The location to unlink	path	integer

204 No Content

List neurons matching filtering criteria.

GET /{project_id}/neurons/

Tags: neurons

List neurons matching filtering criteria.

The result set is the intersection of neurons matching criteria (the criteria are conjunctive) unless stated otherwise.

project_id		path	string
created_by	Filter for user ID of the neurons' creator.	query	integer
reviewed_by	Filter for user ID of the neurons' reviewer.	query	integer
from_date	Filter for neurons with nodes created after this date.	query	string
to_date	Filter for neurons with nodes created before this date.	query	string
nodecount_gt	Filter for neurons with more nodes than this threshold. Removes all other criteria.	query	integer

200 OK

Retrieve neuron IDs modeled by particular entities, eg skeletons.

POST /{project_id}/neurons/from-models

Tags: neurons

Retrieve neuron IDs modeled by particular entities, eg skeletons.

From a list of source entities (class instances), the IDs of all modeled neurons are returned. There are currently only skeletons that model neurons.

application/x-www-form-urlencoded

project_id		path	string
model_ids[]	IDs of models to find neurons for (e.g. skeleton IDs)	formData	string[]

201 Created

Rename a neuron.

POST /{project_id}/neurons/{neuron_id}/rename

Tags: neurons

Rename a neuron.

If a neuron is not locked by a user on which the current user has no permission, the name of neuron can be changed through this endpoint. Neuron names are currently not allowed to contain pipe characters ("|").

application/x-www-form-urlencoded

neuron_id	ID of neuron to rename	path	integer
project_id		path	string
name	New name of the neuron	formData	string

201 Created

Retrieve all nodes intersecting a bounding box

POST /{project_id}/nodes/

Tags: nodes

Retrieve all nodes intersecting a bounding box

The intersection bounding box is defined in terms of its minimum and maximum project space coordinates. The number of returned nodes can be limited to constrain query execution time. Optionally, lists of treenodes and connector IDs can be provided to make sure they are included in the result set, regardless of intersection.

Returned is an array with five entries, plus optionally a sixth one

[[treenodes], [connectors], {labels}, node_limit_reached, {relation_map}, {exstraNodes}]

The list of treenodes has elements of this form:

[id, parent_id, location_x, location_y, location_z, confidence, radius, skeleton_id, edition_time, user_id]

The list connectors has elements of this form:

[id, location_x, location_y, location_z, confidence, edition_time, user_id, [partners]]

The partners arrary represents linked partner nodes, each one represented like this:

[treenode_id, relation_id, link_confidence, link_edition_time, link_id]

If labels are returned, they are represented as an object of the following form, with the labels just being simple strings:

{treenode_id: [labels]}

The fourth top level entry, node_limit_reached, is a boolean that represents if there are more nodes available than the ones returned.

With the last top level element returned the present connector linked relations are mapped to their textural representations:

{relation_id: relation_name}

application/x-www-form-urlencoded

project_id		path	string
treenode_ids	Whether linked connectors should be returned.	formData	string[]
connector_ids	Whether tags should be returned.	formData	string[]
limit	Limit the number of returned nodes.	formData	integer
left	Minimum world space X coordinate	formData	float
top	Minimum world space Y coordinate	formData	float
z1	Minimum world space Z coordinate	formData	float
right	Maximum world space X coordinate	formData	float
bottom	Maximum world space Y coordinate	formData	float
z2	Maximum world space Z coordinate	formData	float
format	Either "json" (default) or "msgpack", optional.	formData	string
with_relation_map	Whether an ID to name mapping for the used relations should be included and which extent it should have.	formData	string
n_largest_skeletons_limit	Maximum number of the largest skeletons in view	formData	integer
n_last_edited_skeletons_limit	Maximum number of most recently edited skeletons.	formData	integer
hidden_last_editor_id	No nodes edited last by this user will be retuned.	formData	integer

201 Created

List nodes with labels matching a query, ordered by distance.

POST /{project_id}/nodes/find-labels

Tags: nodes

List nodes with labels matching a query, ordered by distance.

Find nodes with labels (front-end node tags) matching a regular expression, sort them by ascending distance from a reference location, and return the result. Returns at most 50 nodes.

application/x-www-form-urlencoded

project_id		path	string
x	X coordinate of the distance reference in project space.	formData	number
y	Y coordinate of the distance reference in project space.	formData	number
z	Z coordinate of the distance reference in project space.	formData	number
label_regex	Regular expression query to match labels	formData	string

201 Created

Get locations for a particular set of nodes in a project.

POST /{project_id}/nodes/location

Tags: nodes

Get locations for a particular set of nodes in a project.

A list of lists is returned. Each inner list represents one location and hast the following format: [id, x, y, z].

application/x-www-form-urlencoded

project_id		path	string
node_ids	A list of node IDs to get the location for	formData	string[]

201 Created

List all available point clouds or optionally a sub set.

GET /{project_id}/pointclouds/

Tags: pointclouds

List all available point clouds or optionally a sub set.

application/x-www-form-urlencoded

project_id	Project of the returned point clouds	path	integer
simple	Wheter or not only ID and name should be returned	formData	bool
with_images	Wheter linked images should returned as well.	formData	bool
with_points	Wheter linked points should returned as well.	formData	bool
sample_ratio	Number in [0,1] to optionally sample point cloud	formData	number
pointcloud_ids	A list of point cloud IDs to which the query is constrained.	path	string[]

200 OK

List all available point clouds or optionally a sub set.

POST /{project_id}/pointclouds/

Tags: pointclouds

List all available point clouds or optionally a sub set.

application/x-www-form-urlencoded

project_id	Project of the returned point clouds	path	integer
simple	Wheter or not only ID and name should be returned	formData	bool
with_images	Wheter linked images should returned as well.	formData	bool
with_points	Wheter linked points should returned as well.	formData	bool
sample_ratio	Number in [0,1] to optionally sample point cloud	formData	number
pointcloud_ids	A list of point cloud IDs to which the query is constrained.	path	string[]

201 Created

Create a new pointcloud by providing.

PUT /{project_id}/pointclouds/

Tags: pointclouds

Create a new pointcloud by providing.

application/x-www-form-urlencoded

project_id	Project of the new point cloud	path	integer
name	Name of the new point cloud	formData	string
description	Description of the new point cloud	formData	string
points	Points of point cloud in project space. Can be a stringified JSON array.	formData	string[]
group_id	A group for which this point cloud will be visible exclusivly.	formData	integer

200 OK

Delete a point cloud.

DELETE /{project_id}/pointclouds/{pointcloud_id}/

Tags: pointclouds

Delete a point cloud.

project_id		path	string
pointcloud_id		path	string

204 No Content

Return a point cloud.

GET /{project_id}/pointclouds/{pointcloud_id}/

Tags: pointclouds

Return a point cloud. parameters:

• name: project_id description: Project of the returned point cloud type: integer paramType: path required: true
• name: simple description: Wheter or not only ID and name should be returned type: bool paramType: form required: false defaultValue: false
• name: with_images description: Wheter linked images should returned as well. type: bool paramType: form required: false defaultValue: false
• name: with_points description: Wheter linked points should returned as well. type: bool paramType: form required: false defaultValue: false

project_id		path	string
pointcloud_id		path	string

200 OK

Return a point cloud.

GET /{project_id}/pointclouds/{pointcloud_id}/images/{image_id}/

Tags: pointclouds

Return a point cloud. parameters:

• name: project_id description: Project of the returned point cloud image type: integer paramType: path required: true
• name: pointcloud_id description: Point cloud this image is linked to type: integer paramType: path required: true
• name: image_id description: The image to load type: integer paramType: path required: true

image_id		path	string
project_id		path	string
pointcloud_id		path	string

200 OK

List points, optionally constrained by various properties.

GET /{project_id}/points/

Tags: points

List points, optionally constrained by various properties.

project_id	Project of points	path	integer

200 OK

Add a new point. Expect at least the location as parameters.

PUT /{project_id}/points/

Tags: points

Add a new point. Expect at least the location as parameters.

application/x-www-form-urlencoded

project_id	Project of points	path	integer
location_x	X coordinate	formData	float
location_y	Y coordinate	formData	float
location_z	Z coordinate	formData	float
radius	Optional radius	formData	float
confidence	Optional confidence in [0,5]	formData	integer

200 OK

Delete one particular point.

DELETE /{project_id}/points/{point_id}/

Tags: points

Delete one particular point.

point_id	ID of point	path	integer
project_id	Project point is part of	path	integer

204 No Content

Return details on one particular point.

GET /{project_id}/points/{point_id}/

Tags: points

Return details on one particular point.

point_id	ID of point	path	integer
project_id	Project point is part of	path	integer

200 OK

Update one particular point.

POST /{project_id}/points/{point_id}/

Tags: points

Update one particular point.

Requires at least one field to change.

application/x-www-form-urlencoded

point_id	ID of point	path	integer
project_id	Project point is part of	path	integer
location_x	X coordinate	formData	float
location_y	Y coordinate	formData	float
location_z	Z coordinate	formData	float
radius	Optional radius	formData	float
confidence	Optional confidence in [0,5]	formData	integer

201 Created

Get a collection of available samplers.

GET /{project_id}/samplers/

Tags: samplers

Get a collection of available samplers.

Optionally, the "skeleton_ids" parameter can provide a list of skeleton IDs. If this is the case, only samplers for the respective skeletons are returned.

application/x-www-form-urlencoded

project_id		path	string
skeleton_ids	Optional skeleton IDs to constrain result set to.	formData	integer
with_domains	Optional flag to include all domains of all result sampler results.	formData	boolean
with_intervals	Optional flag to include all intervals of all domains. Implies with_domains.	formData	boolean

200 OK

Create a new sampler for a skeleton.

POST /{project_id}/samplers/add

Tags: samplers

Create a new sampler for a skeleton.

application/x-www-form-urlencoded

project_id		path	string
skeleton_id	Skeleton this sampelr is for	formData	integer
interval_length	Length of a intervals with domains (nm).	formData	integer
interval_error	Maximum allowed error for a single interval.	formData	float
review_required	Whether reviews should be enforced in this sampler	formData	boolean
create_interval_boundaries	Whether new nodes for interval boundaries should be created.	formData	boolean
leaf_segment_handling	How leaf segments should be handled, can be 'ignore', 'merge' or 'short-interval'.	formData	string
merge_limit	A leaf handling option for merge-or-create mode. A value between 0 and 1 representing the interval length ratio up to which a merge is allowed.	formData	string

201 Created

Get a list of connectors that already have a state associated with them.

GET /{project_id}/samplers/connectors/

Tags: samplers

Get a list of connectors that already have a state associated with them.

If a connector is not part of this list it is implicetely assumed to be in an "untouched" state.

application/x-www-form-urlencoded

project_id		path	string
interval_id	The interval all results should be part of	formData	integer
connector_id	The connector to get sampler information for	formData	integer
state_id	The state all result sets have to have.	formData	integer

200 OK

Get a list of all available connectors states and their IDs.

GET /{project_id}/samplers/connectors/states/

Tags: samplers

Get a list of all available connectors states and their IDs.

project_id		path	string

200 OK

Get a list of all available interval states.

GET /{project_id}/samplers/domains/intervals/states/

Tags: samplers

Get a list of all available interval states.

project_id		path	string

200 OK

Set state of sampler connector

POST /{project_id}/samplers/domains/intervals/{interval_id}/connectors/{connector_id}/set-state

Tags: samplers

Set state of sampler connector

application/x-www-form-urlencoded

interval_id	Interval the connector is part of	formData	integer
project_id		path	string
connector_id	Connector to set state of	formData	integer
state_id	The new state	formData	integer

201 Created

Get details on a particular interval.

GET /{project_id}/samplers/domains/intervals/{interval_id}/details

Tags: samplers

Get details on a particular interval.

interval_id		path	string
project_id		path	string

200 OK

Set state of an interval.

POST /{project_id}/samplers/domains/intervals/{interval_id}/set-state

Tags: samplers

Set state of an interval.

application/x-www-form-urlencoded

interval_id	Interval to update state of	formData	integer
project_id		path	string

201 Created

Get a list of all available domain types.

GET /{project_id}/samplers/domains/types/

Tags: samplers

Get a list of all available domain types.

project_id		path	string

200 OK

Get details on a particular domain.

GET /{project_id}/samplers/domains/{domain_id}/details

Tags: samplers

Get details on a particular domain.

domain_id		path	string
project_id		path	string

200 OK

Get a collection of available sampler domains intervals.

GET /{project_id}/samplers/domains/{domain_id}/intervals/

Tags: samplers

Get a collection of available sampler domains intervals.

application/x-www-form-urlencoded

domain_id	Domain to list intervals for	formData	integer
project_id		path	string

200 OK

Create all intervals in a particular domain.

POST /{project_id}/samplers/domains/{domain_id}/intervals/add-all

Tags: samplers

Create all intervals in a particular domain.

domain_id		path	string
project_id		path	string

201 Created

Get a list of all available sampler states and their IDs.

GET /{project_id}/samplers/states/

Tags: samplers

Get a list of all available sampler states and their IDs.

project_id		path	string

200 OK

Get details on a particular sampler.

GET /{project_id}/samplers/{sampler_id}/

Tags: samplers

Get details on a particular sampler.

application/x-www-form-urlencoded

sampler_id	The sampler to return.	path	integer
project_id	The project to operate in.	path	integer
with_domains	Optional flag to include all domains of all result sampler results.	formData	boolean
with_intervals	Optional flag to include all intervals of all domains. Implies with_domains.	formData	boolean

200 OK

Set fields of a particular sampler.

POST /{project_id}/samplers/{sampler_id}/

Tags: samplers

Set fields of a particular sampler.

application/x-www-form-urlencoded

sampler_id	The sampler to return.	path	integer
project_id	The project to operate in.	path	integer
leaf_handling_mode	Optional flag to include all domains of all result sampler results.	formData	boolean

201 Created

Delete a sampler if permissions allow it.

POST /{project_id}/samplers/{sampler_id}/delete

Tags: samplers

Delete a sampler if permissions allow it.

If the sampler was created with allowing the creation of new boundary nodes, these nodes are removed by default if they have not been modified since their insertion. This can optionally be disabled using the

<delete_created_nodes> parameter.

application/x-www-form-urlencoded

sampler_id		path	string
project_id		path	string
delete_created_nodes	Optional flag to disable automatic removal of untouched nodes created for this sampler's intervals.	formData	boolean

201 Created

Get a collection of available sampler domains.

GET /{project_id}/samplers/{sampler_id}/domains/

Tags: samplers

Get a collection of available sampler domains.

application/x-www-form-urlencoded

sampler_id	Sampler to list domains for	formData	integer
project_id		path	string

200 OK

Create a new domain for a sampler.

POST /{project_id}/samplers/{sampler_id}/domains/add

Tags: samplers

Create a new domain for a sampler.

application/x-www-form-urlencoded

sampler_id	Sampeler the new domain is part of	formData	integer
project_id		path	string
domain_type_id	The type of the new domain	formData	integer
start_node_id	Start node of domain	formData	integer
end_node_ids	A list of all end nodes for the new domain	formData	string[]
parent_interval_id	Optional parent inerval ID.	formData	integer

201 Created

Create a new domain for a sampler.

POST /{project_id}/samplers/{sampler_id}/domains/add-all

Tags: samplers

Create a new domain for a sampler.

sampler_id		path	string
project_id		path	string

201 Created

List all available NBLAST configurations.

GET /{project_id}/similarity/configs/

Tags: similarity

List all available NBLAST configurations.

application/x-www-form-urlencoded

project_id	Project of the returned configurations	path	integer
simple	Wheter or not only ID and name should be returned	formData	bool

200 OK

Create a new similarity/NBLAST configuration either by providing

PUT /{project_id}/similarity/configs/

Tags: similarity

Create a new similarity/NBLAST configuration either by providing parameters to have the back-end queue a job or by providing the complete matrix data.

project_id		path	string

200 OK

Delete a NBLAST configuration.

DELETE /{project_id}/similarity/configs/{config_id}/

Tags: similarity

Delete a NBLAST configuration.

project_id		path	string
config_id		path	string

204 No Content

Delete a NBLAST configuration.

GET /{project_id}/similarity/configs/{config_id}/

Tags: similarity

Delete a NBLAST configuration.

project_id		path	string
config_id		path	string

200 OK

List all available NBLAST similarity tasks.

GET /{project_id}/similarity/queries/

Tags: similarity

List all available NBLAST similarity tasks.

application/x-www-form-urlencoded

project_id	Project of the returned similarities	path	integer
config_id	Return only similarities linked to this config	formData	integer

200 OK

Compare two sets of objects (skeletons or point clouds) and return an

POST /{project_id}/similarity/queries/similarity

Tags: similarity

Compare two sets of objects (skeletons or point clouds) and return an NBLAST scoring based on an existing NBLAST configuration.

application/x-www-form-urlencoded

project_id	Project to operate in	path	integer
config_id	ID of the new NBLAST configuration to use	formData	integer
query_ids	Set of objects (skeletons or point clouds) to query similarity for.	formData	string[]
target_ids	Set of objects (skeletons or point clouds) or point clouds to compare against.	formData	string[]
target_type	Type of target objects, 'skeleton' or 'pointcloud'.	formData	string
name	Name for the similarity lookup task	formData	string
normalized	Whether and how scores should be normalized.	formData	string
use_alpha	Whether to consider local directions in the similarity computation	formData	boolean
query_type_id	Type of query data	formData	string
target_type_id	Type of query data	formData	string
query_meta	Extra data for the selected query type. A JSON encoded string is expected.	formData	string
target_meta	Extra data for the selected target type. A JSON encoded string is expected.	formData	string
remove_target_duplicates	Remove all target objects that appear also in the query.	formData	boolean
simplify	Whether or not to simplify neurons and remove parts below a specified branch point level.	formData	boolean
required_branches	The required branch levels if neurons should be simplified.	formData	boolean

201 Created

Delete a NBLAST similarity task.

DELETE /{project_id}/similarity/queries/{similarity_id}/

Tags: similarity

Delete a NBLAST similarity task.

project_id		path	string
similarity_id		path	string

204 No Content

Get a particular similarity query result.

GET /{project_id}/similarity/queries/{similarity_id}/

Tags: similarity

Get a particular similarity query result.

project_id		path	string
similarity_id		path	string

200 OK

Return a sparse connectivity matrix representation for the given skeleton

POST /{project_id}/skeleton/connectivity_matrix

Tags: skeleton

Return a sparse connectivity matrix representation for the given skeleton IDs. The returned dictionary has a key for each row skeleton having outgoing connections to one or more column skeletons. Each entry stores a dictionary that maps the connection partners to the individual outgoing synapse counts.

application/x-www-form-urlencoded

project_id	Project of skeletons	path	integer
rows	IDs of row skeletons	formData	string[]
columns	IDs of column skeletons	formData	string[]
with_locations	Whether or not to return locations of connectors	formData	boolean

201 Created

List skeletons matching filtering criteria.

GET /{project_id}/skeletons/

Tags: skeletons

List skeletons matching filtering criteria.

The result set is the intersection of skeletons matching criteria (the criteria are conjunctive) unless stated otherwise.

project_id		path	string
created_by	Filter for user ID of the skeletons' creator.	query	integer
reviewed_by	Filter for user ID of the skeletons' reviewer.	query	integer
from_date	Filter for skeletons with nodes created after this date.	query	string
to_date	Filter for skeletons with nodes created before this date.	query	string
nodecount_gt	Filter for skeletons with more nodes than this threshold. Removes all other criteria.	query	integer

200 OK

Get the cable length of a set of skeletons.

POST /{project_id}/skeletons/cable-length

Tags: skeletons

Get the cable length of a set of skeletons.

Returns a mapping from skeleton ID to cable length.

application/x-www-form-urlencoded

project_id	Project of landmark	path	integer
skeleton_ids[]	IDs of the skeletons whose partners to find	formData	string[]

201 Created

Get a compact treenode representation of a list of skeletons, optionally

POST /{project_id}/skeletons/compact-detail

Tags: skeletons

Get a compact treenode representation of a list of skeletons, optionally with the history of individual nodes and connectors.

Returns, in JSON, [[nodes], [connectors], {nodeID: [tags]}], with connectors and tags being empty when 0 == with_connectors and 0 == with_tags, respectively.

Each element in the [nodes] array has the following form:

[skeleton_id, id, parent_id, user_id, location_x, location_y, location_z, radius, confidence].

Each element in the [connectors] array has the following form, with the third element representing the connector link as 0 = presynaptic, 1 = postsynaptic, 2 = gap junction, -1 = other:

[treenode_id, connector_id, 0|1|2|-1, location_x, location_y, location_z]

If history data is requested, each row contains a validity interval. Note that for the live table entry (the currently valid version), there are special semantics for this interval: The upper bound is older than or the same as the lower bound. This is done to encode the information of this row being the most recent version and including the original creation time at the same time, plus it requires less queries on the back-end to retireve data. This requires the client to do slightly more work, but unfortunately the original creation time is needed for data that was created without history tables enabled.

application/x-www-form-urlencoded

project_id		path	string
		formData	string
with_connectors	Whether linked connectors should be returned.	formData	boolean
with_tags	Whether tags should be returned.	formData	boolean
with_history	Whether history information should be returned for each treenode and connector.	formData	boolean
with_merge_history	Whether the history of arbors merged into the requested skeleton should be returned. Only used if history is returned.	formData	boolean
with_reviews	Whether a node index should be returned that maps node IDs to the list of reviews done on them, respects history parameter.	formData	boolean
with_annotations	Whether the list of linked annotations should be returned. If history should be returned, returns all link versions.	formData	boolean
with_user_info	Whether all result elements should contain also the creator ID.	formData	boolean

201 Created

Get a synaptic graph between skeletons compartmentalized by confidence.

POST /{project_id}/skeletons/confidence-compartment-subgraph

Tags: skeletons

Get a synaptic graph between skeletons compartmentalized by confidence.

Given a set of skeletons, retrieve presynaptic-to-postsynaptic edges between them, annotated with count. If a confidence threshold is supplied, compartmentalize the skeletons at edges in the arbor below that threshold and report connectivity based on these compartments.

When skeletons are split into compartments, nodes in the graph take an string ID like {skeleton_id}_{compartment #}.

application/x-www-form-urlencoded

project_id		path	string
skeleton_ids[]	IDs of the skeletons to graph	formData	string[]
confidence_threshold	Confidence value below which to segregate compartments	formData	integer
bandwidth	Bandwidth in nanometers	formData	number
cable_spread	Cable spread in nanometers	formData	number
expand[]	IDs of the skeletons to expand	formData	string[]
link_types[]	IDs of link types to respect	formData	string[]

201 Created

Retrieve a list of down/up-stream partners of a set of skeletons.

POST /{project_id}/skeletons/connectivity

Tags: skeletons

Retrieve a list of down/up-stream partners of a set of skeletons.

From a queried set of source skeletons, find all upstream and downstream partners, the number of synapses between each source and each partner, and a list of reviewers for each partner set. Confidence distributions for each synapse count are included. Optionally find only those partners that are common between the source skeleton set.

application/x-www-form-urlencoded

project_id		path	string
source_skeleton_ids[]	IDs of the skeletons whose partners to find	formData	string[]
boolean_op	Whether to find partners of any source skeleton ("OR") or partners common to all source skeletons ("AND")	formData	string
with_nodes	Whether to return detailed connectivity information that includes partner sites.	formData	voolean
link_types,	A list of allowed link types: incoming, outgoing, abutting, gapjunction, tightjunction, desmosome, attachment, close_object.	formData	string[]

201 Created

Get the number of synapses per type for r a set of skeletons.

GET /{project_id}/skeletons/connectivity-counts

Tags: skeletons

Get the number of synapses per type for r a set of skeletons.

Returns an object with to fields. The first, connectivity, is a mapping from skeleton ID to objects that map a relation ID to connectivity count for that particular relation. The second field of the returned object, relations, maps relation IDs used in the first field to relation names.

application/x-www-form-urlencoded

project_id	Project of work in	path	integer
count_partner_links	Whether to count partner links or links to a connector.	path	boolean
source_relations[]	A list of pre-connector relations that have to be used	formData	string[]
target_relations[]	A list of post-connector relations that have to be used	formData	string[]
skeleton_ids[]	IDs of the skeletons whose partners to count	formData	string[]

200 OK

Get the number of synapses per type for r a set of skeletons.

POST /{project_id}/skeletons/connectivity-counts

Tags: skeletons

Get the number of synapses per type for r a set of skeletons.

Returns an object with to fields. The first, connectivity, is a mapping from skeleton ID to objects that map a relation ID to connectivity count for that particular relation. The second field of the returned object, relations, maps relation IDs used in the first field to relation names.

application/x-www-form-urlencoded

project_id	Project of work in	path	integer
count_partner_links	Whether to count partner links or links to a connector.	path	boolean
source_relations[]	A list of pre-connector relations that have to be used	formData	string[]
target_relations[]	A list of post-connector relations that have to be used	formData	string[]
skeleton_ids[]	IDs of the skeletons whose partners to count	formData	string[]

201 Created

Return a CSV file that represents the connectivity matrix of a set of row

POST /{project_id}/skeletons/connectivity_matrix/csv

Tags: skeletons

Return a CSV file that represents the connectivity matrix of a set of row skeletons and a set of column skeletons.

application/x-www-form-urlencoded

project_id	Project of skeletons	path	integer
rows	IDs of row skeletons	formData	string[]
columns	IDs of column skeletons	formData	string[]

201 Created

Import a neuron modeled by a skeleton from an uploaded file.

POST /{project_id}/skeletons/import

Tags: skeletons

Import a neuron modeled by a skeleton from an uploaded file.

Currently only SWC representation is supported.

application/x-www-form-urlencoded

A skeleton representation file to import.

project_id		path	string
neuron_id	If specified, the imported skeleton will model this existing neuron.	formData	integer
name	If specified, the name of a new neuron will be set to this.	formData	string

201 Created

Get a list of all skeletons that intersect with the passed in bounding

GET /{project_id}/skeletons/in-bounding-box

Tags: skeletons

Get a list of all skeletons that intersect with the passed in bounding box. Optionally, only a subsed of passed in skeletons can be tested against.

application/x-www-form-urlencoded

project_id		path	string
limit	Limit the number of returned nodes.	formData	integer
minx	Minimum world space X coordinate	formData	float
miny	Minimum world space Y coordinate	formData	float
minz	Minimum world space Z coordinate	formData	float
maxx	Maximum world space X coordinate	formData	float
maxy	Maximum world space Y coordinate	formData	float
maxz	Maximum world space Z coordinate	formData	float
min_nodes	A minimum number of nodes per result skeleton	formData	float
min_cable	A minimum number of cable length per result skeleton	formData	float
volume_id	Alternative to manual bounding box definition. The bounding box of the volume is used.	formData	integer
skeleton_ids	An optional list of skeleton IDs that should only be tested againt. If used, the result will only contain skeletons of this set.	formData	string[]

200 OK

Get a list of all skeletons that intersect with the passed in bounding

POST /{project_id}/skeletons/in-bounding-box

Tags: skeletons

Get a list of all skeletons that intersect with the passed in bounding box. Optionally, only a subsed of passed in skeletons can be tested against.

application/x-www-form-urlencoded

project_id		path	string
limit	Limit the number of returned nodes.	formData	integer
minx	Minimum world space X coordinate	formData	float
miny	Minimum world space Y coordinate	formData	float
minz	Minimum world space Z coordinate	formData	float
maxx	Maximum world space X coordinate	formData	float
maxy	Maximum world space Y coordinate	formData	float
maxz	Maximum world space Z coordinate	formData	float
min_nodes	A minimum number of nodes per result skeleton	formData	float
min_cable	A minimum number of cable length per result skeleton	formData	float
volume_id	Alternative to manual bounding box definition. The bounding box of the volume is used.	formData	integer
skeleton_ids	An optional list of skeleton IDs that should only be tested againt. If used, the result will only contain skeletons of this set.	formData	string[]

201 Created

Return relationship between label IDs and skeleton IDs

GET /{project_id}/skeletons/node-labels

Tags: skeletons

Return relationship between label IDs and skeleton IDs

application/x-www-form-urlencoded

project_id		path	string
label_ids[]	IDs of the labels to find skeletons associated with	formData	string[]
label_names[]	Alternative to label_ids to pass in a list label names.	formData	string[]

200 OK

Return relationship between label IDs and skeleton IDs

POST /{project_id}/skeletons/node-labels

Tags: skeletons

Return relationship between label IDs and skeleton IDs

application/x-www-form-urlencoded

project_id		path	string
label_ids[]	IDs of the labels to find skeletons associated with	formData	string[]
label_names[]	Alternative to label_ids to pass in a list label names.	formData	string[]

201 Created

Retrieve the review status for a collection of skeletons.

POST /{project_id}/skeletons/review-status

Tags: skeletons

Retrieve the review status for a collection of skeletons.

The review status for each skeleton in the request is a tuple of total nodes and number of reviewed nodes (integers). The reviews of only certain users or a reviewer team may be counted instead of all reviews.

application/x-www-form-urlencoded

project_id		path	string
skeleton_ids[]	IDs of the skeletons to retrieve.	formData	string[]
whitelist	ID of the user whose reviewer team to use to filter reviews (exclusive to user_ids)	formData	integer
user_ids[]	IDs of the users whose reviews should be counted (exclusive to whitelist)	formData	string[]

201 Created

Get the number of samplers associated with each skeleton in the passed in

POST /{project_id}/skeletons/sampler-count

Tags: skeletons

Get the number of samplers associated with each skeleton in the passed in last.

project_id	Project of skeleton	path	integer
skeleton_ids	IDs of the skeleton to get the sampler count for.	path	string[]

201 Created

Find skeletons within a given L-infinity distance of a treenode.

POST /{project_id}/skeletons/within-spatial-distance

Tags: skeletons

Find skeletons within a given L-infinity distance of a treenode.

Returns at most 100 results.

application/x-www-form-urlencoded

project_id		path	string
treenode_id	ID of the origin treenode to search around	formData	integer
distance	L-infinity distance in nanometers within which to search	formData	integer
size_mode	Whether to return skeletons with only one node in the search area (1) or more than one node in the search area (0).	formData	integer

201 Created

Get the cable length for a skeleton

GET /{project_id}/skeletons/{skeleton_id}/cable-length

Tags: skeletons

Get the cable length for a skeleton

skeleton_id	IDs of the skeleton to get the cable length for	path	integer
project_id	Project of landmark	path	integer

200 OK

Get a compact treenode representation of a skeleton, optionally with the

GET /{project_id}/skeletons/{skeleton_id}/compact-detail

Tags: skeletons

Get a compact treenode representation of a skeleton, optionally with the history of individual nodes and connectors.

Returns, in JSON, [[nodes], [connectors], {nodeID: [tags]}], with connectors and tags being empty when 0 == with_connectors and 0 == with_tags, respectively.

Each element in the [nodes] array has the following form:

[id, parent_id, user_id, location_x, location_y, location_z, radius, confidence].

Each element in the [connectors] array has the following form, with the third element representing the connector link as 0 = presynaptic, 1 = postsynaptic, 2 = gap junction, -1 = other:

[treenode_id, connector_id, 0|1|2|-1, location_x, location_y, location_z]

If history data is requested, each row contains a validity interval. Note that for the live table entry (the currently valid version), there are special semantics for this interval: The upper bound is older than or the same as the lower bound. This is done to encode the information of this row being the most recent version and including the original creation time at the same time, plus it requires less queries on the back-end to retireve data. This requires the client to do slightly more work, but unfortunately the original creation time is needed for data that was created without history tables enabled.

application/x-www-form-urlencoded

skeleton_id		path	string
project_id		path	string
with_connectors	Whether linked connectors should be returned.	formData	boolean
with_tags	Whether tags should be returned.	formData	boolean
with_history	Whether history information should be returned for each treenode and connector.	formData	boolean
with_merge_history	Whether the history of arbors merged into the requested skeleton should be returned. Only used if history is returned.	formData	boolean
with_reviews	Whether a node index should be returned that maps node IDs to the list of reviews done on them, respects history parameter.	formData	boolean
with_annotations	Whether the list of linked annotations should be returned. If history should be returned, returns all link versions.	formData	boolean
with_user_info	Whether all result elements should contain also the creator ID.	formData	boolean
ordered	Whether result skeletons should be ordered by ID.	formData	boolean

200 OK

List nodes in a skeleton with labels matching a query.

POST /{project_id}/skeletons/{skeleton_id}/find-labels

Tags: skeletons

List nodes in a skeleton with labels matching a query.

Find all nodes in this skeleton with labels (front-end node tags) matching a regular expression, sort them by ascending path distance from a treenode in the skeleton, and return the result.

application/x-www-form-urlencoded

skeleton_id		path	string
project_id		path	string
treenode_id	ID of the origin treenode for path length distances	formData	integer
label_regex	Regular expression query to match labels	formData	string

201 Created

Export a morphology-only skeleton in neuroglancer's binary format.

GET /{project_id}/skeletons/{skeleton_id}/neuroglancer

Tags: skeletons

Export a morphology-only skeleton in neuroglancer's binary format.

skeleton_id		path	string
project_id		path	string

200 OK

Get information on a skeleton's treenodes, reviews and labels.

GET /{project_id}/skeletons/{skeleton_id}/node-overview

Tags: skeletons

Get information on a skeleton's treenodes, reviews and labels.

skeleton_id	The skeleton to get information on	path	integer
project_id	The project to operate in	path	integer

200 OK

List open leaf nodes in a skeleton.

POST /{project_id}/skeletons/{skeleton_id}/open-leaves

Tags: skeletons

List open leaf nodes in a skeleton.

Return a list of the ID and location of open leaf nodes in a skeleton, their path length distance to the specified treenode, and their creation time.

Leaves are considered open if they are not tagged with a tag matching a particular regex.

.. note:: This endpoint is used interactively by the client so performance is critical.

application/x-www-form-urlencoded

skeleton_id		path	string
project_id		path	string
treenode_id	ID of the origin treenode for path length distances	formData	integer

201 Created

Export skeleton as a set of segments with per-node review information.

POST /{project_id}/skeletons/{skeleton_id}/review

Tags: skeletons

Export skeleton as a set of segments with per-node review information.

Export the skeleton as a list of segments of non-branching node paths, with detailed information on reviewers and review times for each node.

application/x-www-form-urlencoded

skeleton_id		path	string
project_id		path	string
subarbor_node_id	If provided, only the subarbor starting at this treenode is returned.	formData	integer

201 Created

Retrieve ID and location of the skeleton's root treenode.

GET /{project_id}/skeletons/{skeleton_id}/root

Tags: skeletons

Retrieve ID and location of the skeleton's root treenode.

skeleton_id		path	string
project_id		path	string

200 OK

Get the number of samplers associated with this skeleton.

GET /{project_id}/skeletons/{skeleton_id}/sampler-count

Tags: skeletons

Get the number of samplers associated with this skeleton.

skeleton_id	ID of the skeleton to get the sampler count for.	path	integer
project_id	Project of skeleton	path	integer

200 OK

Get the largest skeletons based on cable length.

GET /{project_id}/stats/cable-length

Tags: stats

Get the largest skeletons based on cable length.

application/x-www-form-urlencoded

project_id		path	string
n_skeletoons	How many skeletons should be returned	formData	integer

200 OK

Get the total number of edited nodes per user.

GET /{project_id}/stats/editor

Tags: stats

Get the total number of edited nodes per user.

project_id		path	string

200 OK

Get the total number of created nodes per user.

GET /{project_id}/stats/nodecount

Tags: stats

Get the total number of created nodes per user.

application/x-www-form-urlencoded

project_id		path	string
with_imports	Whether data added through imports should be respected.	formData	boolean

200 OK

Get per user contribution statistics

GET /{project_id}/stats/user-history

Tags: stats

Get per user contribution statistics

A date range can be provided to limit the scope of the returned statiscis. By default, the statistics for the last ten days is returned. The returned data includes created cable length, the number of created synaptic connections and the number of reviews made, per day and user.

application/x-www-form-urlencoded

project_id		path	string
start_date	If provided (YYYY-MM-DD), only statistics from this day on are returned (inclusive).	formData	string
end_date	If provided (YYYY-MM-DD), only statistics to this day on are returned (inclusive).	formData	string
time_zone	Optional time zone for the date range, e.g. "US/Eastern"	formData	string

200 OK

Get a collection of all available transactions in the passed in project.

GET /{project_id}/transactions/

Tags: transactions

Get a collection of all available transactions in the passed in project.

application/x-www-form-urlencoded

project_id		path	string
range_start	The first result element index.	formData	integer
range_length	The maximum number result elements.	formData	integer

200 OK

Try to associate a location in the passed in project for a particular

GET /{project_id}/transactions/location

Tags: transactions

Try to associate a location in the passed in project for a particular transaction.

application/x-www-form-urlencoded

project_id		path	string
transaction_id	Transaction ID in question	formData	integer
execution_time	Execution time of the transaction	formData	string
label	Optional label of the transaction to avoid extra lookup	formData	string

200 OK

Retrieve node information in a compact form. A list of elements of the

POST /{project_id}/treenodes/compact-detail

Tags: treenodes

Retrieve node information in a compact form. A list of elements of the following form is returned:

[ID, parent ID, x, y, z, confidence, radius, skeleton_id, edition_time, user_id]

The returned edition time is an epoch number.

application/x-www-form-urlencoded

project_id	Project to work in	formData	string
treenode_ids	A list of treeonde IDs to return information on	formData	string
label_ids	A list of label IDs that must be linked to result treenodes. Alternative to explicit treenode IDs and label names.	formData	string
label_names	A list of label names that must be linked to result treenodes. Alternative to explicit treenode IDs and label IDs	formData	string
skeleton_ids	A list of skeleton IDs that result skeletons have to be part of.	formData	string

201 Created

Retrieve node information in a compact form. A list of the following form

GET /{project_id}/treenodes/{treenode_id}/compact-detail

Tags: treenodes

Retrieve node information in a compact form. A list of the following form is returned:

[ID, parent ID, x, y, z, confidence, radius, skeleton_id, edition_time, user_id]

The returned edition time is an epoch number.

project_id		path	string
treenode_id		path	string

200 OK

Update confidence of edge between a node to either its parent or its

POST /{project_id}/treenodes/{treenode_id}/confidence

Tags: treenodes

Update confidence of edge between a node to either its parent or its connectors.

The connection between a node and its parent or the connectors it is linked to can be rated with a confidence value in the range 1-5. If connector links should be updated, one can limit the affected connections to a specific connector. Returned is an object, mapping updated partners to their old confidences.

application/x-www-form-urlencoded

project_id		path	string
treenode_id		path	string
new_confidence	New confidence, value in range 1-5	formData	integer
to_connector	Whether all linked connectors instead of parent should be updated	formData	boolean
partner_ids	Limit update to a set of connectors if to_connector is true	formData	string[]
partner_confidences	Set different confidences to connectors in <partner_ids>	formData	string[]

201 Created

Retrieve skeleton and neuron information about this treenode.

GET /{project_id}/treenodes/{treenode_id}/info

Tags: treenodes

Retrieve skeleton and neuron information about this treenode.

project_id		path	string
treenode_id		path	string

200 OK

List suppressed virtual nodes along the edge to this node.

GET /{project_id}/treenodes/{treenode_id}/suppressed-virtual/

Tags: treenodes

List suppressed virtual nodes along the edge to this node.

project_id		path	string
treenode_id		path	string

200 OK

Suppress a virtual treenode along the edge to this node.

POST /{project_id}/treenodes/{treenode_id}/suppressed-virtual/

Tags: treenodes

Suppress a virtual treenode along the edge to this node.

Suppress a virtual treenode along the edge between this treenode and its parent from being traversed during normal topology navigation and review.

application/x-www-form-urlencoded

project_id		path	string
treenode_id		path	string
orientation	Stack orientation to determine which axis is the coordinate of the plane where virtual nodes are suppressed. 0 for z, 1 for y, 2 for x.	formData	integer
location_coordinate	Coordinate along the edge from this node to its parent where virtual nodes are suppressed.	formData	number

201 Created

Unsuppress a virtual treenode.

DELETE /{project_id}/treenodes/{treenode_id}/suppressed-virtual/{suppressed_id}

Tags: treenodes

Unsuppress a virtual treenode.

suppressed_id		path	string
project_id		path	string
treenode_id		path	string

204 No Content

Get a collection of all available volumes.

GET /{project_id}/volumes/

Tags: volumes

Get a collection of all available volumes.

application/x-www-form-urlencoded

project_id	Project to operate in	path	integer
volume_ids	Only return specified volumes	formData	string[]

200 OK

Create a new volume

POST /{project_id}/volumes/add

Tags: volumes

Create a new volume

The ID of the newly created volume is returned. Currently, box volumes and triangle meshes are supported. Which one is created depends on the "type" parameter, which can be either set to "box" or to "trimesh".

If a triangle mesh should be created, the "mesh" parameter is expected to hold the complete volume. It is expected to be a string that encodes two lists in JSON format: [[points], [triangles]]. The list of points contains lists of three numbers, each one representing a vertex in the mesh. The array of triangles also contains three element lists as items. Each one represents a triangle based on the points in the other array, that are referenced by the triangle index values.

application/x-www-form-urlencoded

project_id		path	string
type	Type of volume to create	formData	string
title	Title of volume	formData	string
comment	An optional comment	formData	string
mesh	Triangle mesh	formData	string
minx	Minimum x coordinate of box	formData	integer
miny	Minimum y coordinate of box	formData	integer
minz	Minimum z coordinate of box	formData	integer
maxx	Maximum x coordinate of box	formData	integer
maxy	Maximum y coordinate of box	formData	integer
maxz	Maximum z coordinate of box	formData	integer

201 Created

Retrieve a mapping of volume IDs to entity (class instance) IDs.

POST /{project_id}/volumes/entities/

Tags: volumes

Retrieve a mapping of volume IDs to entity (class instance) IDs.

project_id		path	string
volume_ids	A list of volume IDs to map	query	string

201 Created

Import triangle mesh volumes from an uploaded files.

POST /{project_id}/volumes/import

Tags: volumes

Import triangle mesh volumes from an uploaded files.

Currently only STL representation is supported.

application/x-www-form-urlencoded

Triangle mesh file to import. Multiple files can be provided, with each being imported as a mesh named by its base filename.

project_id		path	string

201 Created

Test environment only contains two skeletons - based on that, sql query

GET /{project_id}/volumes/skeleton-innervations

Tags: volumes

Test environment only contains two skeletons - based on that, sql query always returns list of all SKIDs but all data (about both skeletons) is contained in the first SKID in the list - if this changes, write an else statement for: len(cleanResults) >1.

application/x-www-form-urlencoded

project_id	The project to operate in	path	integer
skeleton_ids	Constrain results to these skeletons	formData	string[]
annotation	An annotation potential target volumes need to have	formData	string
min_nodes	A minimum number of nodes result skeleton need to have.	formData	boolean
min_cable	A minimum number of cable length esult skeleton need to have.	formData	boolean

200 OK

Test environment only contains two skeletons - based on that, sql query

POST /{project_id}/volumes/skeleton-innervations

Tags: volumes

Test environment only contains two skeletons - based on that, sql query always returns list of all SKIDs but all data (about both skeletons) is contained in the first SKID in the list - if this changes, write an else statement for: len(cleanResults) >1.

application/x-www-form-urlencoded

project_id	The project to operate in	path	integer
skeleton_ids	Constrain results to these skeletons	formData	string[]
annotation	An annotation potential target volumes need to have	formData	string
min_nodes	A minimum number of nodes result skeleton need to have.	formData	boolean
min_cable	A minimum number of cable length esult skeleton need to have.	formData	boolean

201 Created

Get detailed information on a spatial volume or set its properties..

DELETE /{project_id}/volumes/{volume_id}/

Tags: volumes

Get detailed information on a spatial volume or set its properties..

The result will contain the bounding box of the volume's geometry and the actual geometry encoded in X3D format. The response might might therefore be relatively large.

volume_id		path	string
project_id		path	string

204 No Content

Get detailed information on a spatial volume or set its properties..

POST /{project_id}/volumes/{volume_id}/

Tags: volumes

Get detailed information on a spatial volume or set its properties..

The result will contain the bounding box of the volume's geometry and the actual geometry encoded in X3D format. The response might might therefore be relatively large.

volume_id		path	string
project_id		path	string

201 Created

Export volume as a triangle mesh file.

GET /{project_id}/volumes/{volume_id}/export\.(P{extension}\w+)

Tags: volumes

Export volume as a triangle mesh file.

The extension of the endpoint and ACCEPT header media type are both used to determine the format of the export.

Supported formats by extension and media type:

STL

• model/stl, model/x.stl-ascii: ASCII STL

volume_id		path	string
project_id		path	string
extension		path	string

200 OK

Test if a point intersects with the bounding box of a given volume.

GET /{project_id}/volumes/{volume_id}/intersect

Tags: volumes

Test if a point intersects with the bounding box of a given volume.

volume_id		path	string
project_id		path	string
x	X coordinate of point to test	query	number
y	Y coordinate of point to test	query	number
z	Z coordinate of point to test	query	number

200 OK