API ReferenceΒΆ

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: 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: 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.

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: skeletons

Operation Description
GET /{project_id}/skeletons/

List skeletons matching filtering criteria.

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.

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/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/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.

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.

Tag: stats

Operation Description
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: 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

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

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

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}/intersect

Test if a point intersects with 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/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/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

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.

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 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 information 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

connector_id path string
project_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
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

project_id

Project containing node of interest

formData string
node_type

Either 'connector', 'treenode' or 'location'

formData string
node_id

ID of node to list labels for

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
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

project_id

The project the landmark group is part of.

path integer
landmarkgroup_id

The ID of the landmark group.

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

project_id

The project the landmark group is part of.

path integer
landmarkgroup_id path string
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.

project_id

Project of landmark group

path integer
location_id

Existing location ID

path integer
landmarkgroup_id

The landmark group to link

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.

project_id

Project of landmark group

path integer
location_id

Existing location ID

path integer
landmarkgroup_id

The landmark group to link

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

project_id

Project of landmark groups

path integer
landmarkgroup_id

The starting landmark group

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.

project_id

The project the landmark is part of.

path integer
landmark_id

The ID of the landmark.

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

project_id

The project the landmark is part of.

path integer
landmark_id

The ID of the landmark.

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

project_id

The project the landmark is part of.

path integer
landmark_id

The ID of the landmark.

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.

project_id

Project of landmark group

path integer
landmark_id

The landmark to unlink from

path integer
group_id

The group to unlink from

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

project_id

Project of landmark group

path integer
landmark_id

The landmark to link

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.

project_id

Project of landmark group

path integer
landmark_id

The landmark to unlink

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
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 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
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

connector_id

Connector to set state of

formData integer
project_id path string
interval_id

Interval the connector is part 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.

project_id path string
interval_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

project_id path string
interval_id

Interval to update state of

formData integer
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
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 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 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
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.

application/x-www-form-urlencoded

project_id path 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
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[]
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
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

project_id

Project of landmark

path integer
skeleton_id

IDs of the skeleton to get the cable length for

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

project_id path string
skeleton_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
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

project_id path string
skeleton_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.

project_id path string
skeleton_id path string
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

project_id path string
skeleton_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

project_id path string
skeleton_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.

project_id path string
skeleton_id path string
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, user_id, radius, skeleton_id, user_id].

project_id path 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, user_id, radius, skeleton_id, user_id].

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.

project_id path string
treenode_id path string
suppressed_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.

project_id path 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
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.

project_id path string
volume_id path string
204 No Content
Get detailed information on a spatial volume or set its properties..

GET /{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.

project_id path string
volume_id path string
200 OK
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.

project_id path string
volume_id path string
201 Created
Test if a point intersects with a given volume.

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

Tags: volumes

Test if a point intersects with a given volume.

project_id path string
volume_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