This changelog notes changes to API endpoints that are documented and listed through Swagger. Changes to undocumented, internal CATMAID APIs are not included in this changelog.
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POST /{project_id}/skeletons/cable-length: The POST version of the already existing GET endpoint. It allows passing in more skeleton IDs for which to get the cable length. -
POST /{project_id}/skeletons/connectivity-counts: Allows to get the number connector links per relation type for each passed in skeleton. Also accepts GET parameters. -
POST /{project_id}/skeletons/connectivity_matrix/csv: Return a CSV file containing the connectivity matrix for the passed inrowsandcolumns. -
POST /{project_id}/skeletons/sampler-count: Return the number of samplers linked to each skeleton in the passed inskeleton_idslist. -
GET /{project_id}/skeletons/{skeleton_id}/sampler-count: Return the number of samplers linked to this skeleton. -
GET /{project_id}/labels/detail: Returns a list of of label objects, each with a name field and an ID field. -
POST /{project_id}/volumes/import: Import volumes as STL files. -
GET /{project_id}/volumes/{volume_id}/export.{extension}: Export a particular volume. Currentl only exports AS STL are supported. -
GET /{projec_id}/stats/cable-length: Get the top N largest skeletons. N can be specified using the 'n_skeletons' parameter. -
POST /{project_id}/volumes/skeleton-innervations: Get a list of all volume/skeleton combinations that intersect. Skeletons are provided with a 'skeleton_ids' parameter. This can be constrained by volume annotation, cable length and node count. -
POST /{project_id}/volumes/: Previously only the GET method would be supported. With the introduction of an optionalvolume_idsparameter, POST can be used as well. This parameter can be used to constrain the returned set of volumes.
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POST /{project_id}/skeletons/node-label: The newlabel_namesparameter accepts a list of strings that an be used instead of or together with label IDs to get skeletons with nodes that have particular labels. -
GET /{project_id}/stacks/{stack_id}/info: Now includes thecommentfield for each stack. -
GET /{project_id}/connectors/: The partner data returned when thewith_partnersis set, includes now additionally the creator of the link and the creation and edition time (in epoch format). -
GET /user-list: Accepts a new boolean parameterwith_passwordsto export encrypted passwords, which in turn can be imported into other CATMAID instances. This requires the requesting user to be a superuser. -
GET /{project_id}/skeleton/{skeleton_id}/swc: A new optional parametersoma_markerscan be supplied. It is a list of 'tag:soma', 'radius:' and 'root'. These are conditions for when a node is marked as soma in the SWC export. The first matching condition in this order wins. -
GET /{project_id}/volumes/: The return format changed. Instead of a list of volume objects an object with a 'columns' field and a 'data' field are returned. The data fields contains a list of lists, with each inner list being a volume. The entries are described by the 'columns' field. Along with the already returned fields, annotations are now retuned as well. -
GET /{project_id}/volumes/: An optionalvolume_idsparameter can now be used and the POST method is supported as well (to transfer larger volume ID lists). This parameter can be used to constrain the returned set of volumes. -
POST /{project_id}/skeletons/connectivity: A new optional option 'link_types' allows to specify which connectivity types should be returned. By default 'incoming' and 'outgoing' is returned. Additionally, the following options are allowed: gapjunction, abutting, attachment, close_object. The return field names have also been adapted to these parameters and match them. Instead of 'gapjunctions' and 'attachments', the fields are now named 'gapjunction' and 'attachment'. -
GET /{project_id}/annotations/: Supports now an optional boolean parameter namedsimple, which returns only names and IDs and is therefore much faster.
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POST /{project_ids}/connectors/links: Accepts the same parameters as the GET variant, but allows for larger skeleton_ids list. -
POST /{project_ids}/skeletons/in-bounding-box: Accepts the same parameters as the GET variant, but allows for larger skeleton_ids list. -
GET /{project_id}/volumes/entities: Return a mapping of volume IDs to their respective class instance ID.
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GET /{project_id}/skeletons/in-bounding-box: Themin_nodesandmin_cableparameters can be used to further filter the result. Thesrcparameter can be 'postgis2d' and 'postgis3d', with the former being the default spatial query type. Thevolume_idparameter can optionally be used to return the skeletons in the bounding box of a specific volume, alternative to explicit bounding box. Optionally, theskeleton_idsparameter can provide a list of skeletons to test for intersections. Without it, all skeletons in the project are considered. -
GET /{project_id}/skeletons/{skeleton_id}/review: The user ID of each node is now returned as well. -
POST|GET /{project_id}/node/list: Offers a new optional parameter "n_largest_skeletons_limit", which can be used to constrain the returned neurons to only those of the N largest skeletons in the result set. -
POST /{project_id}/skeleton/connectivity_matrix: The new parameter 'with_locations' includes more data in the result set. Each connector and its contributions to the link count is returned as well. -
GET|POST /{project_id}/skeletons/compact-detail: The new parameter 'format' can now be used to returned the skeleton data in different formats. Supported are 'msgpack' and 'json'. -
GET /{project_id}/skeletons/{skeleton_id}/compact-detail: The new parameter 'format' can now be used to returned the skeleton data in different formats. Supported are 'msgpack' and 'json'. -
POST /{project_id}/treenodes/compact-detail: Thetreenode_idsparameter is now optional and two new parameters can be used instead:label_idsandlabel_names. They can be used to constrain the result set by their labels. This effectively allows querying treenodes and skeletons based on linked labels. -
GET /{project_id/samplers/{sampler_id}/domains/: Returns now also end nodes for each domain.
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POST /{project_id}/treenodes/compact-detail: Retrieve treenode information for multiple nodes in the format of regular node queries, accepts a parameter "treenode_ids". -
GET /{project_id}/treenodes/{treenode_id}/compact-detail: Retrieve treenode information for a single node. -
DELETE /{project_id}/landmarks/{landmark_id}/groups/{group_id}/: Delete landmark location links to the same locations from a landmark and group. -
PUT /{project_id}/landmarks/groups/links/: Add new links between groups, e.g. "adjacent_to". -
DELETE /{project_id}/landmarks/groups/links/{link_id}/: Delete a single landmark group link. -
GET /{project_id}/landmarks/groups/{landmarkgroup_id}/transitively-linked: Get a list of landmark groups that are linked to the referenced group using a passed in relation, respects reciprocal relations. -
POST /{project_id}/landmarks/groups/materialize: Create pairs of landmark groups along with their landmarks based on a simple description. -
GET /{project_id}/skeletons/cable-length: Get the cable length for multiple skeletons using the skeleton_ids parameter. -
GET /{project_id}/skeletons/{skeleton_id}/cable-length: Get the cable length for a single skeleton. -
GET /{project_id}/skeletons/in-bounding-box: Get IDs of all skeltons that intersect with the passed in bounding box.
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POST /{project_id}/annotations/query-targets: Accepts now a "annotation_reference" parameter which can either be 'id' (default) or 'name'. If it is set to 'name', all annotation references in annotated_with, not_annotated_with and sub_annotated_with are interpreted as annotation names instead of IDs. -
POST /{project_id}/skeleton/split: Returns now also the split location as fields x, y and z. -
POST|GET /{project_id}/node/listoffers a new optional parameter "with_relation_map", which controls which relation map information is returned. Can be 'none', 'used' and all with 'used' being the default. -
GET /{project_id}/landmarks/groups/: Accepts the new optional parameter "with_links", "with_names" and "with_relations", to include links between landmark groups along with a list of linked landmark names and a map of used relations -
GET /{project_id}/landmarks/groups/{group_id}/: Accepts the new optional parameter "with_names" to include landmark names along with linked landmark locations. -
GET /{project_id}/stats/user-history: Returns actual node count in "new_treenodes" field, cable length is returned in "new_cable_length" field (previously new_treenodes).
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GET /{project_id}/useranalytics: ReplacesGET /useranalytics.
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GET /{project_id}/samplers/: Accepts now also a boolean with_intervals parameter to return information on each instantiated interval in each returned domain. Implies with_domains. -
POST|GET /{project_id}/node/listoffers a new optional parameter "src", which can be used to override the node provider selected by the back-end. -
POST|GET /{project_id}/node/listoffers new options for the optional parameter "format": "gif" and "png" to return an imageof the tracing data.
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GET /useranalytics: Has been replaced withGET /{project_id}/useranalytics.
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POST /{project_id}/nodes/location: Get the location of multiple nodes, expects anode_idsparameter. -
GET /{project_id}/connectors/now provides a new API to query connectors directly and not only links. The previous API is available asGET /{project_id}/connctors/links/(see below). -
GET /{project_id}/skeletons/{skeleton_id}/neuroglancer: Export a morphology-only skeleton in neuroglancer's binary format.
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GET /{project_id}/connector/user-infohas been replaced withGET /{project_id}/connectors/user-info. Functionality is the same. -
GET /{project_id}/connectors/has been replaced withGET /{project_if}/connectors/links/. Functionality is the same. -
POST /{project_id}/node/listoffers a new optional parameter "format", which is set by default to 'json', but can be set to 'msgpack' to use msgpack binary encoding of the result.
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GET /{project_id}/samplers/domains/intervals/{interval_id}/details: Get detailed information about a particular interval. -
GET /{project_id}/neurons/: List all neurons in a project. Optionally, the parameters created_by, reviewed_by, from, to and nodecount_gt can be provided.
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POST /{project_id}/treenodes/{treenode_id}/info: This API endpoint is changed to only accept GET requests. Using POST will raise an error. -
GET /{project_id}/stats/nodecount: The response format changed. Now a dictionary mapping user IDs to node counts is returned. -
GET /{project_id}/stats/editor: The response format changed. Now a dictionary mapping user IDs to the number of edited nodes is returned. -
GET /{project_id}/projects/export: Stacks include now also their translation and orientation relative to project space.
GET /{project_id}/annotationdiagram/nx_json: This API has a confusing name, because it uses 'annotation' differently than others. There are different APIs available to get skeleton IDs and treenode IDs.
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POST /{project_id}/skeletons/import: The new 'name' parameter can be used to set the name of a new neuron. -
POST /{project_id}/annotations/query-target: A boolean 'name_not' parameter is now accepted to get results not matching the name passed in with the regular 'name' parameter. Also, an integer list parameter named 'not_annotated_with' is now supported. Like the 'annotated_with' list, it contains annotation IDs. Results will not have the annotations passed in with thenot_annotated_withlist. -
GET /{project_id}/skeletons/{skeleton_id}/compact-detailandGET /{project_id}/skeletons/compact-detailAccepts two new parameters: with_reviews and with_annotations. To also return a list of reviews and a list of linked skeleton IDs respectively for each returned skeleton. -
POST /{project_id}/volumes/{volume_id}/Individual fields can now be updated selectively. Only fields that are passed in as arguments will be updated. This allows for instance to only change the name of a volume.
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POST /{project_id}/skeletons/connectivity: If the new "with_nodes" parameter is true, the involved treenode links are also returned for each partner.
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GET /messages/mark_read: This API took a message ID as parameter before and is replaced by:POST /messages/{message_id}/mark_read -
POST /{project_id}/node/user-info: Thenode_idparameter has been replaced with anode_idsparameter, which is expected to be a list of node IDs. The response maps now individual info objects to their respective node IDs. -
GET /{project_id}/connectors/Each result link now contains one additional column: the link's creation time. It replaces the edition_time in column nine. The edition time is now available in column ten.
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POST /{project_id}/node/listandPOST /{project_id}/node/list: The returned timestamps are now second based UTC epoch numbers instead of UTC strings.
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/{project_id}/analytics/broken-section-nodes: Get s list of all nodes that are currently located in a broken section of any stack linked to their project. Obtionally, specific skeletons can be checked.
POST /{project_id}/skeleton/analyticsIs renamed toPOST /{project_id}/analytics/skeletons.
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GET /{project_id}/stack/{stack_id}/modelsMeshes have been replaced with volumes.
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GET /{project_id}/labels/statsGet statistics on node label usage for the project. -
POST /{project_id}/skeletons/node-labelsReturn mappings from node label IDs to IDs of skeletons which include a node with that label.
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GET /{project_id}/skeletons/{skeleton_id}/compact-detailProvides same functionality asGET/POST /{project_id}/{skeleton_id}/[0|1]/[0|1]/compact-skeleton, but uses explicit GET parameters. -
POST /{project_id}/nodes/Provides the same data as the formerPOST /{project_id}/nodes/listand takes the same parameters.
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GET/POST /{project_id}/{skeleton_id}/[0|1]/[0|1]/compact-skeletonThis endpoint will be replaced in the future with the newly introduced endpointGET /{project_id}/skeletons/{skeleton_id}/compact-detail. -
POST /{project_id}/node/listThis endpoint will be replaced in the future with the newly introduced endpointPOST /{project_id}/nodes/. It takes the same parameters.
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GET /{project_id}/connectors/Replaces thePOST /{project_id}/connector/table/listendpoint, but also changes the parameter names. Additionally, the "relation_type" parameter is now expected to contain the actual relation name instead of a numeric alias: The value "0" is replaced with "postsynaptic_to" and "1" is replaced with "presynaptic_to". See /apis documentation for details.
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GET/POST /{project_id}/[0|1]/[0|1]/compact-skeletonThe new parameter with_history allows to include historic data in th response. Will also include timestamps for regular nodes.
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POST /{project_id}/connector/table/listThis endpoint is replaced by theGET /{project_id}/connectorsendpoint, described above.
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GET /{project_id}/statsThis endpoint returned an HTML document displayed by CATMAIDs statistics widget.
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GET projects/export: Provides all available information on the structure and properties of projects and stacks. Supports application/json and application/yaml content types. A return YAML document matches the format supported by the importer. -
POST /{project_id}/connector/info: This endpoint replaces the/{project_id}/connector/pre-post-infosendpoint. Thepreandpostparameters are now optional. -
POST /{project_id}/neurons/from-models: Get the IDs of all neurons modeled by a list of entities, e.g. skelton IDs. -
POST /{project_id}/skeletons/import: Import a neuron modeled by a skeleton from an uploaded file. Currently only SWC representation is supported. -
GET /{project_id}}/transactions/Get a list of transaction objects, ordered by time (latest first). A sub-range can be specified optionally. -
GET /{project_id}}/transactions/locationGet a location representing the change in a given transaction. Returns error if no location was found.
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GET /projects/: Does not include the catalogueable property of projects anymore. Use ontology queries to filter by the "driver_line" class for the same semantics. -
POST /{project_id}/annotations/forskeletons: Parameterskeleton_idsnow correctly parses with and without explicit indices. -
POST /{project_id}/annotations/query: Parameterobject_idsnow correctly parses with and without explicit indices. -
POST /{project_id}/annotations/query-targets: Parametertypesnow correctly parses with and without explicit indices. -
GET /{project_id}/ontology/list: Return format has been made simpler, contains still same information. -
GET /{project_id}/ontology/relations/list: Return format has been made simpler, contains still same information. -
GET /{project_id}/ontology/classes/list: Return format has been made simpler, contains still same information.
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POST /{project_id}/connector/pre-post-info: This endpoint was renamed to/{project_id}/connector/infoendpoint.
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GET /{project_id}/labels/[treenode|connector]/{label_id}/: Returns a list of labels for a node. -
GET /{project_id}/connectors/{connector_id}/: Returns information on a connector and its partners. -
POST /{project_id}/skeletons/within-spatial-distance: Find skeletons within a given L-infinity distance of a treenode.
POST /{project_id}/skeletons/connectivity:
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Response object now includes
gapjunctionsandgapjunctions_reviewersproperties for gap junction connectors. -
Documentation has correct parameter name:
source_skeleton_idsnotsource.
POST /{project_id}/label/[treenode|connector]/{label_id}/update:
- Returns now also information about what labels were added, which were duplicates and which labels were deleted.
POST /{project_id}/label/[treenode|connector]/{label_id}/remove:
- Returns now also information about which label label was eventually removed. If nothing went wrong the field deleted_link has the input label ID.
POST /{project_id}/annotations/remove:
- The return field
deleted_annotationsis now calleddeleted_linksand continues to contain a list of class_instance_class_instance IDs that were removed. The newdeleted_annotationsfield contains a mapping of removed annotation IDs to the IDs of the object they were removed from.
POST /{project_id}/connector/delete:
- The response contains now detailed information about the removed connector, including its partners.
POST /{project_id}/node/list:
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Edition times of nodes and connectors-links are now returned, too. Therefore some array indices changed.
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Link and connector types are now returned in a more general fashion. Instead of providing four different arrays for pre, post, gap-junction and other connectors (previously index 5, 6, 7, 8), each connector entry now contains one list with all links (index 5), each link is represented as [<treenode_id>, <relation_id>, <link_confidence>].
POST /{project_id}/treenode/delete:
- A list of removed links is now returned as well. Each entry has the following format: [, , , ].
POST /{project_id}/treenodes/{treenode_id}/confidence:
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Edition times of nodes and connectors-links are now returned, too. Each location ID in the returned updated_partners object, is now mapped to an object with an "edition_time" and an "old_confidence" field.
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An optional "partner_ids" parameter is now accepted. If the "to_connectors" parameter is set to true, the "partner_ids" parameter allows to update only the links to the provided connector IDs.
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An optional "partner_confidences" parameter is now accepted. If the "partner_ids" parameter is used, the "partner_confidences" parameter allows to specify an individual confidence for each selected partner.
POST /{project_id}/skeleton/join:
- IDs of the result skeleton and the deleted skeleton are now returned.
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-[POST|GET] /{project_id}/label-for-node/[treenode|connector]/{label_id}:
Has been replaced with:
GET /{project_id}/labels/[treenode|connector]/{label_id}/
The CATMAID API now authorizes requests using an API token tied to your account instead of your username and password. To obtain this token, open the CATMAID client in your browser, hover your cursor over your name (next to the "Logout" link), and click "Get API token". As a security measure, you will be prompted to re-enter your password, then shown your token string.
To use the API token, set the HTTP X-Authorization header on all of your
API requests to be 'Token', a space, and the token string, e.g.:
X-Authorization: Token 9944b09199c62bcf9418ad846dd0e4bbdfc6ee4b
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GET /projects/: List projects visible to the requesting user. -
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. -
POST /{project_id}/volumes/{volume_id}/: Get detailed information on a spatial volume or set its properties.
GET /{project_id}/annotations/:
- Params are now correctly documented as form rather than query params.
POST /{project_id}/annotations/:
- Params are now correctly documented as form rather than query params.
POST /{project_id}/annotations/forskeletons:
- Params are now correctly documented as form rather than query params.
POST /{project_id}/skeletons/connectivity:
boolean_opform param now expects string "AND" or "OR" rather than "logic-AND" or "logic-OR".
POST /{project_id}/volumes/add:
- Params are now correctly documented as form rather than query params.
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