Function reference • catmaid

Package Help Provides an overview of key functions and classes
`catmaid-package`	catmaid: R access to the API for the CATMAID web image annotation tool
Catmaid Login Functions handling connections to a catmaid server
`catmaid_login()` `catmaid_connection()` `print(<catmaid_connection>)`	Connect/authenticate to a CATMAID server, returning a connection object
`vfbcatmaid()`	A connection to the vfb catmaid server for a given dataset
`catmaid_connection_setenv()` `catmaid_connection_getenv()` `catmaid_connection_unsetenv()`	Import/Export catmaid connection details to system variables (e.g. for tests)
CATMAID skeleton functions Fetching raw skeleton information
`catmaid_get_compact_skeleton()`	Return the raw data for a CATMAID neuronal skeleton
`catmaid_get_treenode_table()`	Return tree node table for a given neuron
`catmaid_get_node_count()`	Get the number of nodes per skeleton
`catmaid_get_review_status()`	Get review status of neurons from CATMAID
`catmaid_get_treenodes_detail()`	Fetch position and other information for arbitrary treenode ids
`catmaid_change_history()`	Return the edit history of a CATMAID skeleton
`catmaid_islatest()`	Check if CATMAID skeleton ids are up to date
`catmaid_latestid()`	Return the latest skeleton id accounting for edits
Names and Annotations Querying, fetching and setting neuron names and annotations
`catmaid_query_by_name()` `catmaid_query_by_annotation()`	Get list of neurons/annotations querying by neuron/annotation name
`catmaid_get_neuronnames()`	Get names of neurons from CATMAID
`catmaid_rename_neuron()`	Rename (presently) a single neuron or other entity (e.g. annotation)
`catmaid_skids()`	Find skeleton ids (skids) for various inputs including textual queries
`catmaid_get_meta_annotations()` `catmaid_query_meta_annotations()` `catmaid_set_meta_annotations()` `catmaid_remove_meta_annotations()`	Get, query, set and remove CATMAID meta-annotations for annotations
`catmaid_get_annotations_for_skeletons()` `catmaid_set_annotations_for_skeletons()` `catmaid_remove_annotations_for_skeletons()`	Get or set annotations for neurons from CATMAID
`catmaid_get_annotationlist()`	Get list of annotations (including user information) from CATMAID
`catmaid_lock_neurons()` `catmaid_unlock_neurons()`	Lock or unlock a CATMAID neuron reconstruction
Node labels (aka tags) Fetching, setting and removing tags from tree nodes or connectors
`catmaid_get_labels()` `catmaid_set_labels()` `catmaid_remove_labels()`	Get/Set/Remove CATMAID treenode labels (aka tags)
`catmaid_get_label_stats()` `catmaid_get_all_labels()`	Get statistics for all labels in a project from a CATMAID server
`nsoma()`	Return the number of explicitly tagged somata in a (CATMAID) neuron
Synaptic Connections Querying and fetching neuronal connectivity information
`catmaid_query_connected()`	Find neurons connected to a starting neuron
`catmaid_get_connector_table()`	Return connector table for a given neuron
`catmaid_get_connectors_between()`	Return information about connectors joining sets of pre/postsynaptic skids
`catmaid_get_connectors()`	Return skeleton ids for pre/postsynaptic partners of a set of connector_ids
`catmaid_adjacency_matrix()`	Get connectivity adjacency matrix between set of neurons
Interfacing with Nat Fetching and using catmaid skeletons for use with the NeuroAnatomy Toolbox (nat) package.
`read.neuron.catmaid()` `read.neurons.catmaid()`	Read neuron(s) from CATMAID server into NeuroAnatomy Toolbox (nat) format
`catmaid_update_neuronlist()`	Update a local neuronlist with new CATMAID data
`plot3d(<catmaidneuron>)`	Plot skeleton and connectors for neuron retrieved from CATMAID
`connectors()`	Get data.frame of connector (synapse) information from a neuron or `neuronlist`
`soma()` `somaindex()` `somaid()`	Retrieve soma information for skeletons (specified via CATMAID tags)
Handling volume meshes Adding / converting volume meshes to CATMAID from regular R mesh representations
`as.catmaidmesh()`	Convert a mesh to CATMAID format
`catmaid_add_volume()`	Add a 3D mesh surface to catmaid volume manager
`catmaid_get_volume()`	Fetch a mesh volume from CATMAID
`catmaid_get_volumelist()`	Fetch a data frame containing details of all volumes on CATMAID server
CATMAID statistics and users Neuron and user lists and statistics
`catmaid_get_contributor_stats()`	Get contributor statistics for neurons from CATMAID
`catmaid_get_user_list()` `catmaid_userids()`	Fetch or translate catmaid users for current/specified connection/project
`catmaid_user_history()`	Fetch user contribution history
`catmaid_get_time_invested()`	catmaid_get_time_invested
CATMAID URLs and JSON files Working with the URLs or JSON files used to save and exchange CATMAID state
`catmaid_parse_url()`	Parse a CATMAID URL to extract parameters including xyz location
`read_catmaid_selection()`	Read a CATMAID selection file
`write_catmaid_selection()`	Make a CATMAID selection file based on neuronlist or skids
Data Sample data included with the package
`AV4b1`	A sample CATMAID neuron (from the adult lateral horn of class AV4b1)
Low level functions Functions primarily intended for developer use
`catmaid_fetch()`	Send http GET or POST request to a CATMAID server
`copy_tags_connectors()`	Copy the tag / connector info from a catmaid neuron to a new neuron
`catmaid_entities_from_models()` `catmaid_models_from_entities()`	Convert between entity (neuron) and model (skeleton) ids
`catmaid_version()`	Return the CATMAID version running on the server

Reference

Package Help

Catmaid Login

CATMAID skeleton functions

Names and Annotations

Node labels (aka tags)

Synaptic Connections

Interfacing with Nat

Handling volume meshes

CATMAID statistics and users

CATMAID URLs and JSON files

Data

Low level functions