Package Help

Provides an overview of key functions and classes

catmaid-package

Programmatic access to the CATMAID API

Catmaid Login

Functions handling connections to a catmaid server

catmaid_login() catmaid_connection()

Connect/authenticate to a CATMAID server, returning a connection object

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

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_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

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

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

plot3d(<catmaidneuron>)

Plot skeleton and connectors for neuron retrieved from CATMAID

connectors()

Get data.frame of connector (synapse) information from a neuron or neuronlist

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 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()

Return the entity ids for one or more model ids

catmaid_version()

Return the CATMAID version running on the server