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