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_review_status

Get review status of neurons from CATMAID

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

catmaid_get_label_stats

Get statistics for all labels in a project from a CATMAID server

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

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

Fetch list of 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

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