Basic interaction with neuPrint server

Connect to a server, check what datasets are available (or set the default dataset) and get details of the available API calls.

neuprint_connection() neuprint_login()

Connect to/authenticate with a neuPrint server and its Neo4j database, returning a neuPrint connection object

neuprint_datasets() neuprint_database() neuprint_available() neuprint_version()

Find out what some information about your neuPrint server

Simple queries

Find neurons by name/type or by their ROI innervation

neuprint_search() neuprint_ids()

Search for body IDs based on a given name

neuprint_find_neurons() neuprint_bodies_in_ROI()

Find bodies within a given ROI

Fetch neuron data and metadata

Read the name, summary metdata and skeleton, synapse data for neurons

neuprint_get_neuron_names()

Get the name of a neuron

neuprint_get_meta()

Get key metadata for body (including name, type, status, size)

neuprint_read_neurons() neuprint_read_skeletons() neuprint_read_neurons_simple()

Read skeleton and optional synapse information for neuPrint bodies

neuprint_get_synapses()

Get the locations of pre- and post synapses associated with a body.

neuprint_connectors()

Get the IDs and 3D locations of the pre- and post- synapses that make up a synaptic object

Connectivity between neurons

neuprint_connection_table()

Get the upstream and downstream connectivity of a neuron

neuprint_simple_connectivity()

Get a list of connected partners for a neuron

neuprint_ROI_connectivity()

Get connectivity between ROIs (summary or data frame of connecting neurons)

neuprint_common_connectivity()

Get the common synaptic partners for a set of neurons

neuprint_get_adjacency_matrix()

Get a matrix of connectivities between bodies

neuprint_skeleton_connectivity_matrix()

Get a matrix for connectivity between neuron/neuronlist objects

neuprint_get_paths()

Get a list of paths of length n between 2 neurons

neuprint_get_shortest_paths()

Get a list of the shortest paths between two neurons

ROI information

List, visualise or summarise synpases in regions of interest.

neuprint_ROIs()

Get a vector of all the ROIs in a specified dataset

neuprint_get_roiInfo()

Get roiInfo associated with a body

neuprint_ROI_mesh()

Download a region of interest as a 3D mesh

neuprint_ROI_hierarchy()

Get the region of interest (ROI) hierarchy in a dataset

Neuron manipulation

neuprint_assign_connectors() neuprint_locate_soma()

Assign synapses to a neuronal tree

Other queries

neuprint_dump()

Download data from neuprint for specified bodyids / a specified ROI

Low level functions to interact with neuPrint server

neuprint_fetch_custom()

Use a cypher to make a custom query to the neuPrint server specifying the information you want to obtain

neuprint_list2df()

Parse neuprint return list to a data frame

neuprint_get_fields()

Get available metadata fields for Neuron nodes