Read insect neurons from insectbraindb.org

Source: R/read_neurons.R

Read templatebrain-registered neurons from insectbraindb.org (2018 version), given a single ID or vector of neuron IDs. Alternatively, if ids is set to NULL, all neurons in the database that can be read, are read (~100). Metadata for available neurons can be seen, and IDs chosen, by calling insectbraindb_neuron_info. Neurons are returned as a nat package neuronlist object, that can be be plotted in 3D using rgl and analysed with tools from the nat ecosystem. Each neuron in the insectbraindb is represented by a unique numeric ID, a name and is associated with an insect species and a publication, by DOI. Some neurons cannot be read because a SWC file is not available from insectbraindb.org. You can examine the available neurons here here), while the available species may be examined here). Critically, these neurons are registered to standard templates that may be obtained as hxsurf objects in R by using insectbraindb_read_brain.

insectbraindb_read_neurons(ids = NULL, progress = TRUE)

Arguments

ids

a neuron ID, or vector of neuron IDs, as recorded in the insectbraindb.org. If set to NULL (default) then all neurons in the database are read. As of May 2018, this is only 100 readable neurons. A helpful information page on each neuron can be seen by visiting "https://insectbraindb.org/app/neuron/id", where id is a number, e.g. for Bogon moth neuron 219, this is your ticket.
progress

if TRUE or a numeric value, a progress bar is shown to track the state of your download

Value

a nat package neuronlist object, replete with metadata, is returned

Details

Multiple neurons are read, their SWC files as hosted at https://ibdb-file-storage.s3.amazonaws.com/ are downloaded to a temporary directory, and read using read.neurons into a neuronlist object in R. This format and its manipulation is described in detail here. When using insectbraindb_read_neurons, meta data for the neuron is also returned that gives a neuron's ID, short name, long name, associated laboratory and publication, if available, and the associated insect species. As of May 2019, data from the following species is hosted on insectbraindb.org :

  • Agrotis infusa Bogong moth

  • Agrotis segetum Turnip moth

  • Apis mellifera Honeybee

  • Apis mellifera Honeybee

  • Danaus plexippus Monarch Butterfly

  • Helicoverpa armigera Cotton Bollworm,

  • Helicoverpa assulta Oriental tobacco budworm

  • Heliothis virescens Tobacco budworm

  • Macroglossum stellatarum Hummingbird hawk moth

  • Manduca sexta Tobacco hornworm

  • Megalopta genalis Sweat bee

  • Nasonia vitripennis Jewel wasp

  • Scarabaeus lamarcki Diurnal dung beetle

  • Schistocerca gregaria Desert Locust

Note that since neurons are reconstructed from many different neural species, there is no 'standard' orientation between species, but within a species these neurons are registered to a template brain, usually using elastix. To visualise the templatebrain, use plot3d on class hxsurf objects downloaded using insectbraindb_read_brain.

See also

insectbraindb_neuron_info, insectbraindb_read_brain, insectbraindb_species_info