Read 3D insect brain meshes from insectbraindb.org

Source: R/read_brains.R

Read templatebrains, comprised of their different neuropils, for various insect species from from insectbraindb.org (2018 version), given a single latin names for the species desired. Metadata for available neurons can be seen, and IDs chosen, by calling insectbraindb_species_info. 3D triangular brain meshes are returned as a nat package hxsurf object, which mimics the Amira surface format. These can be be plotted in 3D using rgl and analysed with tools from the nat ecosystem. This includes subsetting by neuropil, i.e.. if you only want to visualise or analyse the antennal lobe.

insectbraindb_read_brain(
  species = insectbraindb_species_info()$scientific_name,
  brain.sex = c("UNKNOWN", "MALE", "FEMALE"),
  progress = TRUE
)

Arguments

species

the full scientific name for a species. The available options can be seen here
brain.sex

the sex of the species' brain. The available options can be seen here
progress

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

Value

a nat package hxsurf object, which mimics the Amira surface format, replete with metadata that can be accessed using $

Details

A single 3D brain object is read, a .obj file for each of its neuropils is downloaded from https://ibdb-file-storage.s3.amazonaws.com/ to a temporary directory, and read using read.obj into a hxsurf object in R, which mimics the Amira surface format. 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.

See also

insectbraindb_neuron_info, insectbraindb_read_neurons, insectbraindb_species_info