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)
ids | a neuron ID, or vector of neuron IDs, as recorded in the
insectbraindb.org. If set to |
---|---|
progress | if |
a nat
package neuronlist
object, replete
with metadata, is returned
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
.