mouselight_read_neurons: Read one or more MouseLight tracings into a neuronlist

In natverse/mouselightr: Bridge HHMI Janelia MouseLight Database and nat R Package

Description

read tracings for neurons from the MouseLight Neuron Browser. Each neuron may have multiple tracgings, typically one for its axon and another for its dendrite. To read neuron, a vector of tracing IDs needs to be supplied. To find there, use mouselight_neuron_info.

Usage

mouselight_read_neurons(
  tracing.ids,
  method = c("native", "swc"),
  meta = TRUE,
  ...
)

mouselight_neuron_metadata(tracing.ids)

Arguments

tracing.ids	ids of tracings.ids for MouseLight neurons. Note, this is different from neuron.ids and other ids used by the project. See available neurons and their tracing.ids using mouselight_neuron_info.
method	whether to read from MouseLight's own raw tracing format or stored SWC files
meta	whether or not to read meta data for tracings using mouselight_neuron_metadata
...	methods sent to mouselight_fetch_swc

Details

Note that mouselight neurons have numerous associated identifiers. Some appear to occur only once per neuron:

• UUID (called neuron.id) e.g. "780dfeef-e644-4e85-9aad-b31c9957b440"

• idString e.g. AA0302

Others may reflect multiple entitities:

• tracing.id e.g. "b0cfcfe1-9870-4e61-ad3e-cf09b114fc3a"

• soma.id e.g. 8abce9c1-479b-43a3-b5f2-080de966f068

There are nearly always two tracing ids per neuron (axon, dendrite). And seemingly multiple soma ids.

Neurons read with method = "native" will have, at neuron$d, the brain region within which each node falls and a value, "Label", denoted whether the tracings is an axon (2) or dendrite (3).

Value

A nat::neuronlist

See Also

mouselight_read_brain, mouselight_brain_region_info, mouselight_neuron_info

Examples

ids=c("1ccbc478-88fb-4181-a4de-d0c22ed9738b",
  "3afa5e41-374d-45bc-a546-03f362d93649")
nn=mouselight_read_neurons(ids)
plot3d(nn)

natverse/mouselightr documentation built on July 6, 2020, 2:09 p.m.