mouselight_read_brain: Read the brain mesh and its brain regions from the MouseLight...

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

Description

Save the brain mesh and its brain regions from the MouseLight project

Usage

mouselight_read_brain(
  type = c("outline", "brain_areas"),
  progress = TRUE,
  Force = FALSE
)

Arguments

type	whether just to retreive the outer brain mesh, or the brain constituent neuropils
progress	logical, toggle progress bar
Force	logical, whether or not to overwrite .obj files stored in a temporary directory
...	methods passed to mouselight_fetch

Value

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

References

Winnubst, Johan, Erhan Bas, Tiago A. Ferreira, Zhuhao Wu, Michael N. Economo, Patrick Edson, Ben J. Arthur, et al. 2019. “Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain.” bioRxiv. https://doi.org/10.1101/537233. Economo, Michael N., Nathan G. Clack, Luke D. Lavis, Charles R. Gerfen, Karel Svoboda, Eugene W. Myers, and Jayaram Chandrashekar. 2016. “A Platform for Brain-Wide Imaging and Reconstruction of Individual Neurons.” eLife 5 (January): e10566.

See Also

mouselight_read_brain, mouselight_brain_region_info

Examples

## Not run: 
## First we can quickly just plot the outer mesh for the brain
outline = mouselight_read_brain(type = "outline")
plot3d(outline, col = "pink", alpha = 0.3)

## This is cool, but maybe what we really want are its sub-divisions.
mousebrain = mouselight_read_brain(type = "brain_areas")
clear3d()
plot3d(mousebrain)
### This takes a long time the first time you call this function per session

## What brain regions are on offer?
print(mousebrain$neuropil_full_names)

## Or if we want more information, we can get it like this:
mbr = mouselight_brain_region_info()
View(mouselight_brain_region_info)

## Perhaps we want to plot just the amygdala?
### To do this we can do
amygdala.codes = mousebrain$RegionList[grepl("amygdala",
mousebrain$neuropil_full_names,
ignore.case = TRUE)]
plot3d(outline, col = "pink", alpha = 0.1)
plot3d(subset(mousebrain, amygdala.codes), alpha = 0.5)


## End(Not run)

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