hemibrain_roi_meshes: Get some or all the region of interest meshes in the...

In natverse/hemibrainr: Code for Working with Data from Janelia FlyEM's Hemibrain Project and the flywire data sets``

Get some or all the region of interest meshes in the hemibrain project

Description

This function can retrieve some or all the hemibrain project ROI meshes as rgl::mesh3d objects. They are returned in a named neuronlist object. This allows further subsets and colours to be applied via the standard nat::plot3d.neuronlist semantics. See the examples for further details.

Usage

hemibrain_roi_meshes(
  rois = NULL,
  microns = FALSE,
  superLevel = NULL,
  OmitFailures = TRUE,
  conn = NULL,
  dataset = NULL,
  ...
)

Arguments

rois	The ROIs to fetch (default NULL implies all ROIs)
microns	convert dimensions from raw voxels into microns (template brain: JRCFIB2018F, else JRCFIB2018Fraw).
superLevel	whether not to show 'superlevel' ROIs - ROIs composed of other ROIs. If set to NULL, both low-level and superlevel ROIs are returned.
OmitFailures	Whether to omit neurons for which FUN gives an error. The default value (NA) will result in nlapply stopping with an error message the moment there is an error. For other values, see details.
conn	optional, a neuprintr connection object, which also specifies the neuPrint server. If NULL, the defaults set in your .Rprofile or .Renviron are used. See neuprint_login for details.
dataset	optional, a dataset you want to query. If NULL, the default specified by your R environ file is used or, failing that the current connection, is used. See neuprint_login for details.
...	Additional arguments passed to nlapply

Value

a neuronlist of rgl::mesh3d objects

See Also

hemibrain_skeleton_check, hemibrain.surf, neuprintr::neuprint_ROI_mesh, neuprintr::neuprint_ROI_hierarchy

Examples

## Not run: 
# Get all the roi meshes
hemibrain.rois = hemibrain_roi_meshes()

# Read in these neurons
cols = rainbow(length(hemibrain.rois))
for(m in 1:length(hemibrain.rois)){
    plot3d(hemibrain.rois[[m]],alpha = 0.5, col = cols[m])
}

# Alternatively plot a subset all at once with rainbow colours
# making use of nat::plot3d.neuronlist
plot3d(hemibrain.rois, 1:3, add=TRUE)

# If you have neuprintr >= 1.0 you can easily find groups of meshes
# find just the terminal nodes of the MB ROI hierarchy
library(nat)
mbterms=nat::endpoints(neuprint_ROI_hierarchy(root='MB(R)', rval='graph'))
mb.rois=hemibrain_roi_meshes(mbterms)
plot3d(mb.rois, add=TRUE)

## End(Not run)

natverse/hemibrainr documentation built on Nov. 27, 2024, 9:01 p.m.