Subset points to be in the brain or in the VNC

Subset points to be in the brain or in the VNC

Usage

banc_decapitate(x, y.cut = 325000, invert = FALSE, ...)

# S3 method for class '`NULL`'
banc_decapitate(x, y.cut = 325000, invert = FALSE, ...)

# S3 method for class 'neuron'
banc_decapitate(x, y.cut = 325000, invert = FALSE, ...)

# S3 method for class 'neuronlist'
banc_decapitate(x, y.cut = 325000, invert = FALSE, ...)

# S3 method for class 'matrix'
banc_decapitate(x, y.cut = 325000, invert = FALSE, ...)

# S3 method for class 'data.frame'
banc_decapitate(x, y.cut = 325000, invert = FALSE, ...)

# S3 method for class 'mesh3d'
banc_decapitate(x, y.cut = 325000, invert = FALSE, ...)

# S3 method for class 'hxsurf'
banc_decapitate(x, y.cut = 325000, invert = FALSE, ...)

Arguments

x

an object with 3d points to be subsetted, e.g. an xyz matrix, a neuron, neuronlist or a mesh3d object. Points must be in native BANC space, i.e. plottable inside banc.surf.

y.cut

Numeric, the Y-axis cut point, in nanometers, in BANC space, that separates the head from the neck and ventral nerve cord. For fitting to the MANC data set, a cut height of y.cut=5e05 seems good.

invert

if FALSE returns brain points, if TRUE returns VNC points.

...

Additional arguments passed to nlapply and then prune_vertices

Value

Remove points above or below the midsection of the neck connective of BANC.

See also

banc.surf

Examples

# \donttest{
# DNa02
m = banc_read_neuron_meshes("720575941478275714")
#>   downloading meshes
#> cannot import name 'ssl' from 'urllib3.util.ssl_' (/home/runner/.local/share/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/urllib3/util/ssl_.py)
#> Error: Please install the python cloudvolume package:
#> This should normally work:
#> fafbseg::simple_python('basic')
#> For more details see ?simple_python or the cloud-volume docshttps://github.com/seung-lab/cloud-volume#setup
#> If you have already installed cloudvolume but it is not found
#> then R probably can't find the relevant version of Python
#> Do:
#> usethis::edit_r_environ()
#>  to point to the right python
#> e.g. RETICULATE_PYTHON="/opt/miniconda3/envs/r-reticulate/bin/python"
m.brain = banc_decapitate(m)
#> Error: object 'm' not found
m.vnc = banc_decapitate(m, invert = TRUE)
#> Error: object 'm' not found
# }
if (FALSE) { # \dontrun{
plot3d(m.brain, col = "red")
plot3d(m.vnc, col = "cyan")
plot3d(banc.surf, col = "grey", alpha = 0.1)
} # }