fanc_read_l2skel reads one or more neurons as simplified
L2 skeletons.
fanc_read_l2dp reads one or more neurons as simplified
dotprops format. See read_l2skel.
Usage
fanc_read_l2dp(id, OmitFailures = TRUE, dataset = NULL, ...)
fanc_read_l2skel(id, OmitFailures = TRUE, dataset = NULL, ...)Arguments
- id
One or more flywire ids
- OmitFailures
Whether or not to drop neurons that cannot be read from the results (rather than erroring out). Default
TRUE.- dataset
An optional CAVE dataset name (expert use only, by default will choose the standard FANC dataset). See details.
- ...
Additional arguments passed to the
fafbseg.flywire.l2_skeletonorfafbseg.flywire.l2_dotpropsfunctions.
Value
a neuronlist containing one or more
neuron or dotprops objects. Note that neurons
will be calibrated in nm while dotprops will be calibrated in microns.
Details
fanc_read_l2dp uses a special data structure for rapid
download of the dotprops version of neurons required for NBLASTing. It
leverages the python navis / fafbseg-py packages and you will need to
install these, typically using the simple_python
function.
fanc_read_l2skel treats the dataset argument a little differently
than fanc_read_l2dp because it actually needs to identify two data sources
a CAVE data
See read_l2skel for additional details of
Examples
if (FALSE) { # \dontrun{
# one time install of necessary python packages
fafbseg::simple_python(pkgs="fafbseg")
dnp42=c("648518346507131167", "648518346485772414")
dnp42.latest=fanc_latestid(dnp42)
dnp42.dps <- fanc_read_l2dp(dnp42.latest)
# plot those
nclear3d()
plot3d(dnp42.dps, lwd=3)
# nb dotprops are always in microns
wire3d(FANC.surf/1e3, col='grey')
nclear3d()
dnp42.skel <- fanc_read_l2skel(dnp42.latest)
plot3d(dnp42.skel, lwd=2)
# nb neuron skeletons are in nm
wire3d(FANC.surf, col='grey')
} # }