banc_read_l2skel reads one or more neurons as simplified
L2 skeletons.
banc_read_l2dp reads one or more neurons as simplified
dotprops format. See read_l2skel.
Usage
banc_read_l2dp(id, OmitFailures = TRUE, dataset = NULL, ...)
banc_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 banc 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
banc_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.
banc_read_l2skel treats the dataset argument a little differently
than banc_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")
dna02=c("720575941478275714", "720575941512946243")
dna02.latest=banc_latestid(dna02)
dna02.dps <- banc_read_l2dp(dna02.latest)
# plot those
nclear3d()
plot3d(dna02.dps, lwd=3)
# nb dotprops are always in microns
wire3d(banc.surf/1e3, col='grey')
nclear3d()
dna02.skel <- banc_read_l2skel(dna02.latest)
plot3d(dna02.skel, lwd=2)
# nb neuron skeletons are in nm
wire3d(banc.surf, col='grey')
} # }