Download neuron morphology and connectivity data to a specified directory as .csv and .rda files
neuprint_dump( dir, bodyids = NULL, roi = NULL, preprocess = NULL, connectivity = TRUE, volumes = TRUE, meta = TRUE, nat = TRUE, drvid = FALSE, soma = TRUE, heal = TRUE, connectors = TRUE, all_segments = FALSE, resample = FALSE, scale = 4, voxel.thresh = 1e+07, dataset = NULL, conn = NULL, OmitFailures = TRUE, ... )
the directory to which to save the dump
the body IDs for neurons/segments (bodies) you wish to query.
This can be in any form understood by
a single ROI. Use
neuprint_ROIs to see what is available.
a function that can be applied to a nat::neuronlist object, to be called on neurons once they are read from
the neuprint server using
whether or not to include connectivity information in the dump, i.e. an adjacency matrix between bodyids
whether or not to include neuron volume information in the dump, i.e. voxels. Currently only works by talking to a DVID server using the package drvid
whether or not to fetch a meta data for the given bodyids, using
whether or not to read neurons are
(TRUE) or get SWC data frame (FALSE)
whether or not to use
drvid::read.neuron.dvid rather than
a cypher post request to
neuprint_fetch_custom, in order to read a
neuron. This might be faster, and this might also enable access to
skeletons on an underlying DVID database that have not yet been ported to
whether or not to fetch a possible soma location for the given
whether or not to heal a fragmented skeleton using a minimum
spanning tree, via
whether or not to add synapse data to the retrieved
skeletons in the format used by the
rcatmaid package, for easy use
catnat functions. This can be done for
synapse-less skeletons using
if TRUE, all bodies are considered, if FALSE, only 'Neurons', i.e. bodies with a status roughly traced status.
if a number, the neuron is resampled using
nat::resample, stepsize = resample. If 0 or FALSE (default), no
Resolution of sparse volume starting with 0 where each level beyond 0 has 1/2 resolution of previous level. "coarse" will return the volume in block coordinates.
the size threshold, in number of voxels, a neuron/segment must exceed, to be included in the dump, if read from an ROI
optional, a dataset you want to query. If
default specified by your R environ file is used or, failing that the
current connection, is used. See
neuprint_login for details.
optional, a neuprintr connection object, which also specifies the
neuPrint server. If NULL, the defaults set in your
neuprint_login for details.
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
methods passed to