Download neuron morphology and connectivity data to a specified directory as .csv and .rda files

  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 neuprint_ids.


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 neuprint_read_neurons


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 neuprint_get_meta


whether or not to read neurons are nat::neuronlist objects (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 neuprint.


whether or not to fetch a possible soma location for the given bodyids, using neuprint_locate_soma


whether or not to heal a fragmented skeleton using a minimum spanning tree, via nat::stitch_neurons_mst


whether or not to add synapse data to the retrieved skeletons in the format used by the rcatmaid package, for easy use with rcatmaid or catnat functions. This can be done for synapse-less skeletons using neuprint_assign_connectors


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 resampling occurs.


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 NULL, the 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 .Rprofile or .Renviron are used. See 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 details.


methods passed to neuprint_login