neuprint_dump | R Documentation |
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,
...
)
dir |
the directory to which to save the dump |
bodyids |
the body IDs for neurons/segments (bodies) you wish to query.
This can be in any form understood by |
roi |
a single ROI. Use |
preprocess |
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 |
connectivity |
whether or not to include connectivity information in the dump, i.e. an adjacency matrix between bodyids |
volumes |
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 |
meta |
whether or not to fetch a meta data for the given bodyids, using
|
nat |
whether or not to read neurons are |
drvid |
whether or not to use |
soma |
whether or not to fetch a possible soma location for the given
bodyids, using |
heal |
whether or not to heal a fragmented skeleton using a minimum
spanning tree, via |
connectors |
whether or not to add synapse data to the retrieved
skeletons in the format used by the |
all_segments |
if TRUE, all bodies are considered, if FALSE, only 'Neurons', i.e. bodies with a status roughly traced status. |
resample |
if a number, the neuron is resampled using
|
scale |
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. |
voxel.thresh |
the size threshold, in number of voxels, a neuron/segment must exceed, to be included in the dump, if read from an ROI |
dataset |
optional, a dataset you want to query. If |
conn |
optional, a neuprintr connection object, which also specifies the
neuPrint server. If NULL, the defaults set in your
|
OmitFailures |
Whether to omit neurons for which |
... |
methods passed to |
neuprint_get_synapses
, neuprint_read_neurons
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