neuprint_read_neurons | R Documentation |
neuprint_read_neurons
is a full service function that
tries to build as complete neuron
objects as possible. Choose
whether or not to heal the fetched skeletons, assign a soma (if tagged in
neuprint) and assign synapses to approximate treenode positions, in the
style of neuron objects used by the rcatmaid package.
If neuprint_read_skeletons
is used, just a simple skeleton is
retrieved.
neuprint_read_neurons(
bodyids,
meta = TRUE,
nat = TRUE,
drvid = FALSE,
soma = TRUE,
heal = TRUE,
heal.threshold = 1000,
connectors = TRUE,
all_segments = TRUE,
dataset = NULL,
resample = FALSE,
conn = NULL,
OmitFailures = TRUE,
...
)
neuprint_read_skeletons(
bodyids,
dataset = NULL,
conn = NULL,
heal = TRUE,
heal.threshold = 1000,
...
)
neuprint_read_neurons_simple(bodyids, ...)
bodyids |
the body IDs for neurons/segments (bodies) you wish to query.
This can be in any form understood by |
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 |
heal.threshold |
distance in raw units beyond which isolated fragments
will not be merged onto the main skeleton. The default of |
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. |
dataset |
optional, a dataset you want to query. If |
resample |
if a number, the neuron is resampled using
|
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 |
a data frame in SWC format, or a
nat::neuronlist
/nat::neuron
object as used by
the nat
and catmaid
packages
neuprint_fetch_custom
,
neuprint_get_synapses
,
neuprint_assign_connectors
neurons = neuprint_read_neurons(c(818983130, 1796818119))
library(nat)
plot3d(neurons, col = "purple", lwd = 2)
## In this example, in hemibrain:v1.0, an erroneously connected bit
## of neuron skeleton is removed.
n1 = neuprint_read_neurons(5812980863, heal.threshold = 20e3)
## compare with
n2 = neuprint_read_neurons(5812980863, heal = FALSE)
dl1s=neuprint_read_skeletons('DL1 adPN')
plot(dl1s, WithNode=FALSE)
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