read.neurons.fafbseg | R Documentation |
Reads neurons (or node count data) from the temporary FAFB segmentation instance. containing auto-segmented fragments from Peter Li. Neurons can also be read using a neuroglancer server fafbseg::read.neurons.brainmaps or fafbseg::read_segments2 if from local .zip files
read.neurons.fafbseg(
x,
google = FALSE,
conn = NULL,
seg = "v14seg-Li-190411.0",
...
)
fafbseg_get_node_count(
x,
read.from = c("CATMAID", "Neuroglancer", "local"),
seg = "v14seg-Li-190411.0",
...
)
x |
typically a skeleton ID in from the CATMAID FAFB v14-seg instance neuroglancer ID. |
google |
if TRUE, we treat x as the name of a Google FAFB segment. If name = FALSE, then x can be skeleton ids (numeric or characters) or the name / annotation for a neuron, if given as a character starting with 'name:' or 'annotation:' respectively. When Google FAFB fragments are merged, one name is maintained and the other may be found as an annotation. In order to check for this, annotations can also be read. |
conn |
a CATMAID connection object. If NULL catmaid::catmaid::catmaid_login() is called. |
seg |
the CATMAID segmentation instance, e.g. v14-seg, v14seg-Li-190411.0 |
... |
methods passed to catmaid::read.neurons.catmaid |
read.from |
from where to read FAFB segmented skeletons to generate node count data |
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