neu_morpho¶
neu-morpho: segment morphology from segmentation volumes.
Generate multi-resolution Draco-encoded meshes (via vol2mesh) per segment,
written in neuroglancer-precomputed format, orchestrated across segments with
blockrun and reading segmentation arrays with neu-vol; read, measure and compare
meshes and skeletons. Skeletons themselves are made by neu-skel, a separate
GPL-licensed package that runs as an extra stage of this pipeline.
The pipeline runs from the neu-morpho command; from Python:
import neu_morpho
summary = neu_morpho.pipeline.run(neu_morpho.pipeline.plan(src, dst)) # serial
db = neu_morpho.MetricsDB(path) # per-body metrics
Large segments (whose binary mask over a big bounding box would OOM) are meshed chunked and stitched rather than materialized whole. See the README, and neu-skel for the tracers.