navis.MeshNeuron¶
- class navis.MeshNeuron(x, units=None, process=True, validate=False, **metadata)[source]¶
Neuron represented as mesh with vertices and faces.
- Parameters:
x (mesh-like | tuple | dictionary | filepath | None) –
- Data to construct neuron from:
any object that has
.vertices
and.faces
properties (e.g. a trimesh.Trimesh)a tuple
(vertices, faces)
a dictionary
{"vertices": (N, 3), "faces": (M, 3)}
filepath to a file that can be read by
trimesh.load
None
will initialize an empty MeshNeuronskeletor.Skeleton
will use the mesh and the skeleton (including the vertex to node map)
units (str | pint.Units | pint.Quantity) – Units for coordinates. Defaults to
None
(dimensionless). Strings must be parsable by pint: e.g. “nm”, “um”, “micrometer” or “8 nanometers”.process (bool) – If True (default and highly recommended), will remove NaN and infinite values, and merge duplicate vertices.
validate (bool) – If True, will try to fix some common problems with meshes. See
navis.fix_mesh
for details.**metadata – Any additional data to attach to neuron.
Initialize Mesh Neuron.
Methods
__init__
(x[, units, process, validate])Initialize Mesh Neuron.
convert_units
(to[, inplace])Convert coordinates to different unit.
copy
()Return a copy of the neuron.
map_units
(units[, on_error])Convert units to match neuron space.
memory_usage
([deep, estimate])Return estimated memory usage of this neuron.
plot2d
(**kwargs)Plot neuron using
navis.plot2d()
.plot3d
(**kwargs)Plot neuron using
navis.plot3d()
.skeletonize
([method, heal, inv_dist])Skeletonize mesh.
snap
(locs[, to])Snap xyz location(s) to closest vertex or synapse.
summary
([add_props])Get a summary of this neuron.
validate
([inplace])Use trimesh to try and fix some common mesh issues.
Attributes
CORE_DATA
Core data table(s) used to calculate hash
EQ_ATTRIBUTES
Attributes to be used when comparing two neurons.
SUMMARY_PROPS
Attributes used for neuron summary
TEMP_ATTR
Temporary attributes that need clearing when neuron data changes
bbox
Bounding box (includes connectors).
connectors
Connector table.
core_md5
MD5 checksum of core data.
datatables
Names of all DataFrames attached to this neuron.
extents
Extents of neuron in x/y/z direction (includes connectors).
Faces making up the neuron.
graph
Networkx Graph representation of the vertex connectivity.
id
ID of the neuron.
igraph
iGraph representation of the vertex connectivity.
is_isometric
Test if neuron is isometric.
is_locked
Test if neuron is locked.
is_stale
Test if temporary attributes might be outdated.
label
Label (e.g. for legends).
name
Neuron name.
postsynapses
Table with postsynapses (filtered from connectors table).
presynapses
Table with presynapses (filtered from connectors table).
Average distance between vertices.
skeleton
Skeleton representation of this neuron.
Trimesh representation of the neuron.
type
Neuron type.
units
Units for coordinate space.
units_xyz
Units for coordinate space.
Vertices making up the neuron.
Volume of the neuron.
soma