conversion
navis.conversion.mesh2skeleton
#
Turn mesh neuron into skeleton.
This function is a thin-wrapper for skeletor
. It uses sensible defaults for neurons but if you want to fine-tune your skeletons you should look into using skeletor
directly.
PARAMETER | DESCRIPTION |
---|---|
x |
TYPE: |
method |
TYPE: |
fix_mesh |
TYPE: |
shave |
TYPE: |
heal |
TYPE: |
connectors |
TYPE: |
inv_dist |
TYPE: |
**kwargs |
DEFAULT: |
RETURNS | DESCRIPTION |
---|---|
skeleton | Has a TYPE: |
See Also
navis.drop_fluff
Use this if your mesh has lots of tiny free floating bits to reduce noise and speed up skeletonization.
Examples:
>>> import navis
>>> # Get a mesh neuron
>>> n = navis.example_neurons(1, kind='mesh')
>>> # Convert to skeleton
>>> sk = navis.conversion.mesh2skeleton(n)
>>> # Mesh vertex indices to node IDs map
>>> sk.vertex_map
array([938, 990, 990, ..., 39, 234, 234])
Source code in navis/conversion/converters.py
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navis.conversion.neuron2voxels
#
Turn neuron into voxels.
PARAMETER | DESCRIPTION |
---|---|
x |
TYPE: |
pitch |
TYPE: |
bounds |
TYPE: |
counts |
TYPE: |
vectors |
TYPE: |
alphas |
TYPE: |
smooth |
TYPE: |
RETURNS | DESCRIPTION |
---|---|
VoxelNeuron | Has the voxel grid as |
Examples:
>>> import navis
>>> # Get a skeleton
>>> n = navis.example_neurons(1)
>>> # Convert to voxel neuron
>>> vx = navis.conversion.neuron2voxels(n, pitch='5 microns')
Source code in navis/conversion/converters.py
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navis.conversion.points2skeleton
#
Turn points into skeleton.
This function works by: 1. Compute the k
nearest neighbors for each point 2. Generate a graph from the nearest-neighbor edges 3. Extract a minimum-spanning tree (MST) from the graph 4. Process the MST into a skeleton
PARAMETER | DESCRIPTION |
---|---|
x |
TYPE: |
k |
TYPE: |
max_dist |
TYPE: |
RETURNS | DESCRIPTION |
---|---|
skeleton | TYPE: |
Examples:
>>> import navis
>>> # Get a mesh neuron
>>> n = navis.example_neurons(1)
>>> # Get the points
>>> pts = n.nodes[['x', 'y', 'z']].values
>>> # Convert points back into skeleton
>>> sk = navis.conversion.points2skeleton(pts)
Source code in navis/conversion/converters.py
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navis.conversion.tree2meshneuron
#
Convert TreeNeuron to MeshNeuron.
Uses the radius
to convert skeleton to 3D tube mesh. Missing radii are treated as zeros.
PARAMETER | DESCRIPTION |
---|---|
x |
TYPE: |
tube_points |
TYPE: |
radius_scale_factor |
TYPE: |
use_normals |
TYPE: |
warn_missing_radii |
TYPE: |
RETURNS | DESCRIPTION |
---|---|
TreeNeuron | Data tables (e.g. |
Examples:
>>> import navis
>>> # Get a skeleton
>>> n = navis.example_neurons(1)
>>> # Convert to mesh neuron
>>> m = navis.conversion.tree2meshneuron(n)
Source code in navis/conversion/converters.py
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navis.conversion.voxels2mesh
#
Generate mesh from voxels using marching cubes.
PARAMETER | DESCRIPTION |
---|---|
voxels |
TYPE: |
spacing |
TYPE: |
step_size |
TYPE: |
chunk_size |
TYPE: |
For |
|
pad_chunks |
TYPE: |
merge_fragments |
TYPE: |
progress |
TYPE: |
RETURNS | DESCRIPTION |
---|---|
mesh | Returns a trimesh or MeshNeuron depending on the input. Data tables (e.g. TYPE: |
Source code in navis/conversion/meshing.py
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