Neuron types¶

Depending your data/workflows you will use different ways to represent neurons. If, for example, you work with light-level data you might end up with point clouds or skeletons whereas modern connectomes typically provide meshes.

To cater for these different data types neurons in navis come in four flavours:

Neuron type	Description	Core data
`navis.TreeNeuron`	A hierarchical skeleton consisting of nodes and edges.	`.nodes`: the SWC node table
`navis.MeshNeuron`	A mesh with faces and vertices.	`.vertices`: (N, 3) array of x/y/z vertex coordinates `.faces`: (M, 3) array of faces
`navis.VoxelNeuron`	An image represented by either a 2d array of voxels or a 3d voxel grid.	`.voxels`: (N, 3) array of voxels `.values`: (N, ) array of values (i.e. intensity) `.grid`: (N, M, K) 3D voxelgrid
`navis.Dotprops`	A cloud of points, each with an associated local vector.	`.points`: (N, 3) array of point coordinates `.vect`: (N, 3) array of normalized vectors

Note that some functions in navis will work on some but not all neuron types (see this table in the API reference for details). If need be, navis also offers ways to convert between the different neuron types (see further below). For details on how to load/import your neurons into navis please see the other tutorials.

TreeNeurons¶

TreeNeurons represent a neuron as a tree-like “skeleton” - effectively a directed acyclic graph, i.e. they consist of nodes and each node connects to at most 1 parent. This format is commonly used to describe a neuron’s topology and often shared using SWC files.

A TreeNeuron is typically constructed from an SWC file (see navis.read_swc()) but you can also use a pandas.DataFrame or a networkx.DiGraph. See the skeleton I/O tutorial for details.

navis ships with a couple example Drosophila neurons from the Janelia hemibrain project published in Scheffer et al. (2020) and available at https://neuprint.janelia.org (see also the neuPrint tutorial):

# Import navis
import navis

# Load one of the example neurons
sk = navis.example_neurons(n=1, kind='skeleton')

# Inspect the neuron
sk


type	navis.TreeNeuron
name	DA1_lPN_R
id	1734350788
n_nodes	4465
n_connectors	2705
n_branches	599
n_leafs	618
cable_length	266476.875
soma	[4177]
units	8 nanometer
created_at	2022-05-09 11:52:08.206993
id	1734350788
origin	/Users/philipps/Google Drive/Cloudbox/Github/n...

TreeNeuron stores nodes and other data as attached DataFrames:

sk.nodes.head()

	node_id	x	y	z	radius	parent_id	type
0	1	15784.0	37250.0	28062.0	10.000000	-1	root
1	2	15764.0	37230.0	28082.0	18.284300	1	slab
2	3	15744.0	37190.0	28122.0	34.721401	2	slab
3	4	15744.0	37150.0	28202.0	34.721401	3	slab
4	5	15704.0	37130.0	28242.0	34.721401	4	slab

MeshNeurons¶

MeshNeurons consist of vertices and faces, and are a typical output of e.g. image segmentation.

MeshNeuron can be constructed from any object that has .vertices and .faces properties, a dictionary of vertices and faces or a file that can be parsed by trimesh.load. See the mesh I/O tutorial for details.

Each of the example neurons in navis also comes as mesh representation:

m = navis.example_neurons(n=1, kind='mesh')
m


type	navis.MeshNeuron
name	DA1_lPN_R
id	1734350788
units	8 nanometer
n_vertices	6309
n_faces	13054

MeshNeuron stores vertices and faces as attached numpy arrays:

m.vertices, m.faces

(TrackedArray([[16384.        , 34792.03125   , 24951.88085938],
               [16384.        , 36872.0625    , 25847.89453125],
               [16384.        , 36872.0625    , 25863.89453125],
               ...,
               [ 5328.08105469, 21400.07617188, 16039.99414062],
               [ 6872.10498047, 19560.04882812, 13903.96191406],
               [ 6872.10498047, 19488.046875  , 13927.96191406]]),
 TrackedArray([[3888, 3890, 3887],
               [3890, 1508, 3887],
               [1106, 1104, 1105],
               ...,
               [5394, 5426, 5548],
               [5852, 5926, 6017],
               [ 207,  217,  211]]))

Dotprops¶

Dotprops represent neurons as point clouds where each point is associated with a vector describing the local orientation. This simple representation often comes from e.g. light-level data or as direvative of skeletons/meshes (see navis.make_dotprops()). Dotprops are used e.g. for NBLAST. See the dotprops I/O tutorial for details.

Dotprops consist of .points and associated .vect (vectors). They are typically created from other types of neurons using navis.make_dotprops():

# Turn our above skeleton into dotprops
dp = navis.make_dotprops(sk, k=5)

dp


type	navis.Dotprops
name	DA1_lPN_R
id	1734350788
k	5
units	8 nanometer
n_points	4465

dp.points, dp.vect

(array([[15784., 37250., 28062.],
        [15764., 37230., 28082.],
        [15744., 37190., 28122.],
        ...,
        [14544., 36430., 28422.],
        [14944., 36510., 28282.],
        [15264., 36870., 28282.]], dtype=float32),
 array([[-0.3002053 , -0.39364937,  0.8688596 ],
        [-0.10845336, -0.2113751 ,  0.9713694 ],
        [-0.0435693 , -0.45593134,  0.8889479 ],
        ...,
        [-0.38446087,  0.44485292, -0.80888546],
        [-0.9457323 , -0.1827982 , -0.26865458],
        [-0.79947734, -0.5164282 , -0.30681902]], dtype=float32))

Check out the NBLAST tutorial for further details on dotprops!

VoxelNeurons¶

VoxelNeurons represent neurons as either 3d image or x/y/z voxel coordinates typically obtained from e.g. light-level microscopy.

VoxelNeuron consist of either a 3d (N, M, K) array (=”grid”) or an 2d (N, 3) array of voxel coordinates. You will probably find yourself loading these data from image files (e.g. .nrrd via navis.read_nrrd()). That said we can also “voxelize” other neuron types to produce VoxelNeurons:

# Load an example mesh
m = navis.example_neurons(n=1, kind='mesh')

# Voxelize:
# - with a 0.5 micron voxel size
# - some Gaussian smoothing
# - use number of vertices (counts) for voxel values
vx = navis.voxelize(m, pitch='0.5 microns', smooth=2, counts=True)

vx


type	navis.VoxelNeuron
name	DA1_lPN_R
id	1734350788
units	500.0 nanometer
shape	(298, 392, 286)
dtype	float32

# The grid representation of the neuron
vx.grid.shape

(297, 392, 286)

# The (N, 3) voxel + (N, ) values representation of the neuron
# -> this is the sparse representation of the neuron
vx.voxels.shape, vx.values.shape

((641384, 3), (641384,))

Note

You may have noticed that all neurons share some properties irrespective of their type, for example .id, .name or .units. These properties are optional and can be set when you first create the neuron, or at a later point.

In particular the .id property is important because many functions in navis will return results that are indexed by the neurons’ IDs. If .id is not set explicitly, it will default to some rather cryptic random UUID - you have been warned!

Connectors¶

navis was designed with connectivity data in mind! Therefore, each neuron - regardless of type - can have a .connectors table. Connectors are meant to bundle all kinds of connections: pre- & postsynapses, electrical synapses, gap junctions and so on.

A connector table must minimally contain an x/y/z coordinate and a type for each connector:

n = navis.example_neurons(1)
n.connectors.head()

	connector_id	node_id	type	x	y	z	roi	confidence
0	0	1436	pre	6444	21608	14516	LH(R)	0.959
1	1	1436	pre	6457	21634	14474	LH(R)	0.997
2	2	2638	pre	4728	23538	14179	LH(R)	0.886
3	3	1441	pre	5296	22059	16048	LH(R)	0.967
4	4	1872	pre	4838	23114	15146	LH(R)	0.990

Connector tables aren’t just passive meta data: certain functions in navis make use of or even require them. The most obvious example is probably for plotting.

# Plot neuron including its connectors
# Note we're increasing connector size and decreasing line width
# to illustrate emphasize connectors
fig, ax = navis.plot2d(n, connectors=True, color='k', cn_size=10, lw=.25)
ax.dist = 5

In above plot, red are presynapses (outputs) and cyan are postsynapses (inputs).

Somas¶

Unless a neuron is truncated, it should have a soma somewhere. Knowing where the soma is can be very useful, e.g. as point of reference for distance calculations or for plotting. Therefore, navis neurons have a .soma property:

n = navis.example_neurons(1)
n.soma

array([4177], dtype=int32)

In case of this exemplary TreeNeuron, the .soma points to an ID in the node table. We can also get the position:

n.soma_pos

array([[14957.1, 36540.7, 28432.4]], dtype=float32)

Other neuron types also support soma annotations but they may look slightly different. For a MeshNeuron, annotating a node position makes little sense. Instead, we track the x/y/z position directly:

m = navis.example_neurons(1, kind='mesh')
m.soma_pos

[14957.1, 36540.7, 28432.4]

For the record: .soma / .soma_pos can be set manually like any other property (there are some checks and balances to avoid issues) and can also be None:

# Set the skeleton's soma on node with ID 1
n.soma = 1
n.soma

# Drop soma from MeshNeuron
m.soma_pos = None

Units¶

navis supports assigning units to neurons. The neurons shipping with navis, for example, are in 8x8x8nm voxel space:

m = navis.example_neurons(1, kind='mesh')
m.units

8 nanometer

To assign or change the units simply use a descriptive string:

m.units = '10 micrometers'
m.units

10 micrometer

Tracking units is good practive but can also be very useful: some navis functions let you pass quantities as unit strings:

# Load example neuron in 8x8x8nm
n = navis.example_neurons(1, kind='skeleton')

# Resample to 1 micrometer
rs = navis.resample_skeleton(n, resample_to='1 um')

Lists of Neurons¶

Multiple neurons are typically collected in a NeuronList as container:

# Grab three example TreeNeurons
nl = navis.example_neurons(n=3)
nl

<class 'navis.core.neuronlist.NeuronList'> containing 3 neurons (875.1KiB)

	type	name	id	n_nodes	n_connectors	n_branches	n_leafs	cable_length	soma	units
0	navis.TreeNeuron	DA1_lPN_R	1734350788	4465	2705	599	618	266476.87500	[4177]	8 nanometer
1	navis.TreeNeuron	DA1_lPN_R	1734350908	4847	3042	735	761	304332.65625	[6]	8 nanometer
2	navis.TreeNeuron	DA1_lPN_R	722817260	4332	3136	633	656	274703.37500	None	8 nanometer

A NeuronList works similar to normal lists with a bunch of additional perks:

# Get the first neuron in the list
nl[0]


type	navis.TreeNeuron
name	DA1_lPN_R
id	1734350788
n_nodes	4465
n_connectors	2705
n_branches	599
n_leafs	618
cable_length	266476.875
soma	[4177]
units	8 nanometer

They also allow easy and fast access to data and across all neurons:

# Get the number of nodes in the first skeleton
nl[0].n_nodes

# Use the neuronlist to collect number of nodes across all neurons
nl.n_nodes

array([4465, 4847, 4332])

# Works on any neuron attribute
nl.cable_length

array([266476.88, 304332.66, 274703.38], dtype=float32)

In addition to these attributes, both TreeNeuron and NeuronList have shortcuts (called methods) to other navis functions. These lines of code are equivalent:

sk.reroot(sk.soma, inplace=True)
navis.reroot_skeleton(sk, sk.soma, inplace=True)

sk.plot3d(color='red')
navis.plot3d(sk, color='red')

lh = navis.example_volume('LH')
sk.prune_by_volume(lh, inplace=True)
navis.in_volume(sk, lh, inplace=True)

Note

The inplace parameter is part of many navis functions and works like e.g. in the pandas library:

if inplace=True operations are performed on the original
if inplace=False (default) operations are performed on a copy of the original which is then returned

# Load a neuron
n = navis.example_neurons(1)
# Load an example neuropil
lh = navis.example_volume('LH')

# Prune neuron to neurpil but leave original intact
n_lh = n.prune_by_volume(lh, inplace=False)

print(f'{n.n_nodes} nodes before and {n_lh.n_nodes} nodes after pruning')

4465 nodes before and 344 nodes after pruning

Index by position¶

NeuronList are designed to behave similar to numpy arrays in that they allow some fancing indexing.

You’ve already seen how to extract a single neuron from a NeuronList using a single integer index. Like for numpy arrays, this also works for list of indices…

nl = navis.example_neurons(n=3)

nl[[0, 2]]

<class 'navis.core.neuronlist.NeuronList'> containing 2 neurons (571.4KiB)

	type	name	id	n_nodes	n_connectors	n_branches	n_leafs	cable_length	soma	units
0	navis.TreeNeuron	DA1_lPN_R	1734350788	4465	2705	599	618	266476.875	[4177]	8 nanometer
1	navis.TreeNeuron	DA1_lPN_R	722817260	4332	3136	633	656	274703.375	None	8 nanometer

… or slices

nl[:2]

<class 'navis.core.neuronlist.NeuronList'> containing 2 neurons (577.6KiB)

	type	name	id	n_nodes	n_connectors	n_branches	n_leafs	cable_length	soma	units
0	navis.TreeNeuron	DA1_lPN_R	1734350788	4465	2705	599	618	266476.87500	[4177]	8 nanometer
1	navis.TreeNeuron	DA1_lPN_R	1734350908	4847	3042	735	761	304332.65625	[6]	8 nanometer

Index by attributes¶

You can index by NeuronList by boolean numpy.arrays - that includes TreeNeuron attributes, e.g. n_nodes, cable_length, soma, etc.

Index using node count:

subset = nl[nl.n_branches > 700]
subset

<class 'navis.core.neuronlist.NeuronList'> containing 1 neurons (303.8KiB)

	type	name	id	n_nodes	n_connectors	n_branches	n_leafs	cable_length	soma	units
0	navis.TreeNeuron	DA1_lPN_R	1734350908	4847	3042	735	761	304332.65625	[6]	8 nanometer

Here is an example where we subset to neurons that have a soma:

nl.soma

array([array([4177], dtype=int32), array([6], dtype=int32), None],
      dtype=object)

nl.soma != None

array([ True,  True, False])

subset = nl[nl.soma != None]
subset

<class 'navis.core.neuronlist.NeuronList'> containing 2 neurons (577.6KiB)

	type	name	id	n_nodes	n_connectors	n_branches	n_leafs	cable_length	soma	units
0	navis.TreeNeuron	DA1_lPN_R	1734350788	4465	2705	599	618	266476.87500	[4177]	8 nanometer
1	navis.TreeNeuron	DA1_lPN_R	1734350908	4847	3042	735	761	304332.65625	[6]	8 nanometer

Index by name¶

TreeNeuron can (but don’t have to) have names (.name). If you, for example, import neurons from SWC files they will inherit their name from the file by default.

Our example neurons all have the same name, so to demo this feature we will need to make those names unique:

for i, n in enumerate(nl):
    n.name = n.name + str(i + 1)
nl

<class 'navis.core.neuronlist.NeuronList'> containing 3 neurons (875.1KiB)

	type	name	id	n_nodes	n_connectors	n_branches	n_leafs	cable_length	soma	units
0	navis.TreeNeuron	DA1_lPN_R1	1734350788	4465	2705	599	618	266476.87500	[4177]	8 nanometer
1	navis.TreeNeuron	DA1_lPN_R2	1734350908	4847	3042	735	761	304332.65625	[6]	8 nanometer
2	navis.TreeNeuron	DA1_lPN_R3	722817260	4332	3136	633	656	274703.37500	None	8 nanometer

You can index by single…

nl['DA1_lPN_R1']

<class 'navis.core.neuronlist.NeuronList'> containing 1 neurons (273.8KiB)

	type	name	id	n_nodes	n_connectors	n_branches	n_leafs	cable_length	soma	units
0	navis.TreeNeuron	DA1_lPN_R1	1734350788	4465	2705	599	618	266476.875	[4177]	8 nanometer

… or multiple names:

nl[['DA1_lPN_R1', 'DA1_lPN_R2']]

<class 'navis.core.neuronlist.NeuronList'> containing 2 neurons (577.6KiB)

	type	name	id	n_nodes	n_connectors	n_branches	n_leafs	cable_length	soma	units
0	navis.TreeNeuron	DA1_lPN_R1	1734350788	4465	2705	599	618	266476.87500	[4177]	8 nanometer
1	navis.TreeNeuron	DA1_lPN_R2	1734350908	4847	3042	735	761	304332.65625	[6]	8 nanometer

Using regex¶

Under the hood navis uses re.fullmatch to match neuron names - so you can use regex!

nl['.*DA1.*']

<class 'navis.core.neuronlist.NeuronList'> containing 3 neurons (875.1KiB)

	type	name	id	n_nodes	n_connectors	n_branches	n_leafs	cable_length	soma	units
0	navis.TreeNeuron	DA1_lPN_R1	1734350788	4465	2705	599	618	266476.87500	[4177]	8 nanometer
1	navis.TreeNeuron	DA1_lPN_R2	1734350908	4847	3042	735	761	304332.65625	[6]	8 nanometer
2	navis.TreeNeuron	DA1_lPN_R3	722817260	4332	3136	633	656	274703.37500	None	8 nanometer

Index by ID¶

All neurons have an ID - even if you don’t explicitly assign one, a UUID will assigned under the hood.

nl[0].id

1734350788

Neuron lists can be indexed by their ID (similar to .loc[] in pandas DataFrames) by using the .idx indexer:

nl.idx[1734350908]


type	navis.TreeNeuron
name	DA1_lPN_R2
id	1734350908
n_nodes	4847
n_connectors	3042
n_branches	735
n_leafs	761
cable_length	304332.65625
soma	[6]
units	8 nanometer

Neuron Math¶

navis implements a very simple and intuitive syntax to add and remove items from a NeuronList:

Addition¶

To merge two lists in Python, you can simply add them:

[1] + [3]

[1, 3]

NeuronList works exactly the same:

nl[:2] + nl[2:]

<class 'navis.core.neuronlist.NeuronList'> containing 3 neurons (875.1KiB)

	type	name	id	n_nodes	n_connectors	n_branches	n_leafs	cable_length	soma	units
0	navis.TreeNeuron	DA1_lPN_R1	1734350788	4465	2705	599	618	266476.87500	[4177]	8 nanometer
1	navis.TreeNeuron	DA1_lPN_R2	1734350908	4847	3042	735	761	304332.65625	[6]	8 nanometer
2	navis.TreeNeuron	DA1_lPN_R3	722817260	4332	3136	633	656	274703.37500	None	8 nanometer

This also works on with two single TreeNeurons! You can use that to combine them into a list:

nl[0] + nl[1]

<class 'navis.core.neuronlist.NeuronList'> containing 2 neurons (577.6KiB)

	type	name	id	n_nodes	n_connectors	n_branches	n_leafs	cable_length	soma	units
0	navis.TreeNeuron	DA1_lPN_R1	1734350788	4465	2705	599	618	266476.87500	[4177]	8 nanometer
1	navis.TreeNeuron	DA1_lPN_R2	1734350908	4847	3042	735	761	304332.65625	[6]	8 nanometer

Substraction¶

To remove an item from a Python list, you would call the .pop() method:

l = [1, 2, 3]
l.pop(2)
l

[1, 2]

For NeuronList you can use substraction:

nl - nl[2]

<class 'navis.core.neuronlist.NeuronList'> containing 2 neurons (577.6KiB)

	type	name	id	n_nodes	n_connectors	n_branches	n_leafs	cable_length	soma	units
0	navis.TreeNeuron	DA1_lPN_R1	1734350788	4465	2705	599	618	266476.87500	[4177]	8 nanometer
1	navis.TreeNeuron	DA1_lPN_R2	1734350908	4847	3042	735	761	304332.65625	[6]	8 nanometer

Bitwise AND¶

To find the intersection between two lists, you would use sets and the & operator:

set([0, 1, 2]) &  set([2, 3, 4])

{2}

NeuronList work similarly:

nl[[0, 1]] & nl[[1, 2]]

<class 'navis.core.neuronlist.NeuronList'> containing 1 neurons (303.8KiB)

	type	name	id	n_nodes	n_connectors	n_branches	n_leafs	cable_length	soma	units
0	navis.TreeNeuron	DA1_lPN_R2	1734350908	4847	3042	735	761	304332.65625	[6]	8 nanometer

Multiplication and Division¶

So far, all operations have led to changes in the structure of the NeuronList. Multiplication and division are different! If you multiply/divide a TreeNeuron or NeuronList by a number, you will change the coordinates of nodes and connectors (including radii):

n = nl[0]
n.nodes.head()

	node_id	x	y	z	radius	parent_id	type
0	1	15784.0	37250.0	28062.0	10.000000	-1	root
1	2	15764.0	37230.0	28082.0	18.284300	1	slab
2	3	15744.0	37190.0	28122.0	34.721401	2	slab
3	4	15744.0	37150.0	28202.0	34.721401	3	slab
4	5	15704.0	37130.0	28242.0	34.721401	4	slab

n2 = n / 1000
n2.nodes.head()

	node_id	x	y	z	radius	parent_id	type
0	1	15.784	37.250000	28.062000	0.010000	-1	root
1	2	15.764	37.230000	28.082001	0.018284	1	slab
2	3	15.744	37.189999	28.122000	0.034721	2	slab
3	4	15.744	37.150002	28.202000	0.034721	3	slab
4	5	15.704	37.130001	28.242001	0.034721	4	slab

Note that this also automatically adjusts the neuron’s units (if it has any):

print('Before:', n.units)
print('After:', n2.units)

Before: 8 nanometer
After: 8.0 micrometer

Comparing Neuron/Lists¶

NeuronList implements some of the basic arithmetic and comparison operators that you might know from standard lists or numpy.arrays. Most this should be fairly intuitive (I hope) but there are a few things you should be aware of. The following examples will illustrate that.

Comparisons¶

In Python the == operator compares two elements:

1 == 1

True

2 == 1

False

For TreeNeuron this is comparison done by looking at the neurons’ attribues: morphologies (soma & root nodes, cable length, etc) and meta data (name).

nl[0] == nl[0]

True

nl[0] == nl[1]

False

To find out which attributes are compared, check out:

navis.TreeNeuron.EQ_ATTRIBUTES

['n_nodes',
 'n_connectors',
 'soma',
 'root',
 'n_branches',
 'n_leafs',
 'cable_length',
 'name']

Edit this list to establish your own criteria for equality.

For NeuronList, we do the same comparison pairwise between the neurons in both neuronlists:

nl == nl

True

nl == nl[:2]

False

Because the comparison is done pairwise and in order, shuffling a NeuronList will result in a failed comparison:

nl == nl[[2, 1, 0]]

False

Comparisons are safe against copying but making any changes to the neurons will cause inequality:

nl[0] == nl[0].copy()

True

nl[0] == nl[0].downsample(2, inplace=False)

False

You can also ask if a neuron is in a given NeuronList:

nl[0] in nl

True

nl[0] in nl[1:]

False

Making custom changes¶

Under the hood navis calculates certain properties when you load a neuron: e.g. it produces a graph representation (.graph or .igraph) and a list of linear segments (.segments) for TreeNeurons. These data are attached to a neuron and are crucial for many functions. Therefore navis makes sure that any changes to a neuron automatically propagate into these derived properties. See this example:

n = navis.example_neurons(1, kind='skeleton')

print(f'Nodes in node table: {n.nodes.shape[0]}')
print(f'Nodes in graph: {len(n.graph.nodes)}')

Nodes in node table: 4465
Nodes in graph: 4465

Making changes will cause the graph representation to be regenerated:

n.prune_by_strahler(1, inplace=True)

print(f'Nodes in node table: {n.nodes.shape[0]}')
print(f'Nodes in graph: {len(n.graph.nodes)}')

Nodes in node table: 1770
Nodes in graph: 1770

If, however, you make changes to the neurons that do not use built-in functions there is a chance that navis won’t know that things have changed and properties need to be regenerated!

n = navis.example_neurons(1)

print(f'Nodes in node table before: {n.nodes.shape[0]}')
print(f'Nodes in graph before: {len(n.graph.nodes)}')

# Truncate the node table by 55 nodes
n.nodes = n.nodes.iloc[:-55]

print(f'\nNodes in node table after: {n.nodes.shape[0]}')
print(f'Nodes in graph after: {len(n.graph.nodes)}')

Nodes in node table before: 4465
Nodes in graph before: 4465

Nodes in node table after: 4410
Nodes in graph after: 4410

Here, the changes to the node table automatically triggered a regeneration of the graph. This works because navis generates and checks hash values for neurons to detect changes and because here the node table is the master. It would not work the other way around (i.e. changing the graph to change the node table).

Again: as long as you are using built-in functions, you don’t have to worry about this. If you do run some custom manipulation of neurons be aware that you might want to make sure that the data structure remains intact. If you ever need to manually trigger a regeneration you can do so like this:

# Clear temporary attributes of the neuron
n._clear_temp_attr()

Converting neuron types¶

navis provides a couple functions to move between neuron types:

`navis.make_dotprops`(x[, k, resample, threshold])	Produce dotprops from neurons or x/y/z points.
`navis.skeletonize`(x, **kwargs)	Turn neuron into skeleton.
`navis.mesh`(x, **kwargs)	Generate mesh from object(s).
`navis.voxelize`(x, pitch[, bounds, counts, ...])	Turn neuron into voxels.

In particular meshing and skeletonizing are non-trivial and you might have to play around with the parameters to optimize results with your data! Let’s demonstrate on some example:

# Start with a mesh neuron
m = navis.example_neurons(1, kind='mesh')

# Skeletonize the mesh
s = navis.skeletonize(m)

# Make dotprops (this works from any other neuron type
dp = navis.make_dotprops(s, k=5)

# Voxelize the mesh
vx = navis.voxelize(m, pitch='2 microns', smooth=1, counts=True)

# Mesh the voxels
mm = navis.mesh(vx.threshold(.5))

Inspect the results:

# Co-visualize the mesh and the skeleton
fig = navis.plot3d([m, s], color=[(1, 1, 1, .2), 'r'])

# Co-visualize the mesh and the dotprops
fig = navis.plot3d([m, dp], color=[(1, 1, 1, .2), 'r'])

# Co-visualize the mesh and the dotprops
# (note that plotly is not great at visualizing voxels)
fig = navis.plot3d([m * 8, vx])

# Co-visualize the original mesh and the meshed voxels
fig = navis.plot3d([vx, mm])

Neuron attributes¶

This is a selection of neuron class (i.e. TreeNeuron, MeshNeuron, etc.) attributes.

All neurons have this:

name: a name
id: a (hopefully unique) identifier - defaults to random UUID if not set explicitly
bbox: Bounding box of neuron
units (optional): spatial units (e.g. “1 micrometer” or “8 nanometer” voxels)
connectors (optional): connector table

Only for TreeNeurons:

nodes: node table
cable_length: cable length(s)
soma: node ID(s) of soma (if applicable)
root: root node ID(s)
segments: list of linear segments
graph: NetworkX graph representation of the neuron
igraph: iGraph representation of the neuron (if library available)

Only for MeshNeurons:

vertices/faces: vertices and faces

Only for VoxelNeurons:

voxels: (N, 3) sparse representation
grid: (N, M, K) voxel grid representation

Only for Dotprops:

points (N, 3) x/y/z points
vect: (N, 3) array of the vector associated with each point

All above attributes can be accessed via the NeuronList containing the neurons. In addition you can also get:

is_mixed: returns True if list contains more than one neuron type
is_degenerated: returns True if list contains neurons with non-unique IDs
types: tuple with all types of neurons in the list
shape: size of neuronlist (N, )

All attributes and methods are accessible through auto-completion.

Reference¶

See TreeNeuron, MeshNeuron, Dotprops, VoxelNeuron, NeuronList or API for a full list of attributes and methods.