navis.VoxelNeuron¶
- class navis.VoxelNeuron(x, offset=None, cache=True, units=None, **metadata)[source]¶
Neuron represented as voxels.
- Parameters:
x (
ndarray
) –- Data to construct neuron from:
a 2D (N, 3) array of voxel positions (x, y, z)
a 2D (N, 4) array of voxel positions + values (x, y, z, value)
a 3D (N, M, J) array representing the voxel grid
offset ((3, ) array, optional) – An (optional) offset in voxels. This is useful to keep the voxel grid small while still maintaining correct positioning e.g. for plotting.
cache (bool) – Whether to cache different representations (i.e. grid and voxels) of the data. Set to False to save some memory.
units (str | pint.Units | pint.Quantity) – Units (scales) for voxels. Defaults to
1
(dimensionless). Strings must be parsable by pint: e.g. “nm”, “um”, “micrometer” or “8 nanometers”.**metadata – Any additional data to attach to neuron.
Initialize Voxel Neuron.
Methods
__init__
(x[, offset, cache, units])Initialize Voxel 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.
max
()Maximum value (excludes zeros).
memory_usage
([deep, estimate])Return estimated memory usage of this neuron.
min
()Minimum value (excludes zeros).
plot2d
(**kwargs)Plot neuron using
navis.plot2d()
.plot3d
(**kwargs)Plot neuron using
navis.plot3d()
.strip
([inplace])Strip empty voxels (leading/trailing planes of zeros).
summary
([add_props])Get a summary of this neuron.
threshold
(threshold[, inplace])Drop below-threshold voxels.
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) in units.
connectors
Connector table.
core_md5
MD5 checksum of core data.
datatables
Names of all DataFrames attached to this neuron.
dtype
Data type of voxel values.
extents
Extents of neuron in x/y/z direction (includes connectors).
Voxel grid representation.
id
ID of the neuron.
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Test if temporary attributes might be outdated.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.
offset
Offset (in voxels).
postsynapses
Table with postsynapses (filtered from connectors table).
presynapses
Table with presynapses (filtered from connectors table).
Shape of voxel grid.
type
Neuron type.
units
Units for coordinate space.
units_xyz
Units for coordinate space.
values
(N, ) array of values for each voxel
volume
Volume of neuron.
(N, 3) array of x/y/z voxels locations
soma