webknossos.skeleton.skeleton ¶

Skeleton ¶

Bases: Group

A hierarchical representation of skeleton annotations in WEBKNOSSOS.

The Skeleton class serves as the root container for all skeleton annotation data, organizing nodes and edges into a hierarchical structure of groups and trees. It contains dataset metadata and provides methods for loading, saving, and manipulating skeleton annotations.

Attributes:

voxel_size (Vector3) –

3D tuple (x, y, z) specifying the size of voxels in nanometers.
dataset_name (str) –

Name of the dataset this skeleton belongs to.
organization_id (Optional[str]) –

Optional ID of the organization owning this skeleton.
description (Optional[str]) –

Optional description of the skeleton annotation.
name (str) –

Always set to "Root" as this is the root group of the hierarchy.

The skeleton structure follows a hierarchical organization

Skeleton (root)
- Groups (optional organizational units)
  - Trees (collections of connected nodes)
    - Nodes (3D points with metadata)
    - Edges (connections between nodes)

Examples:

Create and populate a new skeleton:

# Create skeleton through an annotation
annotation = Annotation(
    name="dendrite_trace",
    dataset_name="cortex_sample",
    voxel_size=(11, 11, 24)
)
skeleton = annotation.skeleton

# Add hierarchical structure
dendrites = skeleton.add_group("dendrites")
basal = dendrites.add_group("basal")
tree = basal.add_tree("dendrite_1")

# Add and connect nodes
soma = tree.add_node(position=(100, 100, 100), comment="soma")
branch = tree.add_node(position=(200, 150, 100), radius=1.5)
tree.add_edge(soma, branch)

Load an existing skeleton:

# Load from NML file
skeleton = Skeleton.load("annotation.nml")

# Access existing structure
for group in skeleton.groups:
    for tree in group.trees:
        print(f"Tree {tree.name} has {len(tree.nodes)} nodes")

Notes

The Skeleton class inherits from Group, providing group and tree management methods.
To upload a skeleton to WEBKNOSSOS, create an Annotation with it.
For complex examples, see the skeleton synapse candidates example in the documentation.

children `property` ¶

children: Iterator[GroupOrTree]

Returns an iterator over all immediate children (groups and trees).

This property provides access to both groups and trees that are direct children of this group, in no particular order. For nested access, use flattened_trees() or flattened_groups().

Returns:

Iterator[GroupOrTree] –

Iterator[GroupOrTree]: Iterator yielding all immediate child groups and trees.

Examples:

# Print all immediate children
for child in group.children:
    if isinstance(child, Tree):
        print(f"Tree: {child.name}")
    else:
        print(f"Group: {child.name}")

dataset_id `class-attribute` `instance-attribute` ¶

dataset_id: Optional[str] = None

dataset_name `instance-attribute` ¶

dataset_name: str

description `class-attribute` `instance-attribute` ¶

description: Optional[str] = None

graphs `property` ¶

graphs: Iterator[Tree]

Deprecated, please use trees.

groups `property` ¶

groups: Iterator[Group]

Returns all (immediate) group children as an iterator. Use flattened_groups if you need also need groups within subgroups.

id `property` ¶

id: int

Read-only property.

name `class-attribute` `instance-attribute` ¶

name: str = field(default='Root', init=False, eq=False, repr=False)

Should not be used with Skeleton, this attribute is only useful for sub-groups. Set to Root.

organization_id `class-attribute` `instance-attribute` ¶

organization_id: Optional[str] = None

scale `property` `writable` ¶

scale: Tuple[float, float, float]

Deprecated, please use voxel_size.

trees `property` ¶

trees: Iterator[Tree]

Returns all (immediate) tree children as an iterator. Use flattened_trees if you also need trees within subgroups.

voxel_size `instance-attribute` ¶

voxel_size: Vector3

add_graph ¶

add_graph(name: str, color: Optional[Union[Vector4, Vector3]] = None, _enforced_id: Optional[int] = None) -> Tree

Deprecated, please use add_tree.

add_group ¶

add_group(name: str, _enforced_id: Optional[int] = None) -> Group

Creates and adds a new subgroup to this group.

Parameters:

name (str) –

Name for the new group.
_enforced_id (Optional[int], default: None ) –

Optional specific ID for the group (internal use).

Returns:

Group ( Group ) –

The newly created group.

Examples:

# Create nested group hierarchy
dendrites = neuron.add_group("dendrites")
basal = dendrites.add_group("basal")
apical = dendrites.add_group("apical")

add_nx_graphs ¶

add_nx_graphs(tree_dict: Union[List[Graph], Dict[str, List[Graph]]]) -> None

Import NetworkX graphs as skeleton trees.

Converts NetworkX Graph objects into skeleton trees, preserving node positions and edge connections. The graphs can be provided either as a list or as a dictionary mapping group names to lists of graphs.

Parameters:

tree_dict (Union[List[Graph], Dict[str, List[Graph]]]) –

Either: - A list of NetworkX graphs to be added directly to the skeleton - A dictionary mapping group names to lists of graphs, which will create new groups with the specified names containing the graphs

Raises:

ValueError –

If any graph nodes lack required position attributes.
TypeError –

If tree_dict is neither a list nor a dictionary.

Examples:

Add graphs directly to skeleton:

import networkx as nx

# Create sample graphs
g1 = nx.Graph()
g1.add_node(1, position=(0, 0, 0))
g1.add_node(2, position=(100, 0, 0))
g1.add_edge(1, 2)

g2 = nx.Graph()
g2.add_node(1, position=(0, 100, 0))
g2.add_node(2, position=(100, 100, 0))
g2.add_edge(1, 2)

# Add graphs directly
skeleton.add_nx_graphs([g1, g2])

# Or organize graphs into groups
graphs_by_group = {
    "dendrites": [g1],
    "axons": [g2]
}
skeleton.add_nx_graphs(graphs_by_group)

Note

Each node in the input graphs must have a 'position' attribute containing (x, y, z) coordinates
Other node attributes (e.g., radius, rotation) will be preserved
Edge attributes are currently not preserved in the conversion

add_tree ¶

add_tree(name_or_tree: Union[str, Tree], color: Optional[Union[Vector4, Vector3]] = None, _enforced_id: Optional[int] = None) -> Tree

Adds a new tree or copies an existing tree to this group.

This method supports two ways of adding trees: 1. Creating a new tree by providing a name 2. Copying an existing tree from another location

Parameters:

name_or_tree (Union[str, Tree]) –

Either a string name for a new tree or an existing Tree instance to copy.
color (Optional[Union[Vector4, Vector3]], default: None ) –

Optional RGBA color tuple (r, g, b, a) or RGB tuple (r, g, b). If an RGB tuple is provided, alpha will be set to 1.0.
_enforced_id (Optional[int], default: None ) –

Optional specific ID for the tree (internal use).

Returns:

Tree ( Tree ) –

The newly created or copied tree.

Examples:

# Create new tree
tree = group.add_tree("dendrite_1", color=(1, 0, 0, 1))

# Copy existing tree
copy = group.add_tree(existing_tree)

Notes

When copying a tree, a new ID will be generated if the original ID already exists in this group.

as_nml_group ¶

as_nml_group() -> Group

Converts this group to its NML representation.

This method creates a lightweight representation of the group suitable for serialization in the NML format.

Returns:

Group –

wknml.Group: NML representation of this group.

Notes

This is primarily used internally for file I/O operations.

flattened_graphs ¶

flattened_graphs() -> Iterator[Tree]

Deprecated, please use flattened_trees.

flattened_groups ¶

flattened_groups() -> Iterator[Group]

Returns an iterator of all groups within this group (and its subgroups).

flattened_trees ¶

flattened_trees() -> Iterator[Tree]

Returns an iterator of all trees in this group and its subgroups.

This method performs a recursive traversal of the group hierarchy, yielding all trees regardless of their nesting level.

Returns:

Iterator[Tree] –

Iterator[Tree]: Iterator yielding all contained trees.

Examples:

# Process all trees regardless of grouping
for tree in group.flattened_trees():
    print(f"Tree {tree.name} has {len(tree.nodes)} nodes")

from_path `staticmethod` ¶

from_path(file_path: Union[PathLike, str]) -> Skeleton

Deprecated. Use Skeleton.load instead.

get_graph_by_id ¶

get_graph_by_id(graph_id: int) -> Tree

Deprecated, please use get_tree_by_id.

get_group_by_id ¶

get_group_by_id(group_id: int) -> Group

Returns the group which has the specified group id.

get_max_graph_id ¶

get_max_graph_id() -> int

Deprecated, please use get_max_tree_id.

get_max_node_id ¶

get_max_node_id() -> int

Returns the highest node id of all nodes of all trees within this group (and its subgroups).

get_max_tree_id ¶

get_max_tree_id() -> int

Returns the highest tree id of all trees within this group (and its subgroups).

get_node_by_id ¶

get_node_by_id(node_id: int) -> Node

Retrieves a node by its ID from any tree in this group or its subgroups.

Parameters:

node_id (int) –

The ID of the node to find.

Returns:

Node ( Node ) –

The node with the specified ID.

Raises:

ValueError –

If no node with the given ID exists in any tree.

Examples:

try:
    node = group.get_node_by_id(42)
    print(f"Found node at position {node.position}")
except ValueError:
    print("Node not found")

get_total_node_count ¶

get_total_node_count() -> int

Counts all nodes in all trees within this group and its subgroups.

Returns:

int ( int ) –

Total number of nodes across all contained trees.

Examples:

# Check total annotation points
count = group.get_total_node_count()
print(f"Total annotation points: {count}")

get_tree_by_id ¶

get_tree_by_id(tree_id: int) -> Tree

Retrieves a tree by its ID from this group or its subgroups.

Parameters:

tree_id (int) –

The ID of the tree to find.

Returns:

Tree ( Tree ) –

The tree with the specified ID.

Raises:

ValueError –

If no tree with the given ID exists.

Examples:

try:
    tree = group.get_tree_by_id(42)
    print(f"Found tree '{tree.name}'")
except ValueError:
    print("Tree not found")

has_tree_id ¶

has_tree_id(tree_id: int) -> bool

Checks if a tree with the given ID exists in this group or its subgroups.

Parameters:

tree_id (int) –

The ID to check for.

Returns:

bool ( bool ) –

True if a tree with the ID exists, False otherwise.

Examples:

if group.has_tree_id(42):
    tree = group.get_tree_by_id(42)
    print(f"Tree exists: {tree.name}")

load `staticmethod` ¶

load(file_path: Union[PathLike, str]) -> Skeleton

Load a skeleton annotation from a file.

This method can load skeleton annotations from either a .nml file or a .zip file that contains an NML file. The .zip file may also contain volume layers.

Parameters:

file_path (Union[PathLike, str]) –

Path to the .nml or .zip file containing the skeleton annotation.

Returns:

Skeleton ( Skeleton ) –

A new Skeleton instance containing the loaded annotation data.

Raises:

FileNotFoundError –

If the specified file does not exist.
ValueError –

If the file format is not supported or the file is corrupted.

Examples:

Load from an NML file:

# Load a simple NML file
skeleton = Skeleton.load("dendrite_trace.nml")

# Load from a ZIP archive containing NML and volume data
skeleton = Skeleton.load("full_annotation.zip")

Note

If you need access to volume layers or other annotation data, use Annotation.load() instead, which returns an Annotation object containing both the skeleton and any additional data.

remove_tree_by_id ¶

remove_tree_by_id(tree_id: int) -> None

save ¶

save(out_path: Union[str, PathLike]) -> None

Save the skeleton annotation to a file.

Saves the skeleton data to either a .nml file or a .zip archive. The .zip format is recommended when the annotation includes volume layers or when you want to compress the data.

Parameters:

out_path (Union[str, PathLike]) –

Destination path for the saved file. Must end with either .nml or .zip extension.

Raises:

AssertionError –

If the file extension is not .nml or .zip.
OSError –

If there are permission issues or insufficient disk space.

Examples:

# Save as NML file
skeleton.save("dendrite_annotation.nml")

# Save as ZIP archive (recommended for complex annotations)
skeleton.save("full_annotation.zip")

Note

The name of the annotation will be derived from the filename stem
When saving as .zip, any associated volume layers will be included
The .nml format is human-readable XML but may be larger in size
The .zip format provides compression and can store additional data

write ¶

write(out_path: PathLike) -> None

Deprecated. Use Skeleton.save instead.

webknossos.skeleton.skeleton ¶

Skeleton ¶

children property ¶

dataset_id class-attribute instance-attribute ¶

dataset_name instance-attribute ¶

description class-attribute instance-attribute ¶

graphs property ¶

groups property ¶

id property ¶

name class-attribute instance-attribute ¶

organization_id class-attribute instance-attribute ¶

scale property writable ¶

trees property ¶

voxel_size instance-attribute ¶

add_graph ¶

add_group ¶

add_nx_graphs ¶

add_tree ¶

as_nml_group ¶

flattened_graphs ¶

flattened_groups ¶

flattened_trees ¶

from_path staticmethod ¶

get_graph_by_id ¶

get_group_by_id ¶

get_max_graph_id ¶

get_max_node_id ¶

get_max_tree_id ¶

get_node_by_id ¶

get_total_node_count ¶

get_tree_by_id ¶

has_tree_id ¶

load staticmethod ¶

remove_tree_by_id ¶

save ¶

write ¶

children `property` ¶

dataset_id `class-attribute` `instance-attribute` ¶

dataset_name `instance-attribute` ¶

description `class-attribute` `instance-attribute` ¶

graphs `property` ¶

groups `property` ¶

id `property` ¶

name `class-attribute` `instance-attribute` ¶

organization_id `class-attribute` `instance-attribute` ¶

scale `property` `writable` ¶

trees `property` ¶

voxel_size `instance-attribute` ¶

from_path `staticmethod` ¶

load `staticmethod` ¶