WEBKNOSSOS annotation module for working with skeleton and volume data.
This module provides the Annotation class for handling WEBKNOSSOS annotations, which can contain two types of data:
1. Skeleton Data: Represented by the `Skeleton` class, e.g. for annotating neural pathways
and structures.
2. Volume Annotation Layers: Used for segmentation data, can be exported as
`SegmentationLayer` objects.
The module supports various operations including
- Loading/saving annotations from/to .nml or .zip files
- Downloading/uploading annotations from/to WEBKNOSSOS
- Working with skeleton data and volume layers
- Exporting volume layers to datasets
Typical usage Examples
# Download an annotation from WEBKNOSSOS
annotation = Annotation.download("annotation_id")
# Add a volume layer with fallback for efficient processing
annotation.add_volume_layer(
name="segmentation",
fallback_layer="original_segmentation"
)
# Save the annotation locally
annotation.save("my_annotation.zip")
Notes
For volume annotations, using fallback layers is recommended for better performance in WEBKNOSSOS. Adding volume annotation data programmatically should be avoided when possible.
See Also
- Skeleton documentation: /webknossos/skeleton_annotation/index.html
- Volume annotation documentation: /webknossos/volume_annotation/index.html
Represents an annotation from WEBKNOSSOS containing skeleton and/or volume data.
The Annotation class provides functionality to:
- Load/save annotations from/to .nml or .zip files
- Download/upload annotations from/to WEBKNOSSOS
- Work with skeleton data and volume layers
- Export volume layers to datasets
Attributes:
-
name(str) –Name of the annotation.
-
skeleton(Skeleton) –Skeleton object containing tree/node data.
-
owner_name(str | None) –Name of annotation owner.
-
annotation_id(str | None) –Unique identifier for the annotation.
-
time(int | None) –Creation timestamp in ms since epoch.
-
edit_position(Vector3 | None) –3D position coordinates.
-
edit_rotation(Vector3 | None) –3D rotation angles.
-
zoom_level(float | None) –Current zoom level.
-
metadata(dict[str, str]) –Dictionary of custom metadata.
-
task_bounding_box(NDBoundingBox | None) –Optional bounding box for task annotations.
-
user_bounding_boxes(list[NDBoundingBox]) –List of user-defined bounding boxes.
Examples:
Create a new annotation:
ann = Annotation(
name="my_annotation",
dataset_name="sample_dataset",
voxel_size=(11.2, 11.2, 25.0)
)
Load annotation from file:
ann = Annotation.load("annotation.nml")
Download from WEBKNOSSOS:
ann = Annotation.download("annotation_id")
Save annotation:
ann.save("annotation.zip")
Add volume layer:
ann.add_volume_layer(
name="segmentation",
fallback_layer="segmentation_layer"
)
property
writable
¶
dataset_id: str | None
ID of the dataset this annotation belongs to.
Proxies to skeleton.dataset_id.
property
writable
¶
dataset_name: str
Name of the dataset this annotation belongs to.
Proxies to skeleton.dataset_name.
property
writable
¶
description: str | None
Optional description of the annotation.
Proxies to skeleton.description.
property
writable
¶
organization_id: str | None
ID of the organization owning this annotation.
Proxies to skeleton.organization_id.
class-attribute
instance-attribute
¶
task_bounding_box: NDBoundingBox | None = None
class-attribute
instance-attribute
¶
user_bounding_boxes: list[NDBoundingBox] = Factory(list)
property
writable
¶
voxel_size: tuple[float, float, float]
Voxel dimensions in nanometers (x, y, z).
Proxies to skeleton.voxel_size.
add_volume_layer(name: str, fallback_layer: Layer | str | None = None, volume_layer_id: int | None = None) -> None
Adds a new volume layer to the annotation.
Volume layers can be used to store segmentation data. Using fallback layers is recommended for better performance in WEBKNOSSOS.
Parameters:
-
name(str) –Name of the volume layer.
-
fallback_layer(Layer | str | None, default:None) –Optional reference to existing segmentation layer in WEBKNOSSOS. Can be Layer instance or layer name.
-
volume_layer_id(int | None, default:None) –Optional explicit ID for the layer. Auto-generated if not provided.
Raises:
-
AssertionError–If volume_layer_id already exists.
-
AssertionError–If fallback_layer is provided but not a segmentation layer.
Examples:
# Add basic layer
annotation.add_volume_layer("segmentation")
# Add with fallback
annotation.add_volume_layer("segmentation", fallback_layer="base_segmentation")
delete_volume_layer(volume_layer_name: str | None = None, volume_layer_id: int | None = None) -> None
Removes a volume layer from the annotation.
Parameters:
-
volume_layer_name(str | None, default:None) –Name of the layer to delete if multiple exist.
-
volume_layer_id(int | None, default:None) –ID of the layer to delete if multiple exist.
Raises:
-
ValueError–If neither name nor ID is provided when multiple layers exist.
-
AssertionError–If specified layer doesn't exist.
Examples:
# Delete by name
annotation.delete_volume_layer("unused_layer")
# Delete by ID
annotation.delete_volume_layer(volume_layer_id=2)
classmethod
¶
download(annotation_id_or_url: str, webknossos_url: str | None = None, *, skip_volume_data: bool = False) -> Annotation
download(annotation_id_or_url: str, webknossos_url: str | None = None, *, skip_volume_data: bool = False, _return_context: bool) -> tuple[Annotation, AbstractContextManager[None]]
download(annotation_id_or_url: str, webknossos_url: str | None = None, *, skip_volume_data: bool = False, retry_count: int = 5, _return_context: bool = False) -> Union[Annotation, tuple[Annotation, AbstractContextManager[None]]]
Downloads an annotation from WEBKNOSSOS.
Parameters:
-
annotation_id_or_url(str) –Either an annotation ID or complete WEBKNOSSOS URL. Example URL: https://webknossos.org/annotations/[id]
-
webknossos_url(str | None, default:None) –Optional custom WEBKNOSSOS instance URL.
-
skip_volume_data(bool, default:False) –If True, omits downloading volume layer data.
-
_return_context(bool, default:False) –Internal use only.
Returns:
-
Annotation(Union[Annotation, tuple[Annotation, AbstractContextManager[None]]]) –The downloaded annotation instance.
Examples:
# Download by ID
ann = Annotation.download("5f7d3a...")
# Download by URL
ann = Annotation.download("https://webknossos.org/annotations/5f7d3a...")
# Skip volume data
ann = Annotation.download("5f7d3a...", skip_volume_data=True)
export_volume_layer_to_dataset(dataset: Dataset, layer_name: str = 'volume_layer', volume_layer_name: str | None = None, volume_layer_id: int | None = None) -> SegmentationLayer
Exports a volume layer to a dataset.
Creates a new layer in the target dataset containing the volume annotation data.
Parameters:
-
dataset(Dataset) –Target Dataset instance.
-
layer_name(str, default:'volume_layer') –Name for the new layer (default: "volume_layer").
-
volume_layer_name(str | None, default:None) –Name of source volume layer if multiple exist.
-
volume_layer_id(int | None, default:None) –ID of source volume layer if multiple exist.
Returns:
-
SegmentationLayer(SegmentationLayer) –The created layer in the target dataset.
Raises:
-
AssertionError–If specified volume layer doesn't exist.
-
AssertionError–If volume layer data is not available.
Examples:
# Export to dataset
layer = annotation.export_volume_layer_to_dataset(
dataset,
layer_name="exported_segmentation"
)
get_remote_annotation_dataset() -> Dataset
Returns a streamed dataset of the annotation from WEBKNOSSOS.
Creates a remote dataset that includes fallback layers and potentially any active agglomerate mappings. Requires the annotation to be already stored in WEBKNOSSOS.
Returns:
-
Dataset(Dataset) –Remote dataset instance representing the annotation.
Raises:
-
ValueError–If annotation_id is not set (annotation not in WEBKNOSSOS).
Examples:
# Stream annotation as dataset
dataset = annotation.get_remote_annotation_dataset()
# Access layers
layer = dataset.get_layer("segmentation")
Notes: After an agglomerate mapping was activated in WEBKNOSSOS, it is applied to this method as soon as the first volume editing action is done. Note that this behavior might change in the future.
get_remote_base_dataset(sharing_token: str | None = None, webknossos_url: str | None = None) -> RemoteDataset
Returns a remote dataset connection to the base dataset.
Creates a connection to the dataset referenced by this annotation.
Parameters:
-
sharing_token(str | None, default:None) –Optional token for accessing private datasets.
-
webknossos_url(str | None, default:None) –Optional custom WEBKNOSSOS instance URL.
Returns:
-
RemoteDataset(RemoteDataset) –Connection to the base dataset.
Examples:
# Connect to base dataset
dataset = annotation.get_remote_base_dataset()
# With sharing token
dataset = annotation.get_remote_base_dataset(
sharing_token="abc123"
)
get_volume_layer_names() -> Iterable[str]
Returns names of all volume layers in the annotation.
Returns:
-
Iterable[str]–Iterable[str]: Iterator of volume layer names.
Examples:
# Print all layer names
for name in annotation.get_volume_layer_names():
print(f"Found layer: {name}")
get_volume_layer_segments(volume_layer_name: str | None = None, volume_layer_id: int | None = None) -> dict[int, SegmentInformation]
Returns segment information for a volume layer.
Returns a mutable dictionary mapping segment IDs to their metadata. Changes to the returned dictionary are reflected in the annotation locally.
Parameters:
-
volume_layer_name(str | None, default:None) –Name of the target volume layer if multiple exist.
-
volume_layer_id(int | None, default:None) –ID of the target volume layer if multiple exist.
Returns:
-
dict[int, SegmentInformation]–dict[int, SegmentInformation]: Dictionary mapping segment IDs to their information.
Raises:
-
ValueError–If neither name nor ID is provided when multiple layers exist.
-
AssertionError–If specified layer doesn't exist.
Examples:
# Get segments for a layer
segments = annotation.get_volume_layer_segments("segmentation_layer")
# Update segment name
segments[1].name = "Cell A"
Notes: Any changes performed on the online version of the annotaiton in webknossos are not synced automatically. The annotation needs to be re-downloaded to update segment information.
classmethod
¶
load(annotation_path: str | PathLike) -> Annotation
Loads an annotation from a file.
Supports loading from: - .nml files (skeleton-only annotations) - .zip files (containing .nml and optional volume layers)
Parameters:
-
annotation_path(str | PathLike) –Path to the .nml or .zip file.
Returns:
-
Annotation(Annotation) –The loaded annotation instance.
Raises:
-
AssertionError–If the file doesn't exist or has invalid extension.
-
RuntimeError–If the file format is invalid.
Examples:
# Load from NML
ann = Annotation.load("annotation.nml")
# Load from ZIP
ann = Annotation.load("annotation.zip")
merge_fallback_layer(target: Path, dataset_directory: Path, volume_layer_name: str | None = None, executor: Executor | None = None) -> None
Merges volume annotations with their fallback layer.
Creates a new dataset containing the merged result of volume annotations and fallback layer data.
Parameters:
-
target(Path) –Output path for merged dataset.
-
dataset_directory(Path) –Directory containing the fallback dataset.
-
volume_layer_name(str | None, default:None) –Name of volume layer to merge if multiple exist.
-
executor(Executor | None, default:None) –Optional executor for parallel processing.
Raises:
-
AssertionError–If no volume layers exist.
-
AssertionError–If specified volume layer doesn't exist.
Examples:
# Merge annotations with fallback
annotation.merge_fallback_layer(
Path("merged_dataset"),
Path("original_dataset")
)
classmethod
¶
open_as_remote_dataset(annotation_id_or_url: str, webknossos_url: str | None = None) -> Dataset
Opens an annotation directly as a remote dataset from WEBKNOSSOS.
This is a convenience method that combines downloading an annotation and converting it to a remote dataset in one step. It's useful when you want to work with the annotation data as a dataset without storing it locally.
Parameters:
-
annotation_id_or_url(str) –Either an annotation ID or complete WEBKNOSSOS URL. Example URL: https://webknossos.org/annotations/[id]
-
webknossos_url(str | None, default:None) –Optional custom WEBKNOSSOS instance URL.
Returns:
-
Dataset(Dataset) –A remote dataset instance representing the annotation.
Examples:
# Open by ID
dataset = Annotation.open_as_remote_dataset("5f7d3a...")
# Open by URL
dataset = Annotation.open_as_remote_dataset(
"https://webknossos.org/annotations/5f7d3a..."
)
# Access layers
layer = dataset.get_layer("segmentation")
Notes
This method automatically skips downloading volume data locally for efficiency, as the data will be streamed from the remote source.
classmethod
¶
open_remote(annotation_id_or_url: str, webknossos_url: str | None = None) -> RemoteAnnotation
save(path: str | PathLike) -> None
Saves the annotation to a file.
For skeleton-only annotations, saves as .nml file. For annotations with volume layers, saves as .zip file containing .nml and layers.
Parameters:
-
path(str | PathLike) –Target path ending in .nml or .zip (.zip required if annotation contains volume layers)
Raises:
-
AssertionError–If path has invalid extension or trying to save volume layers to .nml file.
Examples:
# Save skeleton-only annotation
annotation.save("skeleton.nml")
# Save with volume layers
annotation.save("full_annotation.zip")
temporary_volume_layer_copy(volume_layer_name: str | None = None, volume_layer_id: int | None = None, read_only: bool = True) -> Iterator[SegmentationLayer]
Creates a temporary copy of a volume layer as a dataset.
Context manager that provides temporary access to volume layer data as a SegmentationLayer.
Parameters:
-
volume_layer_name(str | None, default:None) –Name of target layer if multiple exist.
-
volume_layer_id(int | None, default:None) –ID of target layer if multiple exist.
-
read_only(bool, default:True) –If True, prevents modifications to the layer.
Yields:
-
SegmentationLayer(SegmentationLayer) –Temporary layer containing volume data.
Examples:
# Temporarily access volume data
with annotation.temporary_volume_layer_copy("segmentation") as layer:
data = layer.get_mag(1).read()
upload() -> str
Uploads the annotation to WEBKNOSSOS.
Uses the current webknossos_context for authentication and target instance. See webknossos.webknossos_context() for configuration.
Returns:
-
str(str) –URL of the uploaded annotation in WEBKNOSSOS.
Raises:
-
RuntimeError–If no valid authentication is configured.
Examples:
with webknossos.webknossos_context(token="my_token"):
url = annotation.upload()
print(f"Uploaded to: {url}")
Bases: Enum
This Enum contains the state of annotations belonging to tasks.
Can be retrieved via Task instances, getting AnnotationInfo from task.get_annotation_infos().
Bases: Enum
Annotations can be of different types which has to be specified when using Annotation.download()
with an annotation id.
class-attribute
instance-attribute
¶
EXPLORATIONAL = 'Explorational'
Explorational annotations are all annotations created without the task system, e.g. by uploading an annotation or using the "Create Annotation" Button in the dataset view in webknossos.
class-attribute
instance-attribute
¶
TASK = 'Task'
The Task type is automatically assigned to all annotations that are instances of a task.
See also Task.
RemoteAnnotation(annotation_id: str, organization_id: str, dataset_id: str | None = None, *, name: str, skeleton: Skeleton, owner_name: str, time: int | None = None, edit_position: Vector3 | None = None, edit_rotation: Vector3 | None = None, zoom_level: float | None = None, task_bounding_box: NDBoundingBox | None = None, user_bounding_boxes: list[NDBoundingBox] | None = None, metadata: dict[str, str] = {})
Bases: Annotation
A remote Annotation instance. Note: Please not initialize this class directly, use Annotation.open_remote() instead.
property
writable
¶
dataset_name: str
Name of the dataset this annotation belongs to.
Proxies to skeleton.dataset_name.
property
writable
¶
voxel_size: tuple[float, float, float]
Voxel dimensions in nanometers (x, y, z).
Proxies to skeleton.voxel_size.
add_volume_layer(name: str, fallback_layer: Layer | str | None = None, volume_layer_id: int | None = None) -> None
Adds a new volume layer to the annotation.
Volume layers can be used to store segmentation data. Using fallback layers is recommended for better performance in WEBKNOSSOS.
Parameters:
-
name(str) –Name of the volume layer.
-
fallback_layer(Layer | str | None, default:None) –Optional reference to existing segmentation layer in WEBKNOSSOS. Can be Layer instance or layer name.
-
volume_layer_id(int | None, default:None) –Optional explicit ID for the layer. Auto-generated if not provided.
Raises:
-
AssertionError–If volume_layer_id already exists.
-
AssertionError–If fallback_layer is provided but not a segmentation layer.
Examples:
# Add basic layer
annotation.add_volume_layer("segmentation")
# Add with fallback
annotation.add_volume_layer("segmentation", fallback_layer="base_segmentation")
delete_volume_layer(volume_layer_name: str | None = None, volume_layer_id: int | None = None) -> None
Removes a volume layer from the annotation.
Parameters:
-
volume_layer_name(str | None, default:None) –Name of the layer to delete if multiple exist.
-
volume_layer_id(int | None, default:None) –ID of the layer to delete if multiple exist.
Raises:
-
ValueError–If neither name nor ID is provided when multiple layers exist.
-
AssertionError–If specified layer doesn't exist.
Examples:
# Delete by name
annotation.delete_volume_layer("unused_layer")
# Delete by ID
annotation.delete_volume_layer(volume_layer_id=2)
classmethod
¶
download(annotation_id_or_url: str, webknossos_url: str | None = None, *, skip_volume_data: bool = False) -> Annotation
download(annotation_id_or_url: str, webknossos_url: str | None = None, *, skip_volume_data: bool = False, _return_context: bool) -> tuple[Annotation, AbstractContextManager[None]]
download(annotation_id_or_url: str, webknossos_url: str | None = None, *, skip_volume_data: bool = False, retry_count: int = 5, _return_context: bool = False) -> Union[Annotation, tuple[Annotation, AbstractContextManager[None]]]
Downloads an annotation from WEBKNOSSOS.
Parameters:
-
annotation_id_or_url(str) –Either an annotation ID or complete WEBKNOSSOS URL. Example URL: https://webknossos.org/annotations/[id]
-
webknossos_url(str | None, default:None) –Optional custom WEBKNOSSOS instance URL.
-
skip_volume_data(bool, default:False) –If True, omits downloading volume layer data.
-
_return_context(bool, default:False) –Internal use only.
Returns:
-
Annotation(Union[Annotation, tuple[Annotation, AbstractContextManager[None]]]) –The downloaded annotation instance.
Examples:
# Download by ID
ann = Annotation.download("5f7d3a...")
# Download by URL
ann = Annotation.download("https://webknossos.org/annotations/5f7d3a...")
# Skip volume data
ann = Annotation.download("5f7d3a...", skip_volume_data=True)
export_volume_layer_to_dataset(dataset: Dataset, layer_name: str = 'volume_layer', volume_layer_name: str | None = None, volume_layer_id: int | None = None) -> SegmentationLayer
Exports a volume layer to a dataset.
Creates a new layer in the target dataset containing the volume annotation data.
Parameters:
-
dataset(Dataset) –Target Dataset instance.
-
layer_name(str, default:'volume_layer') –Name for the new layer (default: "volume_layer").
-
volume_layer_name(str | None, default:None) –Name of source volume layer if multiple exist.
-
volume_layer_id(int | None, default:None) –ID of source volume layer if multiple exist.
Returns:
-
SegmentationLayer(SegmentationLayer) –The created layer in the target dataset.
Raises:
-
AssertionError–If specified volume layer doesn't exist.
-
AssertionError–If volume layer data is not available.
Examples:
# Export to dataset
layer = annotation.export_volume_layer_to_dataset(
dataset,
layer_name="exported_segmentation"
)
get_remote_annotation_dataset() -> Dataset
Returns a streamed dataset of the annotation from WEBKNOSSOS.
Creates a remote dataset that includes fallback layers and potentially any active agglomerate mappings. Requires the annotation to be already stored in WEBKNOSSOS.
Returns:
-
Dataset(Dataset) –Remote dataset instance representing the annotation.
Raises:
-
ValueError–If annotation_id is not set (annotation not in WEBKNOSSOS).
Examples:
# Stream annotation as dataset
dataset = annotation.get_remote_annotation_dataset()
# Access layers
layer = dataset.get_layer("segmentation")
Notes: After an agglomerate mapping was activated in WEBKNOSSOS, it is applied to this method as soon as the first volume editing action is done. Note that this behavior might change in the future.
get_remote_base_dataset(sharing_token: str | None = None, webknossos_url: str | None = None) -> RemoteDataset
Returns a remote dataset connection to the base dataset.
Creates a connection to the dataset referenced by this annotation.
Parameters:
-
sharing_token(str | None, default:None) –Optional token for accessing private datasets.
-
webknossos_url(str | None, default:None) –Optional custom WEBKNOSSOS instance URL.
Returns:
-
RemoteDataset(RemoteDataset) –Connection to the base dataset.
Examples:
# Connect to base dataset
dataset = annotation.get_remote_base_dataset()
# With sharing token
dataset = annotation.get_remote_base_dataset(
sharing_token="abc123"
)
get_volume_layer_names() -> Iterable[str]
Returns names of all volume layers in the annotation.
Returns:
-
Iterable[str]–Iterable[str]: Iterator of volume layer names.
Examples:
# Print all layer names
for name in annotation.get_volume_layer_names():
print(f"Found layer: {name}")
get_volume_layer_segments(volume_layer_name: str | None = None, volume_layer_id: int | None = None) -> dict[int, SegmentInformation]
Returns segment information for a volume layer.
Returns a mutable dictionary mapping segment IDs to their metadata. Changes to the returned dictionary are reflected in the annotation locally.
Parameters:
-
volume_layer_name(str | None, default:None) –Name of the target volume layer if multiple exist.
-
volume_layer_id(int | None, default:None) –ID of the target volume layer if multiple exist.
Returns:
-
dict[int, SegmentInformation]–dict[int, SegmentInformation]: Dictionary mapping segment IDs to their information.
Raises:
-
ValueError–If neither name nor ID is provided when multiple layers exist.
-
AssertionError–If specified layer doesn't exist.
Examples:
# Get segments for a layer
segments = annotation.get_volume_layer_segments("segmentation_layer")
# Update segment name
segments[1].name = "Cell A"
Notes: Any changes performed on the online version of the annotaiton in webknossos are not synced automatically. The annotation needs to be re-downloaded to update segment information.
classmethod
¶
load(annotation_path: str | PathLike) -> Annotation
Loads an annotation from a file.
Supports loading from: - .nml files (skeleton-only annotations) - .zip files (containing .nml and optional volume layers)
Parameters:
-
annotation_path(str | PathLike) –Path to the .nml or .zip file.
Returns:
-
Annotation(Annotation) –The loaded annotation instance.
Raises:
-
AssertionError–If the file doesn't exist or has invalid extension.
-
RuntimeError–If the file format is invalid.
Examples:
# Load from NML
ann = Annotation.load("annotation.nml")
# Load from ZIP
ann = Annotation.load("annotation.zip")
merge_fallback_layer(target: Path, dataset_directory: Path, volume_layer_name: str | None = None, executor: Executor | None = None) -> None
Merges volume annotations with their fallback layer.
Creates a new dataset containing the merged result of volume annotations and fallback layer data.
Parameters:
-
target(Path) –Output path for merged dataset.
-
dataset_directory(Path) –Directory containing the fallback dataset.
-
volume_layer_name(str | None, default:None) –Name of volume layer to merge if multiple exist.
-
executor(Executor | None, default:None) –Optional executor for parallel processing.
Raises:
-
AssertionError–If no volume layers exist.
-
AssertionError–If specified volume layer doesn't exist.
Examples:
# Merge annotations with fallback
annotation.merge_fallback_layer(
Path("merged_dataset"),
Path("original_dataset")
)
classmethod
¶
open_as_remote_dataset(annotation_id_or_url: str, webknossos_url: str | None = None) -> Dataset
Opens an annotation directly as a remote dataset from WEBKNOSSOS.
This is a convenience method that combines downloading an annotation and converting it to a remote dataset in one step. It's useful when you want to work with the annotation data as a dataset without storing it locally.
Parameters:
-
annotation_id_or_url(str) –Either an annotation ID or complete WEBKNOSSOS URL. Example URL: https://webknossos.org/annotations/[id]
-
webknossos_url(str | None, default:None) –Optional custom WEBKNOSSOS instance URL.
Returns:
-
Dataset(Dataset) –A remote dataset instance representing the annotation.
Examples:
# Open by ID
dataset = Annotation.open_as_remote_dataset("5f7d3a...")
# Open by URL
dataset = Annotation.open_as_remote_dataset(
"https://webknossos.org/annotations/5f7d3a..."
)
# Access layers
layer = dataset.get_layer("segmentation")
Notes
This method automatically skips downloading volume data locally for efficiency, as the data will be streamed from the remote source.
classmethod
¶
open_remote(annotation_id_or_url: str, webknossos_url: str | None = None) -> RemoteAnnotation
temporary_volume_layer_copy(volume_layer_name: str | None = None, volume_layer_id: int | None = None, read_only: bool = True) -> Iterator[SegmentationLayer]
Creates a temporary copy of a volume layer as a dataset.
Context manager that provides temporary access to volume layer data as a SegmentationLayer.
Parameters:
-
volume_layer_name(str | None, default:None) –Name of target layer if multiple exist.
-
volume_layer_id(int | None, default:None) –ID of target layer if multiple exist.
-
read_only(bool, default:True) –If True, prevents modifications to the layer.
Yields:
-
SegmentationLayer(SegmentationLayer) –Temporary layer containing volume data.
Examples:
# Temporarily access volume data
with annotation.temporary_volume_layer_copy("segmentation") as layer:
data = layer.get_mag(1).read()
upload() -> str
Uploads the annotation to WEBKNOSSOS.
Uses the current webknossos_context for authentication and target instance. See webknossos.webknossos_context() for configuration.
Returns:
-
str(str) –URL of the uploaded annotation in WEBKNOSSOS.
Raises:
-
RuntimeError–If no valid authentication is configured.
Examples:
with webknossos.webknossos_context(token="my_token"):
url = annotation.upload()
print(f"Uploaded to: {url}")
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