API Reference¶

Core¶

class neuroglancer.UnsynchronizedViewer

class neuroglancer.Viewer

Viewer state¶

class neuroglancer.viewer_state.SidePanelLocation

class neuroglancer.viewer_state.ToolPalette(SidePanelLocation)

class neuroglancer.viewer_state.SelectedLayerState(
    SidePanelLocation)

class neuroglancer.viewer_state.StatisticsDisplayState(
    SidePanelLocation)

class neuroglancer.viewer_state.LayerSidePanelState(
    SidePanelLocation)

class neuroglancer.viewer_state.LayerListPanelState(
    SidePanelLocation)

class neuroglancer.viewer_state.HelpPanelState(SidePanelLocation)

class neuroglancer.viewer_state.DimensionPlaybackVelocity

class neuroglancer.viewer_state.CoordinateSpaceTransform

class neuroglancer.viewer_state.LayerDataSubsource

class neuroglancer.viewer_state.LayerDataSource

class neuroglancer.viewer_state.LayerDataSources

class neuroglancer.viewer_state.InvlerpParameters

class neuroglancer.viewer_state.TransferFunctionParameters

class neuroglancer.viewer_state.SkeletonRenderingOptions

class neuroglancer.viewer_state.StarredSegments(
    MutableMapping[int, bool]
)

class neuroglancer.viewer_state.VisibleSegments(MutableSet[int])

Subset of visible segments within a StarredSegments object.

class neuroglancer.viewer_state.PointAnnotation(Annotation)

class neuroglancer.viewer_state.LineAnnotation(Annotation)

class neuroglancer.viewer_state.AxisAlignedBoundingBoxAnnotation(
    Annotation)

class neuroglancer.viewer_state.EllipsoidAnnotation(Annotation)

class neuroglancer.viewer_state.AnnotationPropertySpec

class neuroglancer.viewer_state.Layers

class neuroglancer.viewer_state.LinkedType[T]

Value linked to another value in the viewer state.

class neuroglancer.viewer_state.LinkedPosition(
    LinkedType[NDArray[float32]]
)

class neuroglancer.viewer_state.LinkedZoomFactor(LinkedType[float])

class neuroglancer.viewer_state.LinkedDepthRange(LinkedType[float])

class neuroglancer.viewer_state.LinkedOrientationState(
    LinkedType[NDArray[float32]]
)

class neuroglancer.viewer_state.CrossSection

class neuroglancer.viewer_state.CrossSectionMap

class neuroglancer.viewer_state.DataPanelLayout

class neuroglancer.viewer_state.StackLayout

neuroglancer.viewer_state.row_layout(children)

Creates a row-oriented StackLayout.

neuroglancer.viewer_state.column_layout(children)

Creates a column-oriented StackLayout.

class neuroglancer.viewer_state.LayerGroupViewer

class neuroglancer.viewer_state.ViewerState

class neuroglancer.Annotation

Segment sets¶

class neuroglancer.EquivalenceMap

Union-find data structure.

URL representation¶

neuroglancer.parse_url(url: str) -> ViewerState

Parses a Neuroglancer state from a URL.

neuroglancer.to_json_dump(state, indent=None, separators=None)

Returns the JSON-encoded text representation of the viewer state object.

neuroglancer.to_url(state: ViewerState, ...)

Encodes a viewer state as a URL.

Coordinate space¶

class neuroglancer.CoordinateArray

class neuroglancer.CoordinateSpace

class neuroglancer.DimensionScale(NamedTuple)

Layers¶

class neuroglancer.viewer_state.Layer

class neuroglancer.viewer_state.PointAnnotationLayer(Layer)

class neuroglancer.viewer_state.ImageLayer(Layer)

class neuroglancer.viewer_state.SegmentationLayer(Layer)

class neuroglancer.viewer_state.SingleMeshLayer(Layer)

class neuroglancer.viewer_state.AnnotationLayer(Layer)

class neuroglancer.viewer_state.LocalAnnotationLayer(
    AnnotationLayer)

class neuroglancer.viewer_state.ManagedLayer

Tools¶

class neuroglancer.viewer_state.Tool

class neuroglancer.viewer_state.LayerTool(Tool)

class neuroglancer.viewer_state.PlacePointTool(Tool)

class neuroglancer.viewer_state.PlaceLineTool(Tool)

class neuroglancer.viewer_state.PlaceBoundingBoxTool(Tool)

class neuroglancer.viewer_state.PlaceEllipsoidTool(Tool)

class neuroglancer.viewer_state.BlendTool(LayerTool)

class neuroglancer.viewer_state.OpacityTool(LayerTool)

class neuroglancer.viewer_state.VolumeRenderingTool(LayerTool)

class neuroglancer.viewer_state.VolumeRenderingGainTool(LayerTool)

class neuroglancer.viewer_state.VolumeRenderingDepthSamplesTool(
    LayerTool)

class neuroglancer.viewer_state.CrossSectionRenderScaleTool(
    LayerTool)

class neuroglancer.viewer_state.SelectedAlphaTool(LayerTool)

class neuroglancer.viewer_state.NotSelectedAlphaTool(LayerTool)

class neuroglancer.viewer_state.ObjectAlphaTool(LayerTool)

class neuroglancer.viewer_state.HideSegmentZeroTool(LayerTool)

class neuroglancer.viewer_state.HoverHighlightTool(LayerTool)

class neuroglancer.viewer_state.BaseSegmentColoringTool(LayerTool)

class neuroglancer.viewer_state.IgnoreNullVisibleSetTool(LayerTool)

class neuroglancer.viewer_state.ColorSeedTool(LayerTool)

class neuroglancer.viewer_state.SegmentDefaultColorTool(LayerTool)

class neuroglancer.viewer_state.MeshRenderScaleTool(LayerTool)

class neuroglancer.viewer_state.MeshSilhouetteRenderingTool(
    LayerTool)

class neuroglancer.viewer_state.SaturationTool(LayerTool)

class neuroglancer.viewer_state.SkeletonRenderingMode2dTool(
    LayerTool)

class neuroglancer.viewer_state.SkeletonRenderingMode3dTool(
    LayerTool)

class neuroglancer.viewer_state.SkeletonRenderingLineWidth2dTool(
    LayerTool)

class neuroglancer.viewer_state.SkeletonRenderingLineWidth3dTool(
    LayerTool)

class neuroglancer.viewer_state.ShaderControlTool(LayerTool)

class neuroglancer.viewer_state.MergeSegmentsTool(LayerTool)

class neuroglancer.viewer_state.SplitSegmentsTool(LayerTool)

class neuroglancer.viewer_state.SelectSegmentsTool(LayerTool)

class neuroglancer.viewer_state.DimensionTool(LayerTool)

Viewer Config state¶

class neuroglancer.viewer_config_state.SegmentIdMapEntry(
    NamedTuple)

neuroglancer.viewer_config_state.layer_selected_value(x)

class neuroglancer.viewer_config_state.LayerSelectionState

class neuroglancer.viewer_config_state.LayerSelectedValues

Specifies the data values associated with the current mouse position.

class neuroglancer.viewer_config_state.PanelResolutionData

class neuroglancer.viewer_config_state.LayerResolutionData

class neuroglancer.viewer_config_state.ScreenshotResolutionMetadata

class neuroglancer.viewer_config_state.ScreenshotReply

class neuroglancer.viewer_config_state.AggregateChunkSourceStatistics

class neuroglancer.viewer_config_state.ChunkSourceStatistics

class neuroglancer.viewer_config_state.ScreenshotStatistics

class neuroglancer.viewer_config_state.ActionState

class neuroglancer.viewer_config_state.Actions

class neuroglancer.viewer_config_state.InputEventBindings

class neuroglancer.viewer_config_state.PrefetchState

class neuroglancer.viewer_config_state.ScaleBarOptions

class neuroglancer.viewer_config_state.VolumeInfo

class neuroglancer.viewer_config_state.VolumeRequest

class neuroglancer.viewer_config_state.ConfigState

Exposing local data as data source¶

class neuroglancer.LocalVolume(ChangeNotifier)

Exposes a local array as a Neuroglancer data source.

Credentials¶

neuroglancer.set_boss_token(token)

Sets the authentication token for connecting to bossDB.

Capturing Screenshots¶

class neuroglancer.ScreenshotSaver

Saves screenshots in sequentially-numbered files.

Server¶

neuroglancer.is_server_running() -> bool

Returns True if the Python integration webserver is running.

neuroglancer.set_server_bind_address(
    bind_address=None, bind_port=0)

Sets the bind adress and port for the Python integration webserver.

neuroglancer.set_static_content_source(*args, **kwargs)

Specifies the Neuroglancer client hosted by the Python integration webserver.

neuroglancer.set_dev_server_content_source()

Builds the Neuroglancer client from source on demand for the Python integration.

neuroglancer.stop() -> None

Stop the server, invalidating any viewer URLs.

Utilities¶

JSON Containers¶

class neuroglancer.json_wrappers.Map[K, V]

Maps keys of type K to values of type V.

class neuroglancer.json_wrappers.List[T]

List of values of type T.

Trackable state¶

exception neuroglancer.trackable_state.ConcurrentModificationError(
    RuntimeError)

Indicates a concurrent modification during an update to TrackableState.

class neuroglancer.trackable_state.ChangeNotifier

Notifies registered callbacks in response to changes.

class neuroglancer.trackable_state.TrackableState[State](
    ChangeNotifier)

State object that supports registering change notification callbacks.