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datasources

ngtools.datasources

Wrappers around neuroglancer classes that can compute metadata and optional attributes that neuroglancer typically delegates to the frontend.

Dependencies
  • nifti:// -> nibabel
  • zarr:// -> zarr
  • precomputed:// -> cloudvolume

LayerDataSources 

LayerDataSources(*args, **kwargs)

Bases: Wraps(LayerDataSources)

List of data sources.

DataSourceInfo

Base class for source-specific metadata.

LayerDataSource 

LayerDataSource(*args, **kwargs)

Bases: Wraps(LayerDataSource)

A wrapper around ng.LayerDataSource that computes metadata.

info property 

info

Lazy access to format-specific metadata.

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.

VolumeInfo 

VolumeInfo(url)

Bases: DataSourceInfo

Base class for volume metadata.

Parameters:

Name Type Description Default
url str

URL to the file

 required

getNbLevels 

getNbLevels()

Compute number of dimensions.

getShape 

getShape(level=0)

Compute array shape.

getRank 

getRank()

Compute number of dimensions.

getSlopeInter 

getSlopeInter()

Affine intensity scaling.

getInputNames 

getInputNames()

Compute names of input axes.

getOutputNames 

getOutputNames()

Compute names of output axes.

getInputUnits 

getInputUnits()

Compute all units.

getOutputUnits 

getOutputUnits()

Compute all units.

getInputScales 

getInputScales()

Compute input scales.

getOutputScales 

getOutputScales()

Compute output scales.

getDataType 

getDataType()

Compute numpy data type.

getInputDimensions 

getInputDimensions()

Compute input dimensions.

getOutputDimensions 

getOutputDimensions()

Compute output dimensions.

getMatrix 

getMatrix()

Compute transformation matrix.

getTransform 

getTransform()

Compute neuroglancer transform.

VolumeDataSource 

VolumeDataSource(*args, **kwargs)

Bases: LayerDataSource

Wrapper for volume source.

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.

SkeletonDataSource 

SkeletonDataSource(*args, **kwargs)

Bases: LayerDataSource

Wrapper for skeleton source.

info property 

info

Lazy access to format-specific metadata.

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.

MeshDataSource 

MeshDataSource(*args, **kwargs)

Bases: LayerDataSource

Wrapper for mesh source.

info property 

info

Lazy access to format-specific metadata.

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.

AnnotationDataSource 

AnnotationDataSource(*args, **kwargs)

Bases: LayerDataSource

Wrapper for annotation source.

info property 

info

Lazy access to format-specific metadata.

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.

LocalDataSource 

LocalDataSource(*args, **kwargs)

Bases: LayerDataSource

Wrapper for local data sources.

info property 

info

Lazy access to format-specific metadata.

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.

LocalAnnotationDataSource 

LocalAnnotationDataSource(*args, **kwargs)

Bases: AnnotationDataSource, LocalDataSource

Wrapper for local annotation sources.

info property 

info

Lazy access to format-specific metadata.

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.

LocalSkeletonDataSource 

LocalSkeletonDataSource(*args, **kwargs)

Bases: SkeletonDataSource, LocalDataSource

Wrapper for data source that wraps a SkeletonSource.

local_skeleton property 

local_skeleton

Points to the underlying SkeletonSource, if any.

info property 

info

Lazy access to format-specific metadata.

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.

LocalVolumeDataSource 

LocalVolumeDataSource(*args, **kwargs)

Bases: VolumeDataSource, LocalDataSource

Wrapper for data source that wraps a LocalVolume.

local_volume property 

local_volume

Points to the underlying LocalVolume, if any.

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.

NiftiVolumeInfo 

NiftiVolumeInfo(url, align_corner=False, affine='best')

Bases: VolumeInfo

Metadata of a NIfTI volume.

Parameters:

Name Type Description Default
url str

URL to the file

 required
align_corner bool

If True, use neuroglancer's native behavior when computing the transform, which is to assume that (0, 0, 0) points to the corner of the first voxel. If False, use NIfTI's spec, which is to assume the (0, 0, 0) points to the center of the first voxel.

 False
affine (qform, sform, best, base)

Which orientation matrix to use. Neuroglancer uses the qform by default.

 "qform"

getShape 

getShape()

Compute array shape.

getInputNames 

getInputNames()

Compute names of input axes.

getOutputNames 

getOutputNames()

Compute names of output axes.

getSpaceUnit 

getSpaceUnit()

Compute spatial unit.

getTimeUnit 

getTimeUnit()

Compute time unit.

getUnits 

getUnits()

Compute all units.

getInputScales 

getInputScales()

Compute input scales.

getOutputScales 

getOutputScales()

Compute output scales.

getDescription 

getDescription()

Compute description string.

getDataType 

getDataType()

Compute numpy data type.

getSlopeInter 

getSlopeInter()

Compute intensity transform.

getMatrix 

getMatrix()

Compute transformation matrix.

getNbLevels 

getNbLevels()

Compute number of dimensions.

getRank 

getRank()

Compute number of dimensions.

getInputDimensions 

getInputDimensions()

Compute input dimensions.

getOutputDimensions 

getOutputDimensions()

Compute output dimensions.

getTransform 

getTransform()

Compute neuroglancer transform.

NiftiDataSource 

NiftiDataSource(*args, **kwargs)

Bases: VolumeDataSource

Wrapper for nifti sources.

Note that by default, neuroglancer assumes that the coordinate (0, 0, 0) in voxel space corresponds to the corner of the first voxel, whereas the nifti spec is that it corresponds to the center of the first voxel. This wrapper follows the nifti convention by default. The neuroglancer default behavior can be recovered with the option align_corner=True.

Also, by default, neuroglancer uses the qform orientation matrix, whereas the intent code must be used to choose between the sform and qform according to the spec (as implemented in e.g. nibabel). This wrapper follows the specification, unless the affine to use is explicitly specified with the option affine="sform", affine="qform", or affine="base".

Parameters:

Name Type Description Default
json_data dict | NiftiDataSource | str

URL to the file

 required

Other Parameters:

Name Type Description
url str

URL to the file
align_corner bool

If True, use neuroglancer's native behavior when computing the transform, which is to assume that (0, 0, 0) points to the corner of the first voxel. If False, use NIfTI's spec, which is to assume the (0, 0, 0) points to the center of the first voxel.
affine (qform, sform, best, base)

Which orientation matrix to use. Neuroglancer uses the qform by default.

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.

ZarrVolumeInfo 

ZarrVolumeInfo(url)

Bases: VolumeInfo

Base class + common methods for Zarr metadata.

Parameters:

Name Type Description Default
url str

URL to the file

 required

getShape 

getShape(level=0)

Array shape at a given level.

getNbLevels 

getNbLevels()

Return the number of levels in the pyramid.

hasOME 

hasOME()

Return True if Zarr has OME metadata.

hasNIfTI 

hasNIfTI()

Return True if Zarr has NIfTI metadata.

getMultiscalesOME 

getMultiscalesOME()

Return content of OME metadata (JSON).

getAxesOME 

getAxesOME()

Return OME axes (JSON).

getDatasetOME 

getDatasetOME(level=0)

Return OME dataset (JSON).

getNames 

getNames()

Return axis names.

getAxisTypes 

getAxisTypes()

Return axis type (space, time, channel).

getUnits 

getUnits()

Return units.

getScales 

getScales()

Return scales.

getTranslations 

getTranslations()

Return translations (in spatial units).

Although OME-NGFF v0.4 requires translations to appear after scales so that translations are expressed in world units, neuroglancer accepts transformations that have the opposite order, i.e., where translations are expressed in voxels. We also handle this case and rescale translations to world units.

getMatrix 

getMatrix()

Return transformation matrix.

getZarrTransform 

getZarrTransform()

Return the pure zarr transform.

getNiftiInputDimensions 

getNiftiInputDimensions()

Return nifti dimensions, but using OME axis names.

getNiftiOutputDimensions 

getNiftiOutputDimensions()

Return nifti output dimensions.

getNiftiMatrix 

getNiftiMatrix()

Return nifti transformation matrix.

getNiftiTransform 

getNiftiTransform()

Return nifti transform.

getNiftiZarrTransform 

getNiftiZarrTransform()

Return the transform to apply to a Zarr layer so that it's oriented according to the nifti metadata.

getTransform 

getTransform()

Return the nifti-zarr transform if it exists, else the ome-zarr transform.

getRank 

getRank()

Compute number of dimensions.

getSlopeInter 

getSlopeInter()

Affine intensity scaling.

getDataType 

getDataType()

Compute numpy data type.

getInputDimensions 

getInputDimensions()

Compute input dimensions.

getOutputDimensions 

getOutputDimensions()

Compute output dimensions.

Zarr2VolumeInfo 

Zarr2VolumeInfo(url, nifti=None)

Bases: ZarrVolumeInfo

Volume info for Zarr v2.

getDataType 

getDataType()

Array shape at a given level.

getNbLevels 

getNbLevels()

Return the number of levels in the pyramid.

getShape 

getShape(level=0)

Array shape at a given level.

getRank 

getRank()

Compute number of dimensions.

getSlopeInter 

getSlopeInter()

Affine intensity scaling.

getInputDimensions 

getInputDimensions()

Compute input dimensions.

getOutputDimensions 

getOutputDimensions()

Compute output dimensions.

getMatrix 

getMatrix()

Return transformation matrix.

getTransform 

getTransform()

Return the nifti-zarr transform if it exists, else the ome-zarr transform.

hasOME 

hasOME()

Return True if Zarr has OME metadata.

hasNIfTI 

hasNIfTI()

Return True if Zarr has NIfTI metadata.

getMultiscalesOME 

getMultiscalesOME()

Return content of OME metadata (JSON).

getAxesOME 

getAxesOME()

Return OME axes (JSON).

getDatasetOME 

getDatasetOME(level=0)

Return OME dataset (JSON).

getNames 

getNames()

Return axis names.

getAxisTypes 

getAxisTypes()

Return axis type (space, time, channel).

getUnits 

getUnits()

Return units.

getScales 

getScales()

Return scales.

getTranslations 

getTranslations()

Return translations (in spatial units).

Although OME-NGFF v0.4 requires translations to appear after scales so that translations are expressed in world units, neuroglancer accepts transformations that have the opposite order, i.e., where translations are expressed in voxels. We also handle this case and rescale translations to world units.

getZarrTransform 

getZarrTransform()

Return the pure zarr transform.

getNiftiInputDimensions 

getNiftiInputDimensions()

Return nifti dimensions, but using OME axis names.

getNiftiOutputDimensions 

getNiftiOutputDimensions()

Return nifti output dimensions.

getNiftiMatrix 

getNiftiMatrix()

Return nifti transformation matrix.

getNiftiTransform 

getNiftiTransform()

Return nifti transform.

getNiftiZarrTransform 

getNiftiZarrTransform()

Return the transform to apply to a Zarr layer so that it's oriented according to the nifti metadata.

Zarr3VolumeInfo 

Zarr3VolumeInfo(url, nifti=None)

Bases: ZarrVolumeInfo

Volume info for Zarr v3.

getDataType 

getDataType()

Array shape at a given level.

getNbLevels 

getNbLevels()

Return the number of levels in the pyramid.

getShape 

getShape(level=0)

Array shape at a given level.

getRank 

getRank()

Compute number of dimensions.

getSlopeInter 

getSlopeInter()

Affine intensity scaling.

getInputDimensions 

getInputDimensions()

Compute input dimensions.

getOutputDimensions 

getOutputDimensions()

Compute output dimensions.

getMatrix 

getMatrix()

Return transformation matrix.

getTransform 

getTransform()

Return the nifti-zarr transform if it exists, else the ome-zarr transform.

hasOME 

hasOME()

Return True if Zarr has OME metadata.

hasNIfTI 

hasNIfTI()

Return True if Zarr has NIfTI metadata.

getMultiscalesOME 

getMultiscalesOME()

Return content of OME metadata (JSON).

getAxesOME 

getAxesOME()

Return OME axes (JSON).

getDatasetOME 

getDatasetOME(level=0)

Return OME dataset (JSON).

getNames 

getNames()

Return axis names.

getAxisTypes 

getAxisTypes()

Return axis type (space, time, channel).

getUnits 

getUnits()

Return units.

getScales 

getScales()

Return scales.

getTranslations 

getTranslations()

Return translations (in spatial units).

Although OME-NGFF v0.4 requires translations to appear after scales so that translations are expressed in world units, neuroglancer accepts transformations that have the opposite order, i.e., where translations are expressed in voxels. We also handle this case and rescale translations to world units.

getZarrTransform 

getZarrTransform()

Return the pure zarr transform.

getNiftiInputDimensions 

getNiftiInputDimensions()

Return nifti dimensions, but using OME axis names.

getNiftiOutputDimensions 

getNiftiOutputDimensions()

Return nifti output dimensions.

getNiftiMatrix 

getNiftiMatrix()

Return nifti transformation matrix.

getNiftiTransform 

getNiftiTransform()

Return nifti transform.

getNiftiZarrTransform 

getNiftiZarrTransform()

Return the transform to apply to a Zarr layer so that it's oriented according to the nifti metadata.

ZarrDataSource 

ZarrDataSource(*args, **kwargs)

Bases: VolumeDataSource

Wrapper for Zarr data sources.

This wrapper will automatically check for the presence of a nifti group in the zarr object, which indicates that the file really has the nifti-zarr format.

This behavior can be changed by setting the option nifti=False (to load the file as a pure OME-Zarr) or nifti=True (which raises an error if the nifti group is not found).

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

guess_version classmethod 

guess_version(url)

Guess zarr version.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.

Zarr2DataSource 

Zarr2DataSource(*args, **kwargs)

Bases: ZarrDataSource

Wrapper for Zarr v2 data sources.

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.

guess_version classmethod 

guess_version(url)

Guess zarr version.

Zarr3DataSource 

Zarr3DataSource(*args, **kwargs)

Bases: ZarrDataSource

Wrapper for Zarr v3 data sources.

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.

guess_version classmethod 

guess_version(url)

Guess zarr version.

N5VolumeInfo 

N5VolumeInfo(url)

Bases: VolumeInfo

Base class + common methods for N5 metadata.

getDataType 

getDataType()

Array data type.

getShape 

getShape(level=0)

Array shape at a given level.

getNbLevels 

getNbLevels()

Return the number of levels in the pyramid.

getNames 

getNames()

Return axis names.

getUnits 

getUnits()

Return units.

getScales 

getScales()

Return scales.

getTranslations 

getTranslations()

Return translations (in spatial units).

getRank 

getRank()

Compute number of dimensions.

getSlopeInter 

getSlopeInter()

Affine intensity scaling.

getInputDimensions 

getInputDimensions()

Compute input dimensions.

getOutputDimensions 

getOutputDimensions()

Compute output dimensions.

getMatrix 

getMatrix()

Compute transformation matrix.

getTransform 

getTransform()

Compute neuroglancer transform.

N5DataSource 

N5DataSource(*args, **kwargs)

Bases: VolumeDataSource

Wrapper for N5 data sources.

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.

PrecomputedInfo 

PrecomputedInfo(url)

Base class for metadate about precomputed objects.

PrecomputedMeshInfo 

PrecomputedMeshInfo(url)

Bases: PrecomputedInfo

Metadata of a precomputed mesh.

PrecomputedLegacyMeshInfo 

PrecomputedLegacyMeshInfo(url)

Bases: PrecomputedInfo

Metadata of a precomputed mesh (legacy).

PrecomputedSkeletonInfo 

PrecomputedSkeletonInfo(url)

Bases: PrecomputedInfo

Metadata of a precomputed skeleton.

PrecomputedAnnotationInfo 

PrecomputedAnnotationInfo(url)

Bases: PrecomputedInfo

Metadata of a precomputed annotation.

PrecomputedVolumeInfo 

PrecomputedVolumeInfo(url)

Bases: PrecomputedInfo

Metadata of a precomputed volume.

getDataType 

getDataType()

TODO.

getShape 

getShape(level=0)

TODO.

getRank 

getRank()

TODO.

getScales 

getScales()

TODO.

getUnits 

getUnits()

TODO.

getNames 

getNames()

TODO.

getDimensions 

getDimensions()

TODO.

getTransform 

getTransform()

TODO.

getNbLevels 

getNbLevels()

TODO.

getVoxelOffset 

getVoxelOffset()

TODO.

getChunkSize 

getChunkSize(level=0, choice=0)

TODO.

PrecomputedDataSource 

PrecomputedDataSource(*args, **kwargs)

Bases: LayerDataSource

Base wrapper for precomputed data sources.

info property 

info

Lazy access to format-specific metadata.

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.

PrecomputedMeshDataSource 

PrecomputedMeshDataSource(*args, **kwargs)

Bases: MeshDataSource, PrecomputedDataSource

Base wrapper for precomputed mesh sources.

info property 

info

Lazy access to format-specific metadata.

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.

PrecomputedLegacyMeshDataSource 

PrecomputedLegacyMeshDataSource(*args, **kwargs)

Bases: MeshDataSource, PrecomputedDataSource

Base wrapper for precomputed mesh (legacy) sources.

info property 

info

Lazy access to format-specific metadata.

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.

PrecomputedSkeletonDataSource 

PrecomputedSkeletonDataSource(*args, **kwargs)

Bases: SkeletonDataSource, PrecomputedDataSource

Base wrapper for precomputed skeleton sources.

info property 

info

Lazy access to format-specific metadata.

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.

PrecomputedAnnotationDataSource 

PrecomputedAnnotationDataSource(*args, **kwargs)

Bases: AnnotationDataSource, PrecomputedDataSource

Base wrapper for precomputed annotations sources.

info property 

info

Lazy access to format-specific metadata.

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.

PrecomputedTractsDataSource 

PrecomputedTractsDataSource(*args, **kwargs)

Bases: PrecomputedAnnotationDataSource

Base wrapper for track precomputed annotations sources.

info property 

info

Lazy access to format-specific metadata.

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.

PrecomputedVolumeDataSource 

PrecomputedVolumeDataSource(*args, **kwargs)

Bases: VolumeDataSource, PrecomputedDataSource

Wrapper for precomputed volumes.

local_url property 

local_url

Path to url, even if file is local.

shape property 

shape

Return the shape of the array (spatial dimensions first).

rank property 

rank

Return the number of dimensions in the array.

dtype property 

dtype

Return the data type of the array.

slope_inter property 

slope_inter

Affine scaling to apply to the stored intensity.

dataobj property 

dataobj

Return an array-like object pointing to the data.

nb_levels property 

nb_levels

Number of pyramid levels.

input_dimensions property 

input_dimensions

Input dimensions.

output_dimensions property 

output_dimensions

Output dimensions.

input_bbox property 

input_bbox

Bounding box, in input_dimensions space and units.

output_bbox property 

output_bbox

Bounding box, in output_dimensions space and units.

input_center property 

input_center

Center of the field of view in input dimensions space and units.

output_center property 

output_center

Center of the field of view in output dimensions space and units.

input_bbox_size property 

input_bbox_size

Center of the field of view in input dimensions space and units.

output_bbox_size property 

output_bbox_size

Center of the field of view in output dimensions space and units.

output_voxel_size property 

output_voxel_size

Voxel size in model space.

get_dataobj 

get_dataobj(level=0, mode='r')

Return an array-like object pointing to a pyramid level.

quantiles 

quantiles(q)

Compute data quantiles.

apply_transform 

apply_transform(*args)

Apply an additional transform in model space.

datasource 

datasource(formats)

Register a format-specific datasource class.

Parameters:

Name Type Description Default
formats str | list[str]

Formats that should fallback to the decorated class.

 required