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NGFF Coordinate Systems and Transforms

Title: NGFF Coordinate Systems and Transforms

Typearray
RequiredNo

Description: Coordinate Systems and transforms for OME-NGFF

Array restrictions
Min items1
Max itemsN/A
Items unicityTrue
Additional itemsFalse
Tuple validationSee below
Each item of this array must beDescription
root items-

1. NGFF Coordinate Systems and Transforms > root items

Typecombining
RequiredNo
Additional propertiesAny type allowed
All of(Requirement)
coordinateTransformation
item 1

1.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > coordinateTransformation

Typecombining
RequiredNo
Additional propertiesAny type allowed
Defined in#/$defs/coordinateTransformation

Description: OME-NGFF coordinate transformation.

All of(Requirement)
item 0
item 1

1.1.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 0

Typeobject
RequiredNo
Additional propertiesAny type allowed
PropertyPatternTypeDeprecatedDefinitionTitle/Description
- nameNostringNo--
+ typeNostringNo--
1.1.1.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 0 > name
Typestring
RequiredNo
1.1.1.2. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 0 > type
Typestring
RequiredYes

1.1.2. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1

Typecombining
RequiredNo
Additional propertiesAny type allowed
One of(Option)
identity
mapAxis
scale
translation
affine
rotation
inverseOf
bijection
sequence
byDimension
displacements
coordinates
1.1.2.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > identity
Typeobject
RequiredNo
Additional propertiesAny type allowed
Defined in#/$defs/identity
PropertyPatternTypeDeprecatedDefinitionTitle/Description
- typeNoconstNo--
1.1.2.1.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 0 > type
Typeconst
RequiredNo

Specific value: "identity"

1.1.2.2. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > mapAxis
Typeobject
RequiredNo
Additional propertiesAny type allowed
Defined in#/$defs/mapAxis

Description: Permute axes by name

PropertyPatternTypeDeprecatedDefinitionTitle/Description
- typeNoconstNo--
- mapAxisNoarray of integerNo-An array of integers representing the new axis order as zero-based indices of the input axes.
- requiredNoobjectNo--
1.1.2.2.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 1 > type
Typeconst
RequiredNo

Specific value: "mapAxis"

1.1.2.2.2. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 1 > mapAxis
Typearray of integer
RequiredNo

Description: An array of integers representing the new axis order as zero-based indices of the input axes.

Array restrictions
Min itemsN/A
Max itemsN/A
Items unicityFalse
Additional itemsFalse
Tuple validationSee below
Each item of this array must beDescription
mapAxis items-
1.1.2.2.2.1. NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 1 > mapAxis > mapAxis items
Typeinteger
RequiredNo
1.1.2.2.3. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 1 > required
Typeobject
RequiredNo
Additional propertiesAny type allowed
1.1.2.3. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > scale
Typecombining
RequiredNo
Additional propertiesAny type allowed
Defined in#/$defs/scale
PropertyPatternTypeDeprecatedDefinitionTitle/Description
- typeNoconstNo--
One of(Option)
item 0
item 1
1.1.2.3.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 2 > oneOf > item 0
Typeobject
RequiredNo
Additional propertiesAny type allowed
PropertyPatternTypeDeprecatedDefinitionTitle/Description
+ pathNostringNo-Path to a zarr array containing the scale factors.
1.1.2.3.1.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 2 > oneOf > item 0 > path
Typestring
RequiredYes

Description: Path to a zarr array containing the scale factors.

1.1.2.3.2. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 2 > oneOf > item 1
Typeobject
RequiredNo
Additional propertiesAny type allowed
PropertyPatternTypeDeprecatedDefinitionTitle/Description
+ scaleNoarray of numberNo--
1.1.2.3.2.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 2 > oneOf > item 1 > scale
Typearray of number
RequiredYes
Array restrictions
Min itemsN/A
Max itemsN/A
Items unicityFalse
Additional itemsFalse
Tuple validationSee below
Each item of this array must beDescription
scale items-
1.1.2.3.2.1.1. NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 2 > oneOf > item 1 > scale > scale items
Typenumber
RequiredNo
Restrictions
Minimum> 0
1.1.2.3.3. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 2 > type
Typeconst
RequiredNo

Specific value: "scale"

1.1.2.4. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > translation
Typecombining
RequiredNo
Additional propertiesAny type allowed
Defined in#/$defs/translation
PropertyPatternTypeDeprecatedDefinitionTitle/Description
- typeNoconstNo--
One of(Option)
item 0
item 1
1.1.2.4.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 3 > oneOf > item 0
Typeobject
RequiredNo
Additional propertiesAny type allowed
PropertyPatternTypeDeprecatedDefinitionTitle/Description
+ pathNostringNo-Path to a zarr array containing the translation vectors.
1.1.2.4.1.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 3 > oneOf > item 0 > path
Typestring
RequiredYes

Description: Path to a zarr array containing the translation vectors.

1.1.2.4.2. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 3 > oneOf > item 1
Typeobject
RequiredNo
Additional propertiesAny type allowed
PropertyPatternTypeDeprecatedDefinitionTitle/Description
+ translationNoarray of numberNo--
1.1.2.4.2.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 3 > oneOf > item 1 > translation
Typearray of number
RequiredYes
Array restrictions
Min itemsN/A
Max itemsN/A
Items unicityFalse
Additional itemsFalse
Tuple validationSee below
Each item of this array must beDescription
translation items-
1.1.2.4.2.1.1. NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 3 > oneOf > item 1 > translation > translation items
Typenumber
RequiredNo
1.1.2.4.3. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 3 > type
Typeconst
RequiredNo

Specific value: "translation"

1.1.2.5. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > affine
Typecombining
RequiredNo
Additional propertiesAny type allowed
Defined in#/$defs/affine
PropertyPatternTypeDeprecatedDefinitionTitle/Description
- typeNoconstNo--
One of(Option)
item 0
item 1
1.1.2.5.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 4 > oneOf > item 0
Typeobject
RequiredNo
Additional propertiesAny type allowed
PropertyPatternTypeDeprecatedDefinitionTitle/Description
+ pathNostringNo-Path to a zarr array containing the affine matrix.
1.1.2.5.1.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 4 > oneOf > item 0 > path
Typestring
RequiredYes

Description: Path to a zarr array containing the affine matrix.

1.1.2.5.2. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 4 > oneOf > item 1
Typeobject
RequiredNo
Additional propertiesAny type allowed
PropertyPatternTypeDeprecatedDefinitionTitle/Description
+ affineNoarray of arrayNo--
1.1.2.5.2.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 4 > oneOf > item 1 > affine
Typearray of array
RequiredYes
Array restrictions
Min itemsN/A
Max itemsN/A
Items unicityFalse
Additional itemsFalse
Tuple validationSee below
Each item of this array must beDescription
affine items-
1.1.2.5.2.1.1. NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 4 > oneOf > item 1 > affine > affine items
Typearray of number
RequiredNo
Array restrictions
Min itemsN/A
Max itemsN/A
Items unicityFalse
Additional itemsFalse
Tuple validationSee below
Each item of this array must beDescription
affine items items-
1.1.2.5.2.1.1.1. NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 4 > oneOf > item 1 > affine > affine items > affine items items
Typenumber
RequiredNo
1.1.2.5.3. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 4 > type
Typeconst
RequiredNo

Specific value: "affine"

1.1.2.6. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > rotation
Typecombining
RequiredNo
Additional propertiesAny type allowed
Defined in#/$defs/rotation
PropertyPatternTypeDeprecatedDefinitionTitle/Description
- typeNoconstNo--
One of(Option)
item 0
item 1
1.1.2.6.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 5 > oneOf > item 0
Typeobject
RequiredNo
Additional propertiesAny type allowed
PropertyPatternTypeDeprecatedDefinitionTitle/Description
+ pathNostringNo-Path to a zarr array containing the rotation matrix.
1.1.2.6.1.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 5 > oneOf > item 0 > path
Typestring
RequiredYes

Description: Path to a zarr array containing the rotation matrix.

1.1.2.6.2. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 5 > oneOf > item 1
Typeobject
RequiredNo
Additional propertiesAny type allowed
PropertyPatternTypeDeprecatedDefinitionTitle/Description
+ rotationNoarray of arrayNo--
1.1.2.6.2.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 5 > oneOf > item 1 > rotation
Typearray of array
RequiredYes
Array restrictions
Min itemsN/A
Max itemsN/A
Items unicityFalse
Additional itemsFalse
Tuple validationSee below
Each item of this array must beDescription
rotation items-
1.1.2.6.2.1.1. NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 5 > oneOf > item 1 > rotation > rotation items
Typearray of number
RequiredNo
Array restrictions
Min itemsN/A
Max itemsN/A
Items unicityFalse
Additional itemsFalse
Tuple validationSee below
Each item of this array must beDescription
rotation items items-
1.1.2.6.2.1.1.1. NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 5 > oneOf > item 1 > rotation > rotation items > rotation items items
Typenumber
RequiredNo
1.1.2.6.3. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 5 > type
Typeconst
RequiredNo

Specific value: "rotation"

1.1.2.7. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > inverseOf
Typeobject
RequiredNo
Additional propertiesAny type allowed
Defined in#/$defs/inverseOf

Description: The inverse of another coordinate transformation.

PropertyPatternTypeDeprecatedDefinitionTitle/Description
- typeNoconstNo--
+ transformationNoobjectNoSame as items_allOf_i0OME-NGFF coordinate transformation.
1.1.2.7.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 6 > type
Typeconst
RequiredNo

Specific value: "inverseOf"

1.1.2.7.2. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 6 > transformation
Typecombining
RequiredYes
Additional propertiesAny type allowed
Same definition asitems_allOf_i0

Description: OME-NGFF coordinate transformation.

1.1.2.8. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > bijection
Typeobject
RequiredNo
Additional propertiesAny type allowed
Defined in#/$defs/bijection

Description: A pair of forward and inverse coordinate transformations.

PropertyPatternTypeDeprecatedDefinitionTitle/Description
- typeNoconstNo--
+ forwardNoobjectNoSame as items_allOf_i0OME-NGFF coordinate transformation.
+ inverseNoobjectNoSame as items_allOf_i0OME-NGFF coordinate transformation.
1.1.2.8.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 7 > type
Typeconst
RequiredNo

Specific value: "bijection"

1.1.2.8.2. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 7 > forward
Typecombining
RequiredYes
Additional propertiesAny type allowed
Same definition asitems_allOf_i0

Description: OME-NGFF coordinate transformation.

1.1.2.8.3. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 7 > inverse
Typecombining
RequiredYes
Additional propertiesAny type allowed
Same definition asitems_allOf_i0

Description: OME-NGFF coordinate transformation.

1.1.2.9. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > sequence
Typeobject
RequiredNo
Additional propertiesAny type allowed
Defined in#/$defs/sequence

Description: A sequence of transformations

PropertyPatternTypeDeprecatedDefinitionTitle/Description
- typeNoconstNo--
+ transformationsNoarrayNo--
1.1.2.9.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 8 > type
Typeconst
RequiredNo

Specific value: "sequence"

1.1.2.9.2. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 8 > transformations
Typearray
RequiredYes
Array restrictions
Min itemsN/A
Max itemsN/A
Items unicityFalse
Additional itemsFalse
Tuple validationSee below
Each item of this array must beDescription
coordinateTransformationOME-NGFF coordinate transformation.
1.1.2.9.2.1. NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 8 > transformations > coordinateTransformation
Typecombining
RequiredNo
Additional propertiesAny type allowed
Same definition asitems_allOf_i0

Description: OME-NGFF coordinate transformation.

1.1.2.10. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > byDimension
Typeobject
RequiredNo
Additional propertiesAny type allowed
Defined in#/$defs/byDimension

Description: A set of transformations applied independently to each dimension.

PropertyPatternTypeDeprecatedDefinitionTitle/Description
- typeNoconstNo--
+ transformationsNoarrayNo--
1.1.2.10.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 9 > type
Typeconst
RequiredNo

Specific value: "byDimension"

1.1.2.10.2. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 9 > transformations
Typearray
RequiredYes
Array restrictions
Min itemsN/A
Max itemsN/A
Items unicityFalse
Additional itemsFalse
Tuple validationSee below
Each item of this array must beDescription
byDimensionTransformationTransformation used inside a byDimension transformation
1.1.2.10.2.1. NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 9 > transformations > byDimensionTransformation
Typecombining
RequiredNo
Additional propertiesAny type allowed
Defined in#/$defs/byDimensionTransformation

Description: Transformation used inside a byDimension transformation

All of(Requirement)
coordinateTransformation
item 1
1.1.2.10.2.1.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 9 > transformations > transformations items > allOf > coordinateTransformation
Typecombining
RequiredNo
Additional propertiesAny type allowed
Same definition asitems_allOf_i0

Description: OME-NGFF coordinate transformation.

1.1.2.10.2.1.2. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 9 > transformations > transformations items > allOf > item 1
Typeobject
RequiredNo
Additional propertiesAny type allowed
PropertyPatternTypeDeprecatedDefinitionTitle/Description
+ input_axesNoarray of stringNo-Names of the input axes for this transformation.
+ output_axesNoarray of stringNo-Names of the output axes for this transformation.
1.1.2.10.2.1.2.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 9 > transformations > transformations items > allOf > item 1 > input_axes
Typearray of string
RequiredYes

Description: Names of the input axes for this transformation.

Array restrictions
Min itemsN/A
Max itemsN/A
Items unicityFalse
Additional itemsFalse
Tuple validationSee below
Each item of this array must beDescription
input_axes items-
1.1.2.10.2.1.2.1.1. NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 9 > transformations > transformations items > allOf > item 1 > input_axes > input_axes items
Typestring
RequiredNo
1.1.2.10.2.1.2.2. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 9 > transformations > transformations items > allOf > item 1 > output_axes
Typearray of string
RequiredYes

Description: Names of the output axes for this transformation.

Array restrictions
Min itemsN/A
Max itemsN/A
Items unicityFalse
Additional itemsFalse
Tuple validationSee below
Each item of this array must beDescription
output_axes items-
1.1.2.10.2.1.2.2.1. NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 9 > transformations > transformations items > allOf > item 1 > output_axes > output_axes items
Typestring
RequiredNo
1.1.2.11. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > displacements
Typeobject
RequiredNo
Additional propertiesAny type allowed
Defined in#/$defs/displacements
PropertyPatternTypeDeprecatedDefinitionTitle/Description
- typeNoconstNo--
+ pathNostringNo-Path to the zarr array containing the displacement field.
- interpolationNoenum (of string)No-Interpolation method to use when applying the displacement field.
1.1.2.11.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 10 > type
Typeconst
RequiredNo

Specific value: "displacements"

1.1.2.11.2. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 10 > path
Typestring
RequiredYes

Description: Path to the zarr array containing the displacement field.

1.1.2.11.3. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 10 > interpolation
Typeenum (of string)
RequiredNo
Default"linear"

Description: Interpolation method to use when applying the displacement field.

Must be one of:

1.1.2.12. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > coordinates
Typeobject
RequiredNo
Additional propertiesAny type allowed
Defined in#/$defs/coordinates
PropertyPatternTypeDeprecatedDefinitionTitle/Description
- typeNoconstNo--
+ pathNostringNo-Path to the zarr array containing the coordinate field.
- interpolationNoenum (of string)No-Interpolation method to use when applying the coordinate field.
1.1.2.12.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 11 > type
Typeconst
RequiredNo

Specific value: "coordinates"

1.1.2.12.2. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 11 > path
Typestring
RequiredYes

Description: Path to the zarr array containing the coordinate field.

1.1.2.12.3. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 0 > allOf > item 1 > oneOf > item 11 > interpolation
Typeenum (of string)
RequiredNo
Default"linear"

Description: Interpolation method to use when applying the coordinate field.

Must be one of:

1.2. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 1

Typeobject
RequiredNo
Additional propertiesAny type allowed
PropertyPatternTypeDeprecatedDefinitionTitle/Description
+ inputNostringNo--
+ outputNostringNo--

1.2.1. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 1 > input

Typestring
RequiredYes

1.2.2. Property NGFF Coordinate Systems and Transforms > root items > allOf > item 1 > output

Typestring
RequiredYes

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