NGFF Coordinate Systems and Transforms

root coordinateSystems

NGFF CoordinateSystem

Type: array

Coordinate systems to combine with transforms to define spatial relationships

All items must be unique

No Additional Items

Each item of this array must be:

root coordinateSystems coordinateSystem

Type: object

Coordinate Systems for OME-NGFF

root coordinateSystems coordinateSystems items name

Type: string

Name of coordinate system. Must be unique among all coordinate systems.

Must be at least 1 characters long

root coordinateSystems coordinateSystems items axes

NGFF Axes

Type: array

JSON from OME-NGFF .zattrs

Must contain a minimum of 1 items

Must contain a maximum of 5 items

All items must be unique

No Additional Items

Each item of this array must be:

root coordinateSystems coordinateSystems items axes axis

Type: object

root coordinateSystems coordinateSystems items axes axes items name

Type: string

Name of the axis. Must be unique within the coordinate system.

Must be at least 1 characters long

root coordinateSystems coordinateSystems items axes axes items longName

Type: string

Longer name or description of the axis.

root coordinateSystems coordinateSystems items axes axes items type

Type: string

Type of the axis. Can be a predefined type or custom type.

root coordinateSystems coordinateSystems items axes axes items discrete

Type: boolean

Whether the dimension is discrete

root coordinateSystems coordinateSystems items axes axes items unit

Type: string

Unit for the axis

At least one of the items must be:

root coordinateSystems coordinateSystems items axes contains

Type: object

root coordinateSystems coordinateSystems items axes contains name

Type: string

root coordinateSystems coordinateSystems items axes contains type

Type: enum (of string)

Must be one of:

"space"

root coordinateSystems coordinateSystems items axes contains unit

Type: string

root coordinateTransformations

NGFF Coordinate Systems and Transforms

Type: array

Coordinate transformations defining spatial relationships between coordinate systems

Must contain a minimum of 1 items

All items must be unique

No Additional Items

Each item of this array must be:

root coordinateTransformations coordinateTransformations items

root coordinateTransformations coordinateTransformations items allOf coordinateTransformation

Type: object

OME-NGFF coordinate transformation.

All of

Requirement 1
Requirement 2

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 0

Type: object

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 0 name

Type: string

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 0 type

Type: string

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1

One of

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf identity

Type: object

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 0 type

Type: const
Specific value: "identity"

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf mapAxis

Type: object

Permute axes by name

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 1 type

Type: const
Specific value: "mapAxis"

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 1 mapAxis

Type: array of integer

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

No Additional Items

Each item of this array must be:

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 1 mapAxis mapAxis items

Type: integer

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 1 required

Type: object

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf scale

Type: object

One of

Option 1
Option 2

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 2 oneOf item 0

Type: object

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 2 oneOf item 0 path

Type: string

Path to a zarr array containing the scale factors.

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 2 oneOf item 1

Type: object

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 2 oneOf item 1 scale

Type: array of number
No Additional Items

Each item of this array must be:

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 2 oneOf item 1 scale scale items

Type: number

Value must be strictly greater than 0

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 2 type

Type: const
Specific value: "scale"

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf translation

Type: object

One of

Option 1
Option 2

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 3 oneOf item 0

Type: object

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 3 oneOf item 0 path

Type: string

Path to a zarr array containing the translation vectors.

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 3 oneOf item 1

Type: object

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 3 oneOf item 1 translation

Type: array of number
No Additional Items

Each item of this array must be:

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 3 oneOf item 1 translation translation items

Type: number

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 3 type

Type: const
Specific value: "translation"

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf affine

Type: object

One of

Option 1
Option 2

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 4 oneOf item 0

Type: object

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 4 oneOf item 0 path

Type: string

Path to a zarr array containing the affine matrix.

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 4 oneOf item 1

Type: object

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 4 oneOf item 1 affine

Type: array of array
No Additional Items

Each item of this array must be:

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 4 oneOf item 1 affine affine items

Type: array of number
No Additional Items

Each item of this array must be:

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 4 oneOf item 1 affine affine items affine items items

Type: number

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 4 type

Type: const
Specific value: "affine"

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf rotation

Type: object

One of

Option 1
Option 2

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 5 oneOf item 0

Type: object

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 5 oneOf item 0 path

Type: string

Path to a zarr array containing the rotation matrix.

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 5 oneOf item 1

Type: object

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 5 oneOf item 1 rotation

Type: array of array
No Additional Items

Each item of this array must be:

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 5 oneOf item 1 rotation rotation items

Type: array of number
No Additional Items

Each item of this array must be:

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 5 oneOf item 1 rotation rotation items rotation items items

Type: number

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 5 type

Type: const
Specific value: "rotation"

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf inverseOf

Type: object

The inverse of another coordinate transformation.

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 6 type

Type: const
Specific value: "inverseOf"

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 6 transformation

Type: object

OME-NGFF coordinate transformation.

Same definition as coordinateTransformations_items_allOf_i0

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf bijection

Type: object

A pair of forward and inverse coordinate transformations.

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 7 type

Type: const
Specific value: "bijection"

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 7 forward

Type: object

OME-NGFF coordinate transformation.

Same definition as coordinateTransformations_items_allOf_i0

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 7 inverse

Type: object

OME-NGFF coordinate transformation.

Same definition as coordinateTransformations_items_allOf_i0

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf sequence

Type: object

A sequence of transformations

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 8 type

Type: const
Specific value: "sequence"

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 8 transformations

Type: array
No Additional Items

Each item of this array must be:

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 8 transformations coordinateTransformation

Type: object

OME-NGFF coordinate transformation.

Same definition as coordinateTransformations_items_allOf_i0

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf byDimension

Type: object

A set of transformations applied independently to each dimension.

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 9 type

Type: const
Specific value: "byDimension"

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 9 transformations

Type: array
No Additional Items

Each item of this array must be:

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 9 transformations byDimensionTransformation

Type: object

Transformation used inside a byDimension transformation

All of

coordinateTransformation
Requirement 2

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 9 transformations transformations items allOf coordinateTransformation

Type: object

OME-NGFF coordinate transformation.

Same definition as coordinateTransformations_items_allOf_i0

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 9 transformations transformations items allOf item 1

Type: object

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 9 transformations transformations items allOf item 1 input_axes

Type: array of string

Names of the input axes for this transformation.

No Additional Items

Each item of this array must be:

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 9 transformations transformations items allOf item 1 input_axes input_axes items

Type: string

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 9 transformations transformations items allOf item 1 output_axes

Type: array of string

Names of the output axes for this transformation.

No Additional Items

Each item of this array must be:

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 9 transformations transformations items allOf item 1 output_axes output_axes items

Type: string

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf displacements

Type: object

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 10 type

Type: const
Specific value: "displacements"

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 10 path

Type: string

Path to the zarr array containing the displacement field.

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 10 interpolation

Type: enum (of string) Default: "linear"

Interpolation method to use when applying the displacement field.

Must be one of:

"nearest"
"linear"
"cubic"

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf coordinates

Type: object

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 11 type

Type: const
Specific value: "coordinates"

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 11 path

Type: string

Path to the zarr array containing the coordinate field.

root coordinateTransformations coordinateTransformations items allOf item 0 allOf item 1 oneOf item 11 interpolation

Type: enum (of string) Default: "linear"

Interpolation method to use when applying the coordinate field.

Must be one of:

"nearest"
"linear"
"cubic"

root coordinateTransformations coordinateTransformations items allOf item 1

Type: object

root coordinateTransformations coordinateTransformations items allOf item 1 input

Type: string

root coordinateTransformations coordinateTransformations items allOf item 1 output

Type: string

NGFF Coordinate Systems and Transforms

coordinateSystems

NGFF CoordinateSystem

Each item of this array must be:

name Required

axes Required

NGFF Axes

Each item of this array must be:

name Required

longName

type

discrete

unit

At least one of the items must be:

name

type

Must be one of:

unit

coordinateTransformations

NGFF Coordinate Systems and Transforms

Each item of this array must be:

All of

All of

name

type Required

One of

type

type

mapAxis

Each item of this array must be:

required

One of

path Required

scale Required

Each item of this array must be:

type

One of

path Required

translation Required

Each item of this array must be:

type

One of

path Required

affine Required

Each item of this array must be:

Each item of this array must be:

type

One of

path Required

rotation Required

Each item of this array must be:

Each item of this array must be:

type

type

transformation Required

type

forward Required

inverse Required

type

transformations Required

Each item of this array must be:

type

transformations Required

Each item of this array must be:

All of

input_axes Required

Each item of this array must be:

output_axes Required

Each item of this array must be:

type

path Required

interpolation

Must be one of:

type

path Required

interpolation

Must be one of:

input Required

output Required

arrayCoordinateSystem