2d / 3d

Two and three dimensional examples.

axis_dependent

These transformations depend on the axes of their input coordinate system. In this case, the input coordinate system is the array's native coordinate system, which is duplicated.

mapAxis.zarr

An example using the rotation transformation type. Note that the rotation is about the origin.

byDimension.zarr

An example using the byDimension transformation type that itself contains scale and translation transformation types. This is a contrived example for demonstration purposes only.

basic

These transformations are all either identical to or slight re-expressions of in NGFF v0.4. All implementations should support these examples.

identity.zarr

An example using the identity transformation type. The physical coordinate system is identical to the array coordinate system.

scale.zarr

An example using the scale transformation type.

scale_multiscale.zarr

An example of a multiscale image using the scale transformation type.

sequenceScaleTranslation.zarr

An example using the sequence transformation type where the sequence contains one scale transformation and one translation transformation.

If an implementation supports all the transformation types contained in a sequence, then that implementation should also support the sequence.

sequenceScaleTranslation_multiscale.zarr

An example of a multiscale images using the sequence transformation type where the sequence contains one scale transformation and one translation transformation.

If an implementation supports all the transformation types contained in a sequence, then that implementation should also support the sequence.

The transformations here are identical to those in the affine_multiscale.zarr example.

translation.zarr

An example using the translation transformation type.

basic_binary

Example of basic transformations that store their parameters in zarr arrays.

scaleParams.zarr

A tranformation of type scale using the path parameter to reference the zarr array containing its parameters.

translationParams.zarr

A tranformation of type translation using the path parameter to reference the zarr array containing its parameters.

simple

Examples of transformations types that are new, but are simple enough that most implementation should support them. Specifically they are affines, or subsets of affines.

affine_multiscales.zarr

An example of a multiscale images using the affine transformation type

The transformations here are identical to those in the sequenceScaleTranslation_multiscale.zarr example.

affine.zarr

An example using the affine transformation type.

affineParams.zarr

An example using the affine transformation type for which its parameters are stored in zarr array.

rotation.zarr

An example using the rotation transformation type. Note that the rotation is about the origin.

rotationParams.zarr

An example using the rotation transformation type for which its parameters are stored in zarr array.

nonlinear

Examples of new, potentially non-linear transformation types. Implementations need not support these transformations.

invDisplacements.zarr

An example using the displacements transformation type wrapped in an inverseOf transformation.

This transformation is identical to that in the invCoordinates.zarr, but represented differently.

invCoordinates.zarr

An example using the coordinates transformation type wrapped in an inverseOf transformation.

This transformation is identical to that in the invDisplacements.zarr, but represented differently.

user_stories

Examples that are motivated by user stories.

stitched_tiles_2d

An example in which a set of 2D images tiles are each transformed to a shard "world" coordinate system using a different (translation) coordinate transformation.

stitched_tiles_3d

An example in which a set of 3D images tiles are each transformed to a shard "world" coordinate system using a different (translation) coordinate transformation.

image_registration_3d.zarr

An example of a two-step, invertible, non-linear, 3D registration. The two steps of 3D registration represented here were: first affine, then deformatble. As a result, one direction of the registration is represented as a sequence containing affine and displacements transformations.

Because displacements transformations are not closed-form invertible, this example uses a bijection transformation to indicate that the inverse is stored explicity.

• a bijection transformation
  • a forward transformation consisting of:
    • a sequence consisting of:
      • a displacement transformation
      • an affine transformation
  • an inverse transformation consisting of:
    • a sequence consisting of:
      • an affine transformation
      • a displacements transformation

lens_correction.zarr

A realistic example of "lens correction" - apply a 2D, nonlinear tranformation to every slice of a 3D image. This example using the byDimension transformation type that itself contains displacements and identity transformation types.

The displacement field for this example is sampled differently (more sparsely) than the image it is applied to.