nat.h5reg: Neuroanatomy Toolbox Support for Saalfeld/Bogovic HDF5 Registration Format

Enables the Neuroanatomy Toolbox (nat) suite to carry out 3D coordinate transformation defined by points encoded in the HDF5 registration format defined by Stephan Saalfeld and John Bogovic.

h5 registration format

The h5 registration format has been defined by John Bogovic and Stephan Saalfeld as an efficient way to distribute deformation fields (and accompanying affine transformations). This provides a standard way to distribute and apply such transforms in an HDF5 wrapper.

Although deformation fields are the most general form of specifying a non-rigid registration, they can be much larger than a parametric deformation. h5 tools provide a substantial (lossy) compression of these fields at the expense of a very small (and usually irrelevant) loss of precision. They also provide the option to have one or more downsampled versions of the original field, again typically with relatively little impact on precision.

This package supports use of `.h5` registration files through the h5reg class and associated functions.

See also

Useful links:

• https://github.com/natverse/nat.h5reg

• https://natverse.github.io/nat.h5reg

• Report bugs at https://github.com/natverse/nat.h5reg/issues

Author

Maintainer: Gregory Jefferis jefferis@gmail.com (ORCID)

Authors:

• Saalfeld Lab (for transform-helpers java library) [copyright holder]