Alignment

ClearMap.Alignment.Annotation

Module to handle label and annotation info from Allen Brain Atlas (v2).

ClearMap.Alignment.Elastix

Interface to Elastix for alignment of volumetric data.

ClearMap.Alignment.Resampling

This module provides methods to resample and reorient data.

ClearMap.Alignment.Stitching

Stitching module for aligning and stitching data sets with ClearMap.

This sub-package provides an interface to alignment tools in order to register cleared samples to atlases or reference samples.

Supported functionality:

  • stitching of tiles in a rigid or non-rigid wobbly fashion in the Stitching module.

  • resampling and reorientation of large volumetric images in the Resampling module.

  • registering volumetric data onto references via Elastix in the Elastix module.

All steps are demonstrated in the the TubeMap tutorial.

The main routines for resampling are resample().

Main routines for elastix registration are align() and transform().