ClearMap.Alignment

This sub-package handles stitching and alignment of volumetric data.

The ClearMap.Alignment module includes methods for

• 3d resampling:

  • Resampling

• 3d alignment to reference atlases (e.g. Allen Brain Institute Atlases) via interfacing to elastix:

  • Elastix

  • Annotation

• 3d rigid and wobbly stitching via WobblyStitcher:

  • StitchingRigid

  • StitchingWobbly

All steps are demonstrated in the TubeMap tutorial.

The main routines for resampling are resample().

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

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Sub-packages and modules

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.
ClearMap.Alignment.Transformation	Transformation classes to track transformations of data, points and shapes.
ClearMap.Alignment.Transformations	Transformation classes to transform data, points and shapes.
ClearMap.Alignment.orientation
ClearMap.Alignment.utils