WlzWarp: An Open-Source Tool for Complex Alignment of Spatial Data
Citation:
Hill, Bill, Husz, Zost, Armit, Chris, Davidson, Duncan R., Murphy, Paula, Baldock, Richard A., WlzWarp: An Open-Source Tool for Complex Alignment of Spatial Data, 2022Download Item:
Abstract:
Background: The spatio-temporal organisation of many biological processes
such as gene-expression and neuronal activity is critical to understanding the
overall biological behaviour, phenotype and disease. This is especially true during
embryonic development. During development spatial patterns of gene expression
are key to segmentation, tissue differentiation and organ development. In situ
techniques can reveal the activity of genes and the presence of proteins to a very
high sub-cellular resolution but typically at high resolution only a few probes can
be used on any sample therefore to compare many such patterns requires
mapping of image-based data to a standard spatial framework. Once mapped
those data can be collated, queried and analysed in purely spatial terms to reveal
unknown combinatorial gene-activity that could not be discovered any other way.
Mapping spatial data to image domains with systematic variation in shape and
pose, such as embryos or elongated organs, presents special problems. Automated
techniques available for more constrained systems can not deliver the mapping
fidelity required to analyse these data therefore we have developed a manual
editing tool, WlzWarp, for mapping 3D image data using the constrained distance
transform (CDT) which uniquely can deliver the complex transforms required.
Results: We have implemented a fully open-source tool (available on GitHub),
WlzWarp to provide interactive complex spatial mapping of 3D image data. We
have applied WlzWarp to map a set of gene-expression patterns in the
developing mouse embryo that could not be mapped by any other technique. The
transform procedure was tested by using multiple images of the same gene from
independent samples and thereby testing the full end-to-end mapping process.
WlzWarp is implemented in C++ using open-source packages Qt, Coin and
SIMVoleon for cross-architecture compatibility. It has been developed under Linux
but also tested on Mac OSX and MS Windows.
Conclusions: WlzWarp is a freely available software tool for non-linear
registration and alignment of complex 2D & 3D spatial patterns from one image
to another or to an atlas model. It has been tested in the context of embryo data
but can be used for any 3D or 2D image registration problem.
Author's Homepage:
http://people.tcd.ie/pmurphy3
Author: Murphy, Paula
Type of material:
Journal ArticleCollections
Availability:
Full text availableKeywords:
3D Images, Image Registration, Spatial Mapping, Gene Expression, Mouse Embryo, Non-linear TransformsSubject (TCD):
Genes & Society , computational biologyDOI:
https://doi.org/10.1101/2022.02.11.480105Metadata
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