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Non-rigid registration to determine strain fields during mouse brain fixation and embedding

文献类型： 会议论文

第一作者： Bert Mueller

作者： Bert Mueller 1 ; Christine Tanner 1 ; Griffin Rodgers 1 ; Georg Schulz 2 ; Willy Kuo 3 ; Mario Scheel 4 ; Vartan Kurtcuoglu 3 ; Timm Weitkamp 4 ;

作者机构： 1.Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland,Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland

2.Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland,Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland,Core Facility Micro- and Nanotomography, Department of Biomedical Engineering, University of Basel, 14, 4123 Allschwil, Switzerland

3.The Interface Group, Institute of Physiology, University of Zurich, 8057 Zurich, Switzerland,National Centre of Competence in Research, Kidney.CH, 8057 Zurich, Switzerland

4.Synchrotron Soleil, 91192 Gif-sur-Yvette, France

关键词： mouse brain;hard Ⅹ-ray computed tomography;microtomography;synchrotron radiation;image registration;strain field;embedding-induced local deformation

会议名称： Conference on Bioinspiration, Biomimetics, and Bioreplication

主办单位：

页码： 115860I.1-115860I.10

摘要： Biological matter may change shape via water absorption or loss. For example, brain tissue shows non-uniform shrinkage during formalin fixation and paraffin embedding, which is the most common tissue preparation for conventional histological analysis. Local deformations can be analyzed with non-rigid registration of non-destructive three-dimensional imaging datasets. We utilized synchrotron radiation microtomography at the ANATOMIX beamline of Synchrotron SOLEIL to image a mouse brain with 3 micron voxel length after formalin fixation, immersion in ascending alcohol series and xylene, and after paraffin embedding. We created a pipeline for non-rigid registration to align the volumes and extract volumetric strain fields. In this way, we could visualize the swelling/shrinkage of anatomical features. This method avoids time-consuming segmentation of brain regions, however it is sensitive to the registration parameters. In this proceedings paper, we discuss the selection of registration parameters in order to generate plausible volumetric strain fields. This protocol can be deployed to any type of shape change of biological matter and allows for the quantification of the related processes.

分类号： q81

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