Shape analysis for phenotype characterisation from high-throughput imaging

Leiden Repository

Shape analysis for phenotype characterisation from high-throughput imaging

Type: Doctoral Thesis
Title: Shape analysis for phenotype characterisation from high-throughput imaging
Author: Guo, Y.
Journal Title: SIKS Dissertation Series
Issue Date: 2017-10-17
Keywords: Shape analysis
High-throughput imaging
Image segmentation
3D reconstruction
Pattern recognition
Abstract: We have studied shape with a particular focus on the zebrafish model system. The shape is an essential appearance of the phenotype of a biological specimen and it can be used to read out a current state or response or to study gene expression. So accurate shape analysis requires a precise shape description. Moreover, a sufficiently large sampling size of the specimens is necessary to ensure a justified and unbiased shape analysis. The latter is very important for high-throughput in compound screening. Therefore, top performance in zebrafish analysis requires high-throughput imaging (HTI). To deal with HTI, we aim to design an elaborate and well-performing HTI architecture. For the essential operations we need computational approaches to obtain the 2D/3D shape representations that are precise and yet can be acquired fast. The quality of the obtained shape descriptions will be validated in a straightforward manner with scalar primitives, i.e., the volume and surface area of a 3D shape. These primitives serve as 3D measurements for a robust primary shape assessment in the phenotype characterisation. Using only shape description is not sufficient, e.g., for high-resolution imaging on tissue and cellular level, so texture should be considered to complement and enhance the shape analysis.
Promotor: Supervisors: F.J. Verbeek; H.J. van den Herik
Faculty: Science
University: Leiden
Uri: urn:isbn:9789462997349
Handle: http://hdl.handle.net/1887/56254
 

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application/pdf Chapter 1 Introduction 445.0Kb View/Open
application/pdf Chapter 2 2.429Mb View/Open
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application/pdf Chapter 7 Conclusion and discussion 203.8Kb View/Open
application/pdf References 192.9Kb View/Open
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