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Shape analysis for phenotype characterisation from high-throughput imaging
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...
Show moreWe 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.
Show less- All authors
- Guo, Y.
- Editor(s)
- Guo Y.
- Supervisor
- Verbeek, F.J.; Herik, H.J. van den
- Committee
- Bäck, T.; Gevers, T.; Spaink, H.P.; Trautmann, H.
- Qualification
- Doctor (dr.)
- Awarding Institution
- Leiden Institute of Advanced Computer Science (LIACS) , Science , Leiden University
- Date
- 2017-10-17
- Title of host publication
- SIKS Dissertation Series
- ISBN (print)
- 9789462997349
Publication Series
- Name
- 2017-36