Hattab, Georges: Analyzing colony dynamics and visualizing cell diversity in spatiotemporal experiments. 2018
Inhalt
- Introduction
- Background
- Abstractions: From ideas to events
- Life begins with cells
- Bioimaging: Insight into the microscale
- Problem statement
- Thesis statement
- Thesis overview
- Cell colony development: aspects of diversity and dynamics
- Microfluidics: A multidisciplinary field
- The Biology: Bacterial growth
- The model organism: Sinorhizobium meliloti
- From Bioimaging to Bioimage Informatics
- Diversity: A multiplicity of properties
- Dynamics: The forces which vary data properties
- biomovies: a particular time lapse image data
- Bioimaging of microfluidics experiments
- Scales of cell colony development: Cell, colony, colonies
- Diversity and dynamics of biomovies
- Bottleneck: Human and computer based limitations
- Visualization: a means to understanding and discovery
- Spatial shift: a hindrance to knowledge discovery
- Related work
- Methods
- Results
- Implementation
- Discussion
- Data abstractions to understand cell growth
- General paradigm
- The idea
- Related work
- Preprocessing
- Particle analysis
- Particle detection
- Particle trajectories
- Particle evaluation
- Particle visualization
- An enriched space-time cube
- Patch lineages
- Patch finding
- Patch trajectory splitting
- Patch trajectory merging
- Parameter space
- Patch visualization
- Patch lineage graphs
- Implementation
- Discussion
- Outlook
- Conclusion
- Appendix Synthetic data
- Appendix Amino Acids
- Appendix Cell segmentation task
- Appendix Data Structures
- Acronyms
- Glossary
- References