This repository contains the LaTeX source code for my bachelors thesis on structured illumination microscopy and the slides used for its defence. The PDF can be found in releases. This is the latest version of the document and the defence slides. Here is the supervisors opinion and the opponents opinion.
- Contents
- Introduction
- Theory
- Nature of Light
- Historical Context
- Wave Theory of Light
- Wave Equation Solutions
- Super-resolution Microscopy
- Comparison of SR Methods
- Principle of SIM
- SIM
- Discussion
- Nature of Light
- Experiment
- SIM Reconstruction
- Parameter Estimation
- Wiener filter Reconstruction
- Inversion Reconstruction
- Discussion
- Measurement of the Transfer Function
- Image Formation
- PSF from Beads
- The Source Model
- Estimating the PSF from the Model
- PSF from SIM
- New Reconstruction
- Discussion
- SIM Reconstruction
- Conclusion
- Bibliography
The document can be compiled using tectonic.
A just build script is included in the repository that builds the figures and compiles the document in one command by
just build-allThe figures that are necessary are included in the repository built from the data.
Important
The data used for building the figures is not included in the repository but can be made available upon request.
Figures are built using Julia (which must be installed and the figure project instantiated).
This is automated with the build script written in just by running
just build-all-figsTo build a concrete figure, you can run
just build-fig <name>and to list the available figures run
just list-figsYou can build the document with the figures available by running
just build # or `tectonic -X build`
Comparison of SIM and deconvolved raw acquired images
Comparison of SIM reconstruction from 3 low resolution images reconstruction and standard 9 images reconstruction
Comparison of the estimated measured PSF and the model PSF
