Imaging 1

Microscopy images contain a wealth of information. Extracting this information in a way that is not subject to error requires 1) understanding of the physics of image formation to assess the limits of physical information present; 2) understanding of the mathematical concepts underlying digital image formation and analysis to allow for objective and complete information extraction; 3) understanding of the concepts of different microscopy methods to assess what method should be used to obtain a specific type of information and 4) the ability to automate image analysis tasks by using a computer and appropriate methods to efficiently, accurately and reproducibly extract objective, complete and physically relevant information.

In this course the student will learn the basic concepts, math and physics of imaging.

The course starts with the basic physics of optical systems:

- Electromagnetic waves, Polarization

- Interference, Diffraction, Resolution limit

- Geometrical optics, Imaging, Paraxial approximation, Thin lenses

- Visual optical systems, Simple microscope, Matrix formalism for imaging

The students will then learn about some basic types of microscopy utilizing the physical concepts learned before:

- Bright field and dark field microscopy and phase contrast microscopy

- Polarisation microscopy

- Fluorescence microscopy and Confocal scanning microscopy

Finally, the student will learn how to quantitatively analyze and extract basic information from the images made by types of microscopy introduced by computer, and will develop the skills to use computational image analysis tools for biological research.