Quantitative Optical Imaging
This course explores the fundamentals of optical imaging in biology, especially molecular and cellular biology. Covered topics include an introduction to optics and microscopes, fluorescence microscopy and image analysis, and biological applications. MATLAB will be taught at the beginning of the course and used throughout for image processing. Prior experience with MATLAB (or Python) is highly recommended but not required.
This course is required for the Interdisciplinary Quantitative Biology (IQBiology) Graduate Certificate program hosted by the BioFrontiers Institute. An additional microscopy lab is offered for one credit for students in the IQBiology program.
- Fall 2020 (current)
- Fall 2019
I develop the curriculum and lecture the image analysis and programming content of the class (about one-third of course). I also develop and teach the microscopy labs (over half the lab content).
IQBiology Microscopy Lab
- Fall 2016 - Present
The Fall 2020 class is currently being taught remotely via Zoom. I have recorded some lecture material which is available on YouTube. More videos will be released as the semester progresses.
PDF of slides from Fall 2019
- Lecture 1: MATLAB and matrices
- Lecture 2: matrix operations and scripts
- Lecture 3: Logical operations and images
- Lecture 4: Segmentation
- Lecture 5: Morphological operators
- Lecture 6: Watershed transform
- Lecture 7: Data types, mean and median filters
- Lecture 8: Plots and curve-fitting
- Lecture 9: Background subtraction, uneven illumination, ratiometric FRET
- Lecture 10: Analyzing videos and tracking bees
- Lecture 11: Particle localization and STORM
- MATLAB Reference Sheet