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img-sys-modeling

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# README #

### Introduction ###
When I joined CREOL at the University of Central Florida as a new assistant professor in 2015, I started to teach a senior level undergraduate course **Imaging and Display (OSE4380)**. I inherited this course from Dr. Bahaa E. A. Saleh, the Dean of the College at the time. Like many fellas working in the field of optics, I read his book [Fundamentals of Photonics](https://www.wiley.com/en-us/Fundamentals+of+Photonics%2C+2+Volume+Set%2C+3rd+Edition-p-9781119506874) before I met him in person. As a prolific author in optics and photonics, Bahaa has some very well-organized manuscripts for introductory chapters of this course. To help students get familiar with the materials, he also included some MATLAB code along with the manuscripts for students to just 'play around'.

It turned out that *the manuscripts with code* format is very popular among students. I suppose all the students agree with [Linus Torvalds](https://en.wikipedia.org/wiki/Linus_Torvalds)'s famous line: **Talk is cheap; show me the code**. So I started to implement the code for the rest of the materials of this course. After teaching this course for a couple of years, I have accumulated enough examples for teaching, but not more. As a researcher in optical imaging, I often draw inspiration from well-established imaging systems, such as phase contrast microscopy, OCT, CT, etc.. When I discussed these systems with graduate students whose backgrounds were in physics or computer vision, they often asked for more details about the data acquisition process and operating principles. I also found out that only sending them the classic papers was not the most efficient way to get them started, so I prepared these materials the same way as I did for the course.

In the beginning, I tried to compile my own handouts with the code in the same manuscript style for the class. However, after a while, the research and other responsibilities stopped me from organizing this like a textbook. I started to use Jupyter notebooks and more recently with MATLAB live scripts. This is by no means a complete work in optical imaging systems, but I hope this serves a quick and concise introduction to the mathematics and physics models of two- and  higher dimensional imaging systems. It is suitable for senior undergraduate and first-year graduate students majoring in optical engineering, electrical engineering, computer science, biomedical engineering, applied physics, or anyone with background in STEM who is just interested in learning about optical imaging.

### Table of contents ###
The scripts are divided in to 3 parts: linear system fundamentals, optical image formation, and imaging system modeling.

**Part 1 Fundamentals** 
> 1. Image Representation
> 1. Linear Systems
> 1. Spectral Analysis
> 1. Transfer Functions and Filtering

**Part 2 Optical Image Formation**
> 5. Geometric Optics
> 1. Scalar Wave and Diffraction-Limited Imaging
> 1. Diffraction-Limited 3D Imaging

**Part 3 Imaging Systems**
> 8. Passive Optical Ranging 
> 1. Active Optical Ranging 
> 1. Interferometric Imaging
> 1. Structured Illumination Microscopy
> 1. Computed Tomography
> 1. Phase Retrieval in Coherent Imaging
> 1. Synthetic Aperture and Ptychography (in progress)

[![YouTube Promo](https://img.youtube.com/vi/HHWVpXB5ZKk/0.jpg)](https://www.youtube.com/watch?v=HHWVpXB5ZKk)

### Acknowledgment ###
Our excellent undergraduate researcher at OISL, Tamara Nelson, was instrumental in implementing the livescripts, making sure the consistency of the style and code of the whole project. Dr. Zheyuan Zhu contributed to Lecture 13. Graduate students Andrew Klein and Zachary Erickson helped with the first round of proof reading.

Special thanks to Prof. Bahaa Saleh for his support to this project and allowing me to use some of the figures from his lecture notes. I would also like to thank my PhD advisor Prof. Changhuei Yang and postdoc supervisor Prof. David Brady for introducing me to the field of imaging.

I would also like to thank my colleagues Prof. Peter Delfyett, Prof. Pieter Kik, Prof. Miguel Bandres, and Prof. Kyle Renshaw at CREOL for reviewing the scripts. Dr. Raktim Sarma (Sandia), Dr. Brandon Redding (NRL), Prof. Jian Ren (Harvard/MGH), Prof. Hong Liu (University of Oklahoma), Prof. Kenith Meissner (UT El Paso) also reviewed the scripts and provided their suggestions.

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