Fall Offering

EN 530.473 Molecular Spectroscopy and Imaging

Juniors, Seniors and Graduate Students

Course Description

The overarching objective of this course is to understand, employ and innovate molecular spectroscopy and optical imaging tools. The emphasis will be to bridge the domain between molecular spectroscopy, which provides exquisite chemical information, and the imaging capabilities of microscopy to seamlessly traverse between structural and biochemical spaces. The course will build on the foundational principles of light-matter interactions and an understanding of light sources, geometrical and wave optics, and detectors. Using vibrational and fluorescence spectroscopy as the tools of choice, we will discuss the design and fabrication of molecular reporters that offer unprecedented sensitivity, specificity and multiplexing capabilities in imaging of live biological specimen. Finally, we will learn about spectral and image-processing algorithms that have fundamentally changed the nature and quantity of useful information and have directly lead to breakthroughs in super-resolution imaging and multi-modal image fusion. All through the course, the focus will be on the underlying concepts and physical insights as we navigate through a diverse array of biophotonics applications.

Principal Course Modules

1. Molecular Spectroscopy:

Following a brief description of the wave-particle duality of light, we will focus on the principles of fluorescence and Raman spectroscopy and how one can employ these methods to elucidate chemical information in live cells. Moreover, application of these methods into tissue specimen and at the organismal level will be discussed.

2. Optical Microscopy:

This module will feature the fundamentals of imaging (generalized and confocal) with special emphasis on the elucidation of biologically important length scales and structures. Microchemical analyses and augmentation of structural detail will also be explored.

3. Spectroscopic imaging:

Blending the ideas of the first two modules, we will explore ideas behind concomitant elucidation of microstructural and biochemical information. Significant portion of the discussion will focus on architecting targeted molecular reporters for cellular and in vivo imaging and development of high-throughput assays.

4. Numerical Methods in Spectral Analysis (Chemometrics) and Image Processing:

We will discuss the foundational numerical techniques with the aim of investigating the optimal approaches for extracting information from hyperspectral datasets and fusing multiple imaging approaches to uncover latent structural and/or chemical information.

Spring Offering

EN 530.441 Introduction to Biophotonics

Juniors, Seniors and Graduate Students

Course Description

The primary aim for this course is to explore the unique and diverse properties of light that makes it suited for diagnosis, imaging, manipulation and control of biological structure and function from the nanoscale to the tissue level. The course will focus on different optical spectroscopic and microscopic modalities that provide biochemical and morphological information, while introducing new ideas on analysis and interpretation of the acquired data. We will also discuss manipulation methods, including optical tweezers and laser scissors, and low-level light therapy. In all of these areas, the idea is to develop a basic understanding of the subject and to use it for finding solutions to real-world problems in healthcare. Discussions and open exchanges of ideas will be strongly emphasized.


Basic knowledge of optics fundamentals and an interest in learning about cutting edge research in biophotonics!

Principal Course Modules

The following is a tentative list of topics that will be covered during the course – although like any biological system, it is expected to evolve over the course lifetime.


  • Fundamentals of Light and Matter (Physical Optics)
  • Basics of Biology
  • Principles of Light-Matter Interactions
  • Optical Spectroscopy: Reflectance/Absorption, Fluorescence and Raman
  • Numerical Methods in Spectral Processing and Information Extraction: Chemometrics
  • Optical Microscopy: Generalized, Confocal and Multi-photon
  • Photonic Manipulation: Laser Tweezers and Laser Scissors
  • Light-Activated Therapy: Photodynamic Therapy

Course Objectives

  • Students will understand the physical principles underlying optical microscopy and spectroscopy
  • Students will learn the concepts of optical imaging and manipulation
  • Students will understand the strengths and limitations of optics for biological applications
  • Students will learn to design biological experiments using the “right” optical instruments
  • Students will learn to analyze and extract information from optical images and datasets