BME 238 Spectroscopy and Imaging of Biological Systems (2013-2014)

BME 238 Spectroscopy and Imaging of Biological Systems

(Not required for any major.)
Catalog Data:

BME 238 Spectroscopy and Imaging of Biological Systems (Credit Units: 4) Principles of spectroscopy; Absorption; Molecular orbitals; Multiphoton transitions; Jablonski diagram; Fluorescence Anisotropy; Fluorescence decay; Quenching; FRET; Excited state reactions; Solvent relaxations; Instruments; Microscopy: Wide field, LSM, TPE; Fluorescent probes, Fluctuations Spectroscopy; optical resolution and super-resolution; CARS and SHG microscopy. Prerequisite: Math 3A, Math 3D; Statistics 8 recommended. Graduate students only. Concurrent with BME 138. (Design units: 0)

Required Textbook:
Recommended Textbook:
Enrico Gratton
Relationship to Student Outcomes
No student outcomes specified.
Course Learning Outcomes. Students will:

1. Understand the nature of Spectroscopy and microscopy biological signals

2. Apply the essential analytical and numerical approaches for analyzing spectral and microscopy images

3. Fluctuations in optical signals related to images

4. Develop analysis skills by using correlation functions for signals analysis

Prerequisites by Topic

Statistical concepts: average, variance. Correlation functions, Fourier Transform. Chemistry: molecular orbitals. Biology: cells and cell organelles.

Lecture Topics:
  • Week 1: Principles of spectroscopy; Extinction coefficients. Einstein coefficients Absorption. Molecular orbitals.
  • Week 2: Multiphoton transitions; Fluorescence Jablonski diagram; Excitation-emission
  • Week 3: Fluorescence Anisotropy; Fluorescence decay; Anisotropy decay
  • Week 4: Fluorescence decay analysis; Quenching; FRET; Excited state reactions. Solvent relaxations
  • Week 4: Instruments: Steady state. Sources, optical setup, detectors; lifetime instruments; Microscopy: Wide field, LSM, TPE; Fluorescent probes, Quantum dots
  • Week 5: Fluctuations. Diffusion; Fluctuations. Chemical reactions; Fluctuations. Chemical reactions
  • Week 6: PCH. Single point; Dynamic imaging
  • Week 7: ICS principles; RISC; N&B
  • Week 8: FLIM; FRET imaging microscopy
  • Week 9: TIRF microscopy; Optical resolution and super-resolution
  • Week 10: Non-linear spectroscopy: CARS and SHG microscopy
Class Schedule:

Meets for 3 hours of lecture each week for 10 weeks.

Computer Usage:
Laboratory Projects:


Professional Component
Design Content Description

The design skills are developed and tested through a number of homework problems such as: * Determine the relationship between energy level transitions and spectrum. * Determine the effect of molecular rotations on the average polarization of an ensemble of molecules * Use intensity and temporal fluctuations to determine the number of molecules in a volume of excitation * Understand the principle of microscopy design for optical sectioning * Design experiments to measure molecular aggregation in biological systems * Identify molecular species in biological tissue on the basis of fluorescence lifetime * Understand the principles of optical super-resolution. * Understand the principles on non-linear optics.

Lectures: 0%
Laboratory Portion: 0%
Grading Criteria:
  • Homework 1:20%
  • Homework 2: 20%
  • Homework 3: 20%
  • Final Exam: e.g. Research paper: 40%
  • Total: 100%
Estimated ABET Category Content:

Mathematics and Basic Science: 0.0 credit units

Computing: 0.0 credit units

Engineering Topics: 4.0 credit units

Engineering Science: 3.0 credit units

Engineering Design: 1.0 credit units

October 16, 2012
Senate Approved:
May 31, 2013
Approved Effective:
2013 Fall Qtr