20.309 Main Page

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20.309 course information

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20.309 master schedule

Module 1: Optics & Microscopy

Important dates	Assignment due	Assignment page links	Useful resources
2/16/20	Assignment 1	Assignment 1 Overview Part 1: Pre-lab questions Part 2: Optics bootcamp Part 3: Build a microscope Part 4: Measure stuff	Lectures 1 through 9 of the 20.309 class Snell's law Understanding log plots
2/23/20	Assignment 2	Assignment 2 Overview Part 1: Noise in images Part 2: Fluorescence microscopy Part 3: Build an epi-illuminator for your microscope	Geometrical optics and ray tracing Physical optics and resolution Optical aberrations Aperture and field stops Optical detectors, noise, and the limit of detection Manta G032 camera measurements
2/25/20	Quiz 1 (in lecture)
3/1/20	Assignment 3	Assignment 3 Overview Part 1: fluorescence imaging Part 2: choosing filters	Flat-field correction of non-uniform illumination Matlab: Scalebars
3/8/20	Assignment 4	Overview Part 1: Make a fake image Part 2: Measure resolution Part 3: Track microspheres over time	Resolution Physical optics and resolution Converting Gaussian fit to Rayleigh resolution MATLAB: Estimating resolution from a PSF slide image Matlab: Scalebars Calculating MSD and Diffusion Coefficients
4/3/20	Assignment 5	Assignment 5 Overview (Spring 2020) Part 1: MSD difference tracking and microscope stability Part 2: Live cell particle tracking of endocytosed beads	Matlab: Scalebars Calculating MSD and Diffusion Coefficients
4/7/20	Exam 1

Module 2: electronics, signals and systems

Important dates	Assignment due	Assignment page links	Useful resources
4/13/20	Assignment 6	Spring 2020 Assignment 6 (Previous semesters' assignment 6 for reference) Assignment 6 overview Assignment 6, Part 1: build a two-color microscope Assignment 6, Part 2: electronics written problems	Electronics primer Khan Academy Material, esp. "Ideal Circuit Elements" and "Voltage Divider" Impedance analysis Input and output impedance
4/20/20	Assignment 7	Spring 2020 Assignment 7 (Previous semesters' assignment 7 for reference) Assignment 7 overview Assignment 7, Part 1: more electronics written problems Assignment 7, Part 2: Electronics bootcamp I	Impedance analysis Transfer functions and Bode plots Complex number review Input and output impedance
4/21/20	Quiz 2 (60 min)
4/27/20	Assignment 8	Spring 2020 Assignment 8 (Previous semester's assignment 8 for reference) Assignment 8 Overview Part 1: feedback systems Part 2: fabricate a microfluidic device Part 3: add flow control and test your device	*The* yeast paper: Mettelal et al., Science (2008)
5/4/20	Assignment 9	Spring 2020 Assignment 9 (Previous semester's assignment 9 for reference) Assignment 9 Overview: Analyzing yeast images Part 0: convolution practice Part 1: Analyze two-color yeast images A10: Measure the osmotic shock response of yeast
5/8/20	Exam 2 (90 min)
5/12/20	Assignment 10	Spring 2020 Assignment 10 (Previous semester's assignment 10 was combined with assignment 9)
cancelled	Assignment 11	Assignment 11: Tell us about your lab visit

Optics and microscopy resources

Background reading

• Geometrical optics and ray tracing
• Physical optics and resolution
• Optical aberrations
• Aperture and field stops
• Optical detectors, noise, and the limit of detection
• Manta G032 camera measurements
• Understanding log plots

Code examples and simulations

• Converting Gaussian fit to Rayleigh resolution
• MATLAB: Estimating resolution from a PSF slide image
• Matlab: Scalebars
• Calculating MSD and Diffusion Coefficients

Electronics resources

Background reading

• Electronics primer
• Khan Academy Material, esp. "Ideal Circuit Elements" and "Voltage Divider"
• Impedance analysis
• Transfer functions and Bode plots
• Complex number review
• Input and output impedance

Limits of detection mini-lab

• Lab Manual: Limits of Detection
• Lab Manual: Atomic Force Microscopy (AFM)
• Limits of Detection: Data Sessions

MRI mini-lab

• MGH tabletop MRI

(Kept for historical reasons.)