20.309 is an “open format” lab. Generally, students should aim to sign up for 6-8 hours of lab time per week, which should be enough to accomplish the week’s goals. Students are responsible for scheduling their own hours. Instructors and TAs will always be present in the lab, but will only be available to answer questions and help you work on your experiments during scheduled hours. (However, if an emergency arises or an injury occurs, get an instructor’s attention immediately).

Lab Guidelines Document: Safety, Lab Notebooks, and Other Issues (PDF)

Four written reports on the labs will comprise 50% of the course grade. You will be working in pairs throughout the semester, but you will be submitting individual lab reports.

Overview of Laboratory Modules


Resistive Networks, Filters, and Op-amp Circuits for Measurement

During the first part of the course we will focus on electronics. Over a series of labs, we will build several types of commonly used electronic circuits and combine them implement a system for measuring DNA melting curves. This section will also provide an introduction to computer control and data acquisition, including LabVIEW and MATLAB® software.


Scanning Probe Microscopy

We will learn to configure and use “home-built” atomic force microscopes (AFMs) for imaging surfaces with nanometer-scale resolution, conducting sensitive force measurements, and exploring the ultimate detection limits of microcantilevers. Such instruments are essential for investigating the mechanics of single biomolecules, cellular adhesion and modulus, as well as the physical properties of biomaterials. The goal of these labs is to gain hands-on experience with these instruments in the lab and understand the basic principles that they use to achieve exquisite sensitivity.

A video tutorial on using the AFM is presented on the tools.


Fluorescent Microscopy, Image Processing, and Optical Traps

Approximately half of the semester, and two lab modules, are devoted to optical microscopy and imaging. The lectures will cover geometric optics, Fourier optics, and optical instrumentation design, the fundamentals of image processing and 3D microscopy. In one lab module, we will build microscopes for white light and fluorescent imaging and apply them to studying cellular mechano-transduction based on particle tracking and immunolabeling. In the second optical lab module, we will use optical traps for high sensitivity measurements of bacterial flagella torque generation, and get some hands-on experience with two-photon and confocal microscopes.

Lab Report Grading Rubric

Presentation of Data (10 pts.)

  • All figures have clear purpose, have a figure number and caption, and are discussed in text
  • Data plots:
    • Appropriately chosen/organized (e.g. curves overlaid or compared, when appropriate, correct scales, etc.)
    • Axes labeled with quantities/units
    • Quality of data
  • No “data dumping” or screen captures (unless explicitly specified)

Analysis/Discussion (10 pts.)

  • Demonstrates understanding of key concepts/methods
  • Coherent, logical reasoning, clear thought process
  • Show key numeric parameters; include important calculations and results
  • Appropriate data processing applied, described and justified
  • Draw conclusions supported by the data

Overall Quality (5 pts.)

  • Report typed, well-organized, length appropriate say what you need to – not more or less
  • Report requirements met
  • Sufficient time spent in the lab
  • Citation of any material that isn’t your own (e.g. things you looked up on the Web, in literature; data from others in the class; be sure to list with whom you worked on the lab)

Part I: Electronics
0 Lab orientation and tour, safety, introduction to electronics

Module 0: introduction to electronics


Introduction to DC measurements, dividers, impedance, photodiode i-v curves, AC measurements, transfer functions, the Wheatstone bridge for temperature measurement


Module 1: measuring DNA melting curves


Build optics for DNA melting experiment, build photodiode readout circuit

Calibrate fluorescence signal

MATLAB® tutorial Part 1: the basics (PDF)

MATLAB® tutorial Part 2: curve fitting, etc. (PDF)


Module 1 (cont.)

Complete DNA melting curves apparatus

Test perfect-match, all-mismatch, and single-base mismatch DNA strands

Part II: Mechanics

Module 2: atomic force microscope


AFM alignment and calibration, AFM imaging I


Module 2 (cont.)

AFM imaging II

Force spectroscopy


Module 2 (cont.)

Thermal fluctuations of microcantilevers: Boltzmann’s constant experiment

Lab exercise on sampling, aliasing, and digital data (PDF)

Part III: Optics
7 Image processing with MATLAB® - see Homework 3 in assignments
8 Optoelectronics: PMT and photon counting - see Homework 3.5 in assignments

Module 3: fluorescence microscope construction


White light imaging and Fourier optics


Module 3 (cont.)

Live-cell imaging and microrheology


Module 3 (cont.)

Actin cytoskeleton imaging


Module 3 (cont.)

Finish construction, conduct experiments

Module 4: optical trapping



Module 4 (cont.)

3D imaging and visualization: two-photon microscopy


Module 4 (cont.)

3D image-stack visualization, imageJ

Course Info

Learning Resource Types
Tutorial Videos
Problem Sets
Design Assignments