20.345:Course Information

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Sophisticated measurement techniques play a central role in modern biological research. 20.345 is a hands-on course that allows students to pursue an in-depth exploration of some of the most advanced methods in use. The course emphasizes the application of optical, electronic, micromechanical, and microfluidic technologies to biological measurement problems on a scale from single molecules to whole organisms. There will be two short lab exercises over the first five weeks of the semester. During this time, you will also develop a written proposal for a substantial, original project that you will execute over the last nine weeks. The final project will be an opportunity to pursue a technique of interest in depth. In addition, you will have many chances to work on your oral and written presentation skills. Active participation is a vital part of this course. Students should have a background in physics, biology, computer programming, and linear systems. Tutorials will be given during the first weeks of class for students who have not previously studied geometric optics or those in need of refreshment.


Lectures will be on Tuesday s and Thursday s at 12:00 PM in room 4-231. The first few lectures will introduce the two lab exercises and discuss final projects. Other lectures will cover multidimensional transforms, microfluidic devices, neural recording, advanced microscopy methods, atomic force microscopy, mass spectrometery, and more. Nine of the 26 meetings will be reserved for student presentations. Attendance at these sessions is required. Each student must fill out written evaluation form for every presentation. The second lecture will include a mandatory discussion of laser safety.

Final project

Students may work individually or in small groups. Working with a partner is encouraged. A good final project must be feasible, relevant and novel. Unfortunately, the demands of novelty are frequently at odds with achievability. For the purposes of this course, feasibility is nearly always the more important goal. Resist the temptation to choose a topic that might be more appropriate for your Ph. D. thesis. Replicating a previously reported method inexpensively, in a teaching lab environment is both noble and novel. Work closely with your mentor to find the right balance. The lab has a modest budget for purchasing new components and equipment, if the case for them is compelling. The milestones for the final project are:

  • Statement of interest
  • Literature search
  • Written proposal
  • Proposal presentation
  • Lab notebook check 1
  • Midway presentation
  • Lab notebook check 2
  • Final presentation
  • Poster submission
  • Final lab notebook submission


The first phase of the project is to develop a proposal. One of the project ideas presented in class may inspire you, or you may decide to develop one of your own ideas. Based on the subject area of your endeavor, you will be paired with a member of the instructional staff to serve as a mentor. Develop your proposal in close consultation with your mentor. There will be four milestones in the proposal process: statement of interest; literature search; proposal submission; and presentation.

Statement of interest

Turn in a short statement of interest with your solutions to the first problem set. The statement should summarize your relevant background, identify techniques you are interested in investigating, and outline your goals this semester. Be as specific as possible. If you would like to work with microcontrollers or super-resolution microscopy, say so. Your statement will help the instructors allocate resources for the semester and identify students that are interested in similar areas.

Literature search

The value of a careful literature review cannot be understated. This frequently neglected step can make the difference between a breakthrough research and a fool’s errand. A conscientious search has many benefits, not the least of which is avoiding time consuming pitfalls that have been identified by others. Turn in your literature search with Problem Set 2, and use the format from this page

Written proposal

Your written proposal is due at the end of the fourth week of class. Follow the outline on this page.The proposal should be less than ten pages, excluding supplementary materials. Have your mentor review the proposal &mdash perhaps more than once &mdash before submitting it. You will present the proposal to the class the following week.

Proposal presentation

Lab notebook

You must maintain a lab notebook or other suitable documentation. Keep a detailed, accurate record of your work. Carbon copy lab notebooks are dependable; however, more technologically advanced solutions are encouraged. Consider using the course wiki instead of a paper notebook. Whatever technology you choose, entries must be contemporaneous and clear. Annotate each entry with the date and time it was made. Group members may elect to maintain individual or joint notebooks. Your lab notebook will be thrice: three weeks into the final project, six weeks in, and at the end of the project.


Project teams must create a 30”x20” poster to display at our open house on the last day of classes. Submit an electronic copy of the poster to stellar in PDF or PowerPoint format.


The course Stellar site (link) has an exhaustive list of assignments and due dates.