20.309:Course Information

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20.309: Biological Instrumentation and Measurement

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Course meetings

Lecture: T/R/F 12:00pm-1:00pm (4-237)

Lab: open scheduling, see below (16-352)

Lab hours and scheduling

Use the lab station reservation system to reserve a place in the lab. (Be careful to reserve a time when the lab is actually open, since the scheduler will allow you to reserve a station outside of lab open hours.) Most lab exercises can be completed in about 6 hours per week; however, some students find the lab work significantly more or less time consuming. If you have little experience building things, you might want to plan for a few extra hours.

Hours for Spring 2018

Monday Tuesday Wednesday Thursday Friday Saturday Sunday
1-6pm closed 1-6pm

During regular lab hours, please sign up at least 24 hours before coming to the lab. If there are no scholars signed up 24 hours in advance, the lab may be closed without notice.

The lab is located in room 16-352.

Lab attendance is mandatory and there will be no make-up labs.


The chief hazards present in the 20.309 Lab come from laser radiation, chemical and biological materials, and electric equipment. Some simple precautions will make your time in the lab much safer.

Get to know the 20.309 Safety Page. Read the safety precautions in each lab manual.

Overview of laboratory modules


Fluorescence microscopy, particle tracking, and image processing

The first half of the semester is devoted to optical microscopy and imaging. Each student group will design and construct a microscope with trans-illuminated brightfield and epifluorescence imaging contrast modes. Students will characterize the resolution and mechanical stability of their microscopes, image a variety of samples, and make quantitative microrheological measurements by particle tracking.


Resistive networks, filters, and op-amp circuits for measurement

The second part of the course focuses 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.

Ultimate limits for force and position detection

Microcantilevers, precision measurement, and thermomechanical noise

Force sensors such as the optical tweezers and atomic force microscope (AFM) provide a unique means for investigating single biomolecules. Examples include the real-time monitoring of enzymatic activity with the optical tweezers and the direct measurement of forces required to unfold individual protein domains with the AFM. At the heart of these force sensors is an ultrasensitive displacement detector that resolves the position of compliant structure (i.e. microcantilever or optically trapped mircobead) with nanometer, or in some cases, sub-nanometer resolution. The performance of the force sensor is determined by the mechanical properties of the structure (spring constant, resonant frequency, damping, etc) and the resolution of the displacement detector. In the last week of class, we will measure the thermomechanical motion of a microcantilever sensor, estimate its detection limit, and compare to theoretical calculations.

Lab facilities

Lab stations

There are 12 lab stations in room 16-352. Each station is equipped with:

  1. anti-vibration optical table
  2. digital oscilloscope
  3. triple output power supply
  4. tools in drawers
  5. computer workstation with data acquisition card (DAQ)

The lab also has several function generators.

Stations 3, 6 and 11 are reserved for instructor use.


Lab stations are equipped with PCs running Windows 10. Each PC has a National Instruments data acquisition system. MATLAB and LabVIEW software are installed on all lab PCs.

Log in to the PCs as user User. Ask an instructor for the password.

Feel free to use the Documents folder while working at the PC, but beware that any data on the PCs could be erased without notice! At the end of your session transfer every file that you care about to your own computer or to a network location of your choice. The lab provides a network share named Student Data. You may access it via the link on the PC desktop or via the address \\win.mit.edu\dfs\departmental\bioeng\bioenglab\CourseMaterials\StudentData. Log in using your kerberos credentials.

Additional course material can be found on our Course Materials share. There is also a link to this network share on the desktop, or you may the address \\win.mit.edu\dfs\departmental\bioeng\bioenglab\CourseMaterials. As before, log in using your kerberos credentials.

Course locker

The 20.309 course locker and Stellar site contain virtually every computer file you will need for the course. To access the locker on an Athena workstation, type attach 20.309 and then cd /mit/20.309. Use the Desktop or Start Menu shortcut to access the locker from any PC in the lab. You can also access the locker with SecureFX.


2 Exams 40%
11 Assignments 40% (lowest grade dropped)
2 Quizzes 15%
Participation 5%


Three lectures per week introduce key concepts behind the labs. An underlying theme throughout all the lectures will be on signals analysis (e.g. Fourier transforms, power spectral density, convolution theorem, etc.) as applied to electrical, mechanical and optical systems.

In some cases, the lectures will be closely related to ongoing lab modules, and in other cases, the lectures will develop material that will be used in a future lab module.


Assignments contain a combination of conceptual problems, coding, lab work, and data analysis. You must complete the lab work in teams of 2 or 3, but each of you will submit your own report. You must keep the same lab team for an entire lab module (i.e. microscopy or electronics), and you must have a different lab group for the second half of the semester than you did from the first half.

For each assignment, you should turn in an answer-book style report, making sure to answer all questions noted throughout the assignment's wiki pages. Answers should be clear and concise, plots should contain axis labels and legends, and measurements should be written with the appropriate number of significant figures.

All assignments should be turned in electronically via the course Stellar site. Check the schedule on Stellar for assignment due dates and times. As a courtesy, we will offer you one free 3-day extension for the semester. Otherwise, late work will not be accepted without an excuse from the Dean's office.

You are encouraged to seek advice from the instructors, TAs and other students; however, the work that is turned in must be your own.