20.309:Schedule

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<b>Please Note: the Schedule has been updated to reflect the Fall 2007 semester; however,
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some of the materials and readings linked from the Schedule are the Fall 2006 versions.  These may change
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and will be updated accordingly.</b>
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Revision as of 10:54, 4 September 2007

20.309: Biological Instrumentation and Measurement

Home        Course Information        Schedule        People        Student Presentations        LAB SIGNUP       

Please Note: the Schedule has been updated to reflect the Fall 2007 semester; however, some of the materials and readings linked from the Schedule are the Fall 2006 versions. These may change and will be updated accordingly.

WEEK LECTURES & RECITATIONS LAB READINGS & ASSIGNMENTS
 
Electronics
0

Thu, Sep. 6
Course Overview & syllabus; Lab Intro & logistics: scheduling, wiki, assignments

Fri, Sep. 7 (LECTURE)
Electronics for DNA analysis; dividers, Thevenin's theorem, impedance and loading, RC circuits

   
1

Tue, Sep. 11
RC circuits: transfer functions, Laplace transforms, impedance, RC filters

Thu, Sep. 13
DNA analysis: SNP detection, chemical equilib. - K and deltaG; description of DNA melting lab apparatus

Fri, Sep. 14 (RECITATION)
Electronics tutorial

Mon, Sep. 10 - Fri, Sep. 14
Lab manual for Week 1: Intro to Electronics.
Intro to DC measurements, dividers, impedance; photodiode i-v curves, AC measurements, black-box transfer functions;
the Wheatstone bridge for temperature measurement

Readings
Resistors, capacitors, voltage & current dividers, RC transients.

Impedance, frequency response, filters.

This brief introduction to diodes will be helpful for working on the labs this week.

2

Tue, Sep. 18
Feedback: Black's formula, the loop;
op-amps: "golden rules" and circuit examples

Thu, Sep. 20 Fourier series & integrals; Fourier transform (continuous & discrete)

Fri, Sep. 21 (RECITATION) MATLAB tutorial and Lab Report Guidelines

Mon, Sep. 18 - Fri, Sep. 22
Lab manual for Weeks 2 - 4: Measuring DNA Melting Curves.
Build optics for DNA melting experiment, build photodiode readout circuit; calibrate fluorescence signal

Readings Operational amplifiers.

Matlab Tutorial file 1 (the basics)

Matlab Tutorial file 2 (curve fitting, etc.)

 

HOMEWORK SET 1 DUE (electronics, circuits).

3

Tue, Sep. 25
Fourier analysis (cont'd)

Thu, Sep. 27
Signals, noise, Power Spectral Density

Fri, Sep. 28
Student presentations (Session #1)

NO LAB MONDAY SEP. 24
(Student holiday)

Tue, Sep. 25 - Fri, Sep. 28
Lab manual for Weeks 2 - 4: Measuring DNA Melting Curves.
Complete DNA melting curves apparatus; test perfect-match, all-mismatch, and single-base mismatch DNA strands

Readings
Fourier Transforms.

FFT reference material

Tutorial 1: Overview of Fourier Transforms
Tutorial 2: Sampling and Aliasing

 
Mechanics
4

Tue, Oct. 2
Correlation/convolution; lock-in amplification & demo; linear systems

Thu, Oct. 4
Equipartition theorem and thermal fluctuations

Fri, Oct. 5 (RECITATION)
Intro to AFM lab module

Mon, Oct. 1 - Fri, Oct. 5
Lab manual for weeks 2 - 4: Measuring DNA Melting Curves.
wrap up DNA melting curve measurements

Readings
One-page handout, with a few convolution clarification examples.

A helpful link that discusses spectral leakage when doing spectral analysis.

5

NO LECTURE TUESDAY, OCT. 9
(Columbus Day)

Thu, Oct. 11
Scanning probe microscopy (and associated critical band audio files)

Fri, Oct. 12
Student presentations (Session #2)

NO LAB MON-TUE
(Columbus Day Weekend)

Wed, Oct. 10 - Fri, Oct. 12
AFM alignment and calibration, AFM imaging I

Lab manual for weeks 5 - 7: The Atomic Force Microscope

LAB REPORT #1 (Measuring DNA Melting Curves) DUE

6

Tue, Oct. 16
Student presentations (Session #3)

Thu, Oct. 18
Image Processing I

Fri, Oct. 19 (RECITATION)
Laser Safety Session; AFM data analysis tutorial

Monday, Oct. 15 - Friday Oct. 19
AFM imaging II; force spectroscopy

Lab manual for weeks 5 - 7: The Atomic Force Microscope

 

HOMEWORK SET 2 DUE (signals, digital sampling, SPM).

 
Optics
7

Tue, Oct. 23
Image processing II
Supplementary slides to image processing lectures

Thu, Oct. 25
Intro to microscopy: geometric optics, lenses, ray tracing

Fri, Oct. 26
Image processing tutorial & Student presentations (Session #4)

Mon, Oct. 22 - Fri, Oct. 26
Thermal fluctuations of microcantilevers: Boltzmann's constant experiment

Lab manual for weeks 5 - 7: The Atomic Force Microscope

Readings

Great Matlab Matrix Indexing Tutorial

Nice online microscopy references:
"MicroscopyU" from Nikon and Molecular Expressions Optical Microscopy Primer

8

Tue, Oct. 30
Optical instrumentation I: physics, sources, lasers

Thu, Nov. 1
Optical instrumentation II: detectors, noise; Statistics I

Fri, Nov. 2 (RECITATION)
Intro to Microscopy lab module and design review presentations

Mon, Oct. 29 - Fri, Nov. 2
Image processing

Handout on Image Processing

Readings
Image Processing Readings (from Gonzalez & Woods):
Chapter 4: histograms, contrast, spatial filtering.
Chapter 8: morphological operations
Chapter 7: segmentation
Chapter 9: recognition & interpretation

LAB REPORT #2 (The Atomic Force Microscope) DUE.

9

Tue, Nov. 6
Statistics II

Thu, Nov. 8
Fluorescence microscopy/spectroscopy

Fri, Nov. 9
Student presentations (Session #5)

Mon, Nov. 5 - Fri, Nov. 9
Lab manual for weeks 9-11: Fluorescence microscope construction I: lenses, white light imaging, resolution/alignment, begin fluorescence

Readings

Nice online microscopy references:
"MicroscopyU" from Nikon and Molecular Expressions Optical Microscopy Primer

HOMEWORK SET 3 DUE (Image Processing).

10

Tue, Nov. 13
Microrheology & particle tracking

Thu, Nov. 15
Optical trapping I (Prof. Matt Lang guest lecture)

Fri, Nov. 16
Student presentations (Session #6)

NO LAB MONDAY NOV. 12
(Veteran's Day)

Tue, Nov. 13 - Fri, Nov. 16
Lab manual for weeks 9-11: Fluorescence microscope construction II: finish construction, live-cell imaging; particle tracking

MATLAB scripts for calculating MSD and G*

11

Tue, Nov. 20
Optical Trapping II
and Intro to Optical Trap lab module

NO LECTURE THU, NOV. 22

NO RECITATION FRI, NOV. 23
(Thanksgiving weekend)

Mon, Nov. 19 - Wed, Nov. 21
Lab manual for weeks 9-11: Fluorescence microscope construction III: live-cell imaging, microrheology, actin cytoskeleton staining & imaging

NO LAB THU-FRI
(Thanksgiving Weekend)

Papers referenced in the lab manual:
The Vukusic paper on photonic structures
and the Mason and Lau papers on microrheology and the complex viscoelastic modulus.

12

Tue, Nov. 27
Interference and diffraction, phase-contrast microscopy

Thu, Nov. 29
Resolution in microscopy, Fourier optics + demo

Fri, Nov. 30
Student presentations (Session #7)

Mon, Nov. 26 - Fri, Nov. 30
Lab manual for weeks 12 - 13: Optical Trapping

Readings AJP paper by Appleyard et al. on the 20.309 traps,
and the wiki page about them.

LAB REPORT #3 (Fluorescence Microscope) DUE.

13

Tue, Dec. 4
3D microscopy: confocal & multiphoton imaging

Thu, Dec. 6
3D microscopy: 3D image processing

Fri, Dec. 7
Student presentations (Session #8)

Mon, Dec. 3 - Thu Dec. 6
Lab manual for weeks 12 - 13: Optical Trapping

Fri, Dec. 7
Mini-Lab & hands-on demo: 3D Imaging - two-photon microscopy

 
14

Tue, Dec. 11
TBD & end-of-term party

Mon, Dec. 10 - Wed, Dec. 12
Mini-Lab & hands-on demo: 3D Imaging - two-photon microscopy
3D Image-stack Visualization, ImageJ

LAB REPORT #4 (Optical Trapping) DUE.

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