20.309:Schedule

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       <p><b>[[Media:OpticsLect1.pdf| Thu, Nov. 1]]</b><br>
       <p><b>[[Media:OpticsLect1.pdf| Thu, Nov. 1]]</b><br>
       Optical instrumentation II: detectors, noise; Statistics I</p>
       Optical instrumentation II: detectors, noise; Statistics I</p>
-
     <p><b>Fri, Nov. 2</b><br>
+
     <p><b>Fri, Nov. 2 (RECITATION)</b><br>
       Intro to [[Media:20.309f06mod3.pdf|Microscopy lab module]] and <b><i>design review presentations</i></b></p>
       Intro to [[Media:20.309f06mod3.pdf|Microscopy lab module]] and <b><i>design review presentations</i></b></p>
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       <p><b>Mon, Nov. 5 - Fri, Nov. 9</b><br>
       <p><b>Mon, Nov. 5 - Fri, Nov. 9</b><br>
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         <u>Lab manual for weeks 9-11: [[Media:20.309f06mod3.pdf|Fluorescence microscope construction I]]: white light imaging and Fourier optics </u></p>
+
         <u>Lab manual for weeks 9-11: [[Media:20.309f06mod3.pdf|Fluorescence microscope construction I]]:</u>
 +
        lenses, white light imaging, resolution/alignment, begin fluorescence</p>
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 +
    <p><b>Readings</b></p>
 +
    <p> Nice online microscopy references: <br>
 +
      [http://www.microscopyu.com/index.html "MicroscopyU" from Nikon]
 +
        and [http://micro.magnet.fsu.edu/primer/index.html Molecular Expressions Optical Microscopy Primer]</p>
     <p><font color=#aa0000>[[Media:HW3.pdf|HOMEWORK SET 3]] (Image Processing) DUE.</font></p>   
     <p><font color=#aa0000>[[Media:HW3.pdf|HOMEWORK SET 3]] (Image Processing) DUE.</font></p>   
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     <td width="5%" valign="top"><b> 10</b></td>
     <td width="5%" valign="top"><b> 10</b></td>
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       <p><b>[[Media:OpticsLect4.pdf|Tuesday, Nov. 14]]</b><br>
+
       <p><b>[[Media:20.309_MicroRheolLect2.pdf|Tue, Nov. 13]]</b><br>
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        Interference and diffraction, resolution in microscopy, Fourier optics</p>
+
        Microrheology & particle tracking</p>
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       <p><b>[[Media:20.309_MicroRheolLect1.pdf|Thursday, Nov. 16]]</b><br>
+
       <p><b>[[Media:309TrappingLect.pdf|Thu, Nov. 15]]</b><br>
-
         Active microrheology</p>
+
        Optical trapping (Prof. Matt Lang guest lecture)</p>
 +
      <p><b>Fri, Nov. 16</b><br>
 +
         [[20.309:Presentations|Student presentations]] (Session #6)</p>
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       <p><i><b>NO LAB MONDAY NOV. 12<br> (Veteran's Day)</b></i></p>  
       <p><i><b>NO LAB MONDAY NOV. 12<br> (Veteran's Day)</b></i></p>  
       <p><b>Tue, Nov. 13 - Fri, Nov. 16</b><br>
       <p><b>Tue, Nov. 13 - Fri, Nov. 16</b><br>
-
       <u>Lab manual for weeks 9-11: [[Media:20.309f06mod3.pdf|Fluorescence microscope construction II]]: Live-cell  
+
       <u>Lab manual for weeks 9-11: [[Media:20.309f06mod3.pdf|Fluorescence microscope construction II]]:</u>
-
        imaging &amp; microrheology </u></p>
+
        finish construction, live-cell imaging; particle tracking &amp; microrheology </p>
     </td>
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     <p>&nbsp;</p>
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     <p>MATLAB scripts for calculating [[Media:getMSD_BE309.m|MSD]] and [[Media:getGstar_Mason_BE309.m|G*]]</p>
-
    <p><font color=#aa0000><b>Thursday, Nov. 16 @ 8:00pm &ndash; Room 56-614</b><br>
+
-
        [[20.309:Presentations|Student Presentations]] (Session #3)</font></p>
+
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    <p>MATLAB scripts for calculating [[Media:getMSD_BE309.m|MSD]] and [[Media:getGstar_Mason_BE309.m|G*]]</p>
 
     <p>Three papers about peacock feathers:<br>
     <p>Three papers about peacock feathers:<br>
       &ndash; [http://www.media.mit.edu/nanoscale/courses/BE309/private/papers/Zi_PeacockColor_PNAS2003.pdf Zi, <i>PNAS</i> (2003)]<br>  
       &ndash; [http://www.media.mit.edu/nanoscale/courses/BE309/private/papers/Zi_PeacockColor_PNAS2003.pdf Zi, <i>PNAS</i> (2003)]<br>  
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     <td width="5%" valign="top"><b> 12</b></td>
     <td width="5%" valign="top"><b> 12</b></td>
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       <p><b>[[Media:309TrappingLect.pdf|Tuesday, Nov. 28]]</b><br>
+
       <p><b>[[Media:OpticsLect4.pdf|Tue, Nov. 27]]</b><br>
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        Optical trapping</p>
+
        Interference and diffraction, phase-contrast microscopy</p>
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       <p><b>[[Media:20.309_OpticsLect6.pdf|Thursday, Nov. 30]]<br>
+
       <p><b>[[Media:20.309_OpticsLect6.pdf|Thu, Nov. 29]]<br>
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         </b>Advanced fluorescence microscopy</p>
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         </b>Resolution in microscopy, Fourier optics + <b><i>demo</i></b></p>
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Revision as of 10:15, 30 August 2007

20.309: Biological Instrumentation and Measurement

Home        Course Information        Schedule        People        Student Presentations        LAB SIGNUP       

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.

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
<p>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.

 
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 (Image Processing) DUE.

10

Tue, Nov. 13
Microrheology & particle tracking

Thu, Nov. 15
Optical trapping (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 & microrheology

MATLAB scripts for calculating MSD and G*

11

Tuesday, Nov. 21
Passive microrheology & Particle tracking

NO LECTURE THURSDAY, NOV. 23
(Thanksgiving)

Monday, Nov. 20 - Wednesday, Nov. 24
Lab manual for weeks 9-11: Fluorescence microscope construction III: Actin cytoskeleton imaging

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.

NO LAB THU-FRI
(Thanksgiving Weekend)

Three papers about peacock feathers:
Zi, PNAS (2003)
Yoshioka, Forma (2002)
Kinoshita, ChemPhysChem (2005)

12

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

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

Monday, Nov. 27 - Wednesday, Nov. 29
Fluorescence microscope construction/experiments

Wednesday, Nov. 29 - Friday, Dec. 1
Lab manual for weeks 12/13: Optical Trapping

Preprint of AJP paper by Appleyard et al. on the 20.309 traps.

Thursday, Nov. 30 @ 8:00pm – Room 56-614
Student Presentations (Session #4)

13

Tuesday, Dec. 5
3D microscopy: Confocal imaging

Thursday, Dec. 7
3D microscopy: 2-photon microscopy, 3D image processing

Monday, Dec. 4 - Wednesday Dec. 6
Lab manual for weeks 12/13: Optical Trapping

Thursday, Dec. 7 - Friday, Dec. 8
3D Imaging & Visualization: two-photon microscopy

LAB REPORT #3 (Fluorescence Microscope) due Monday, Dec. 4, by 12:00 noon.

14

Tuesday, Dec. 12
Student presentations (Session #5)

Thursday, Dec. 14
End-of-Semester Party

Monday, Dec. 11 - Wednesday, Dec. 13
3D Image-stack Visualization, ImageJ

LAB REPORT #4 (Optical Trapping) due Monday, Dec. 11, by 12:00 noon.

Tuesday, Dec. 12 (in class)
Student presentations (Session #5)

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