# 20.309:Schedule

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[[Media:OpticsLect1.pdf| Thu, Nov. 1]]

[[Media:OpticsLect1.pdf| Thu, Nov. 1]]
Optical instrumentation II: detectors, noise; Statistics I

Optical instrumentation II: detectors, noise; Statistics I

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Fri, Nov. 2
+ Intro to Microscopy lab module and design review presentations

## Revision as of 10:01, 30 August 2007

20.309: Biological Instrumentation and Measurement

 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 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 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. 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 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 Thursday, Nov. 9 Interference and diffraction, resolution in microscopy, Fourier optics Mon, Nov. 5 - Fri, Nov. 9 Lab manual for weeks 9-11: Fluorescence microscope construction I: white light imaging and Fourier optics HOMEWORK SET 3 (Image Processing) DUE. 10 Tuesday, Nov. 14 Fluorescence microscopy Thursday, Nov. 16 Active microrheology NO LAB MONDAY NOV. 12 (Veteran's Day) Tue, Nov. 13 - Fri, Nov. 16 Lab manual for weeks 9-11: Fluorescence microscope construction II: Live-cell imaging & microrheology Thursday, Nov. 16 @ 8:00pm – Room 56-614 Student Presentations (Session #3) 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) MATLAB scripts for calculating MSD and G* Three papers about peacock feathers: – Zi, PNAS (2003) – Yoshioka, Forma (2002) – Kinoshita, ChemPhysChem (2005) 12 Tuesday, Nov. 28 Optical trapping Thursday, Nov. 30 Advanced fluorescence microscopy 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. 53D microscopy: Confocal imaging Thursday, Dec. 73D 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)