# Difference between revisions of "20.309:Schedule"

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 (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 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. 43D microscopy: confocal & multiphoton imaging Thu, Dec. 63D 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.