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20.109(S22):Spring 2022 schedule20.109:Lab basics20.109:Module 1
20.109:Module 220.109:Module 320.109:Module 4
20.109:OWW basics20.109:People20.109: Spring 2007 schedule
20.109 (F07): Phage by design20.109 (S07): Atomic force microscopy20.109 (S07): Transmission electron microscopy
20.109 Main Page20.309:Course Information20.309:DAQ System
20.309:Lab Report Guidelines20.309:Learning outcomes20.309:Safety
20.309: Exam 1 Topics20.309 Assignment 1: Optics bootcamp20.309 Main Page
20.309 development to-do list20.345:Course Information20.345:Final project proposal
20.345:Key Factors Table20.345:Literature search20.345:Main page
20.345: Wiki guidelinesA.Williams: Objectives and Literature Review
ANOID ProjectAdditional ResourcesAligning the optical trap
Alumni PageAperture and field stopsAssignment 1, Part 1: Pre-lab questions
Assignment 1, Part 2: Optics bootcampAssignment 1, Part 3: Building your transillumination microscope
Assignment 1, Part 4: Measuring magnification and bead sizeAssignment 10, Part 1: Measuring the osmotic shock response of yeast
Assignment 10 OverviewAssignment 11: Tell us about your lab visit
Assignment 1 Overview: Transillumination microscopyAssignment 2: epi illuminator for fluorescence microscopy
Assignment 2: fluorescence microscopyAssignment 2 Part 1: Noise in imagesAssignment 2 Part 2: Fluorescence microscopy
Assignment 2 Part 3: Build an epi-illuminator for your microscopeAssignment 2 Part 4: Fluorescent imaging of actinAssignment 3, Part 1: visualizing actin with fluorescence contrast
Assignment 3, Part 2: experimental design with fluorescence
Assignment 3 OverviewAssignment 4: finding and measuring thingsAssignment 4 part 1: Make a fake image
Assignment 4 part 2: Measure resolutionAssignment 4 part 3: Track microspheres over timeAssignment 5, Part 1: MSD difference tracking and microscope stability
Assignment 5, Part 1: viscosity and diffusivity in glycerol-water mixturesAssignment 5, Part 2: live cell particle tracking of endocytosed beadsAssignment 5: Spring 2020
Assignment 5 Overview
Assignment 6, Part 1: Pre-lab questionsAssignment 6, Part 1: build a two-color microscopeAssignment 6, Part 2: Electronics bootcamp
Assignment 6, Part 2: electronics written problemsAssignment 6, Part 3: Identifying unknown filter circuitsAssignment 6 Overview
Assignment 6 Overview: two color microscopeAssignment 7, Part 1: op amp golden rules questionsAssignment 7, Part 2: measure temperature and fluorescence
Assignment 7, Part 3: testing your instrument and measuring a DNA melting curveAssignment 7: Amplifiers and feedbackAssignment 7 Overview
Assignment 8, Part 0: convolution practiceAssignment 8, Part 1: convolution
Assignment 8, Part 2: build a two-color microscopeAssignment 8, Part 2: fabricate a microfluidic deviceAssignment 8, Part 2: lock-in amplifier and temperature control
Assignment 8, Part 3: add flow control and test your deviceAssignment 8 OverviewAssignment 8 Overview: flow channel & two-color microscope
Assignment 9, Part 1: Analyze two-color yeast imagesAssignment 9, Part 1: model functionAssignment 9, Part 2: Simulating DNA melting data and testing the model function
Assignment 9, Part 3: Fitting your dataAssignment 9 OverviewAssignment 9 Overview: Analyzing yeast images
BE Classroom Computer DocumentationBE TA Training(Su16):HomepageBE TA Training (Su17)
BE TA Training (Su18)BE TA Training (Su19)Beam Expander Example
Bode plotsBode plots and frequency responseBryan Hernandez/20.109/Lab notebook/Module 1/Day 2
Bryan Hernandez/20.109/Lab notebook/Module 1/Day 3Bryan Hernandez/20.109/Lab notebook/Module 1/Day 4Bryan Hernandez/20.109/Lab notebook/Module 1/Day 5
Bryan Hernandez/20.109/Lab notebook/Module 1/Day 6Bryan Hernandez/20.109/Lab notebook/Module 2/Day 2CM March14
CM March28CRISPRi module, Part II: Increasing ethanol yield in E. coli MG1655Calculating MSD and Diffusion Coefficients
Capacitors and inductorsCartridge ManipulationCell Printing
Cell Printing ExperimentationCell ReservationsCellular microrheology
Complex Number ReviewCompound Microscope ExampleConfocal Wiki
Converting Gaussian fit to Rayleigh resolutionCourse Journal -- Nathan S LachenmyerCoursework
Creating 20.109(S17):Scan slides to identify FKBP12 binders (Day5)DAQ Ribbon CableDNA Melter Improvements
DNA Melting: DNA SequencesDNA Melting: Model function and parameter estimation by nonlinear regression
DNA Melting: Processing DNA Melting DataDNA Melting: Simulating DNA Melting - BasicsDNA Melting: Simulating DNA Melting - Intermediate Topics
DNA Melting: Using the Basic DNAMelter GUIDNA Melting: Using the LockIn DNAMelter GUIDNA Melting: Using the Matlab DNAMelter GUI
DNA Melting II: Using the Matlab DNALockIn GUIDNA Melting Part 1: Measuring Temperature and Fluorescence
DNA Melting Part 2: Lock-in Amplifier and Temperature Control
DNA Melting Report Requirements
DNA Melting Report Requirements for Part 1DNA Melting Thermodynamics
DNA melting: Identifying the unknown sampleDNA melting lab wiki pagesData Sheets
Deconvolved ImageDevelop Research proposal ideas and presentationsDevice Creation
ESTORMElectronics Mini-Lab
Electronics boot camp I: passive circuits and transfer functionsElectronics boot camp lab part 1
Electronics bootcamp II: feedback systemsElectronics primerElectronics written problems
Electronics written problems IIEmmanuel QuirozEquipment on loan
Error analysisEstimating second order system parameters from noise power spectra using nonlinear regressionExam 2 study guide
FPGA Design EnvironmentFall 2010: DNA melting report outline
Fall 2010: Problem Set 3Fall 2010 SyllabusFall 2012: Journal Presentations
Final Project -- Nathan S LachenmyerFinal Project Proposal Williams
Final ProjectsFinding and measuring thingsFlat-field correction
Geometrical OpticsGeometrical optics and ray tracing
Hattie ChungImpedance Analysis
In silico cloning of pdCas9 constructInkjet TechnologiesInput and output impedance
Intro Electronics Lab ReportIntroductionKey Project Elements
Key estimatesLab 1 Report -- Nathan S LachenmyerLab 2 Report -- Nathan S Lachenmyer
Lab Manual:Introduction to electronics
Lab Manual:Optical Trapping
Lab Manual: Atomic Force Microscopy (AFM)Lab Manual: Limits of Detection
Lab Manual: Measuring DNA Melting CurvesLab Manual: Optical Microscopy
Lab orientationLaser cutter safe operating procedureLecture Notes:Modeling real systems with ideal elements
Limits of Detection:Report RequirementsLimits of Detection: Data Sessions
Locating objects in a fluorescent microscopic imageMATLAB: Estimating resolution from a PSF slide imageMATLAB: Estimating viscoelastic spectrum using Mason's method
MATLAB: Intensity-weighted centroid noise formulaMRI lab: FPGA controller documentationMSD of Sum and Difference Trajectories
Main PageManta G032 camera measurementsMarch14
Matlab:Division operatorsMatlab:Image Processing for Fluorescent MicroscopyMatlab:Matlab Fundamentals
Matlab: Scalebars
Matlab: Simulating Brownian motionMeasuring biological forces mini-labMeasuring optical magnification
MethodsMicroscope Objective Lenses
Microscopy report general guidelinesMicroscopy report outlineMore info on BJC2100 Attempt
Nonlinear regressionObjective
Optical Microscopy: Brownian motion and microscopy stability
Optical Microscopy: Part 1 Report OutlineOptical Microscopy: Part 2 Report OutlineOptical Microscopy: Part 3 Report Outline
Optical Microscopy: Part 4 Report OutlineOptical Microscopy Data Sheets
Optical Microscopy Part 1: Brightfield Microscopy
Optical Microscopy Part 2: Fluorescence Microscopy
Optical Microscopy Part 3: Resolution, Stability, and Particle TrackingOptical Microscopy Part 3: Resolution and Stability
Optical Microscopy Part 4: Particle Tracking
Optical Microscopy Week 1: Build a brightfield microscopeOptical Microscopy Week 3: Experiments
Optical Trap Code
Optical Trap GraphsOptical aberrationsOptical detectors, noise, and the limit of detection
Optical microscopy lab wiki pagesOptical resolutionOptical trap
Optics BootcampPapersPapers to read
Part 3 Combined Report OutlineParticle Tracking ExercisePhotobleaching Model
Physical optics and resolutionPower spectral densityProbability and statistics
Problem Set 1Problem Set 2Problem Set 2 Fall 2010
Procedure: Diffusion in biological gelsProcedure: Particle trackingProcedure: Peptide-DNA Tethering Assay
Project ideasProtocolsProtocols for cell culture
Protocols for making microscopy samplesPython:DNA melting data analysis
Python:Simulating DNA MeltingQRT-PCRQRT-PCR:Get Started
QRT-PCR:Heated LidQRT-PCR:LabView-versionsReal electronics
Recording, displaying and saving images in MATLABReference ListRelay Lens Example
Resource list: DNA melting and PCR
Resource list: ElectronicsResource list: Fiber opticsResource list: Image Enhancement
Resource list: Image processingResource list: Magnetic Resonance ImagingResource list: Matlab
Resource list: MicroscopyResource list: Optical trappingResource list: Optics
Resource list: Particle trackingResource list: SuppliersResults
Review of probability conceptsSToNCalculator.mSandbox
Save the curve to a USB memory stickShot noise and centroid findingSimulating diffusing microspheres in MATLAB