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20.309 Assignment 1: Optics bootcamp20.309 Main Page20.309 development to-do list
20.345:Course Information20.345:Final project proposal20.345:Key Factors Table
20.345:Literature search20.345:Main page20.345: Wiki guidelines
A.Williams: Objectives and Literature ReviewANOID Project
Additional ResourcesAligning the optical trapAlumni Page
Aperture and field stopsAssignment 1, Part 1: Pre-lab questionsAssignment 1, Part 2: Optics bootcamp
Assignment 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 yeastAssignment 10 Overview
Assignment 11: Tell us about your lab visit
Assignment 1 Overview: Transillumination microscopyAssignment 2: epi illuminator for fluorescence microscopyAssignment 2: fluorescence microscopy
Assignment 2 Part 1: Noise in imagesAssignment 2 Part 2: Fluorescence microscopyAssignment 2 Part 3: Build an epi-illuminator for your microscope
Assignment 2 Part 4: Fluorescent imaging of actinAssignment 3, Part 1: visualizing actin with fluorescence contrastAssignment 3, Part 2: experimental design with fluorescence
Assignment 3 Overview
Assignment 4: finding and measuring thingsAssignment 4 part 1: Make a fake imageAssignment 4 part 2: Measure resolution
Assignment 4 part 3: Track microspheres over timeAssignment 5, Part 1: MSD difference tracking and microscope stabilityAssignment 5, Part 1: viscosity and diffusivity in glycerol-water mixtures
Assignment 5, Part 2: live cell particle tracking of endocytosed beadsAssignment 5: Spring 2020
Assignment 5 OverviewAssignment 6, Part 1: Pre-lab questions
Assignment 6, Part 1: build a two-color microscopeAssignment 6, Part 2: Electronics bootcampAssignment 6, Part 2: electronics written problems
Assignment 6, Part 3: Identifying unknown filter circuitsAssignment 6 OverviewAssignment 6 Overview: two color microscope
Assignment 7, Part 1: op amp golden rules questionsAssignment 7, Part 2: measure temperature and fluorescenceAssignment 7, Part 3: testing your instrument and measuring a DNA melting curve
Assignment 7: Amplifiers and feedbackAssignment 7 OverviewAssignment 8, Part 0: convolution practice
Assignment 8, Part 1: convolutionAssignment 8, Part 2: build a two-color microscope
Assignment 8, Part 2: fabricate a microfluidic deviceAssignment 8, Part 2: lock-in amplifier and temperature controlAssignment 8, Part 3: add flow control and test your device
Assignment 8 OverviewAssignment 8 Overview: flow channel & two-color microscopeAssignment 9, Part 1: Analyze two-color yeast images
Assignment 9, Part 1: model functionAssignment 9, Part 2: Simulating DNA melting data and testing the model functionAssignment 9, Part 3: Fitting your data
Assignment 9 OverviewAssignment 9 Overview: Analyzing yeast imagesBE Classroom Computer Documentation
BE TA Training(Su16):HomepageBE TA Training (Su17)BE TA Training (Su18)
BE TA Training (Su19)Beam Expander ExampleBode plots
Bode plots and frequency responseBryan Hernandez/20.109/Lab notebook/Module 1/Day 2Bryan Hernandez/20.109/Lab notebook/Module 1/Day 3
Bryan Hernandez/20.109/Lab notebook/Module 1/Day 4Bryan Hernandez/20.109/Lab notebook/Module 1/Day 5Bryan Hernandez/20.109/Lab notebook/Module 1/Day 6
Bryan Hernandez/20.109/Lab notebook/Module 2/Day 2CM March14CM March28
CRISPRi module, Part II: Increasing ethanol yield in E. coli MG1655Calculating MSD and Diffusion CoefficientsCapacitors and inductors
Cartridge ManipulationCell PrintingCell Printing Experimentation
Cell ReservationsCellular microrheologyComplex Number Review
Compound Microscope ExampleConfocal WikiConverting Gaussian fit to Rayleigh resolution
Course Journal -- Nathan S LachenmyerCourseworkCreating 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 regressionDNA Melting: Processing DNA Melting Data
DNA Melting: Simulating DNA Melting - BasicsDNA Melting: Simulating DNA Melting - Intermediate TopicsDNA Melting: Using the Basic DNAMelter GUI
DNA Melting: Using the LockIn DNAMelter GUIDNA Melting: Using the Matlab DNAMelter GUIDNA Melting II: Using the Matlab DNALockIn GUI
DNA Melting Part 1: Measuring Temperature and FluorescenceDNA Melting Part 2: Lock-in Amplifier and Temperature Control
DNA Melting Report RequirementsDNA Melting Report Requirements for Part 1
DNA Melting ThermodynamicsDNA melting: Identifying the unknown sample
DNA melting lab wiki pagesData SheetsDeconvolved Image
Develop Research proposal ideas and presentationsDevice CreationESTORM
Electronics Mini-Lab
Electronics boot camp I: passive circuits and transfer functionsElectronics boot camp lab part 1Electronics bootcamp II: feedback systems
Electronics primerElectronics written problemsElectronics written problems II
Emmanuel QuirozEquipment on loanError analysis
Estimating second order system parameters from noise power spectra using nonlinear regressionExam 2 study guideFPGA Design Environment
Fall 2010: DNA melting report outlineFall 2010: Problem Set 3
Fall 2010 SyllabusFall 2012: Journal Presentations
Final Project -- Nathan S LachenmyerFinal Project Proposal WilliamsFinal Projects
Finding and measuring thingsFlat-field correction
Geometrical OpticsGeometrical optics and ray tracingHattie Chung
Impedance AnalysisIn silico cloning of pdCas9 construct
Inkjet TechnologiesInput and output impedanceIntro Electronics Lab Report
IntroductionKey Project ElementsKey estimates
Lab 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 DetectionLab Manual: Measuring DNA Melting Curves
Lab Manual: Optical MicroscopyLab orientation
Laser cutter safe operating procedureLecture Notes:Modeling real systems with ideal elementsLimits of Detection:Report Requirements
Limits of Detection: Data SessionsLocating objects in a fluorescent microscopic image
MATLAB: Estimating resolution from a PSF slide imageMATLAB: Estimating viscoelastic spectrum using Mason's methodMATLAB: Intensity-weighted centroid noise formula
MRI lab: FPGA controller documentationMSD of Sum and Difference TrajectoriesMain Page
Manta G032 camera measurementsMarch14Matlab:Division operators
Matlab:Image Processing for Fluorescent MicroscopyMatlab:Matlab Fundamentals
Matlab: ScalebarsMatlab: Simulating Brownian motion
Measuring biological forces mini-labMeasuring optical magnificationMethods
Microscope Objective LensesMicroscopy report general guidelines
Microscopy report outlineMore info on BJC2100 AttemptNonlinear regression
ObjectiveOptical Microscopy: Brownian motion and microscopy stability
Optical Microscopy: Part 1 Report Outline
Optical Microscopy: Part 2 Report OutlineOptical Microscopy: Part 3 Report OutlineOptical Microscopy: Part 4 Report Outline
Optical Microscopy Data SheetsOptical Microscopy Part 1: Brightfield Microscopy
Optical Microscopy Part 2: Fluorescence Microscopy
Optical Microscopy Part 3: Resolution, Stability, and Particle Tracking
Optical Microscopy Part 3: Resolution and Stability
Optical Microscopy Part 4: Particle Tracking
Optical Microscopy Week 1: Build a brightfield microscope
Optical Microscopy Week 3: Experiments
Optical Trap CodeOptical Trap Graphs
Optical aberrationsOptical detectors, noise, and the limit of detectionOptical microscopy lab wiki pages
Optical resolutionOptical trapOptics Bootcamp
PapersPapers to readPart 3 Combined Report Outline
Particle Tracking ExercisePhotobleaching ModelPhysical optics and resolution
Power spectral densityProbability and statisticsProblem Set 1
Problem Set 2Problem Set 2 Fall 2010Procedure: Diffusion in biological gels
Procedure: Particle trackingProcedure: Peptide-DNA Tethering AssayProject ideas
ProtocolsProtocols for cell culture
Protocols for making microscopy samplesPython:DNA melting data analysisPython:Simulating DNA Melting
QRT-PCRQRT-PCR:Get StartedQRT-PCR:Heated Lid
QRT-PCR:LabView-versionsReal electronicsRecording, displaying and saving images in MATLAB
Reference ListRelay Lens Example
Resource list: DNA melting and PCRResource list: Electronics
Resource list: Fiber opticsResource list: Image EnhancementResource list: Image processing
Resource list: Magnetic Resonance ImagingResource list: MatlabResource list: Microscopy
Resource list: Optical trappingResource list: OpticsResource list: Particle tracking
Resource list: SuppliersResultsReview of probability concepts
SToNCalculator.mSandboxSave the curve to a USB memory stick
Shot noise and centroid findingSimulating diffusing microspheres in MATLAB
Spring09:Todo listSpring 11:CellPrinterSpring 11:Chemotaxis Assay
Spring 11:Confocal MicroscopeSpring 11:Directed EvolutionSpring 11:Directed Evolution/KAF95
Spring 11:Directed Evolution/Perfusion ChambersSpring 11:Directed Evolution/Week of 3-14-2011 StatusSpring 11:Directed Evolution/Week of 3-21-2011 Status
Spring 11:Directed Evolution/Week of 3-28-2011 StatusSpring 11:Directed Evolution/Week of 4-04-2011 StatusSpring 11:Directed Evolution/Week of 4-11-2011 Status
Spring 11:Directed Evolution/Week of 4-18-2011 StatusSpring 11:Directed Evolution/Week of 4-25-2011 StatusSpring 11:Directed Evolution/Week of 5-02-2011 Status
Spring 11:Directed Evolution/Week of 5-09-2011 StatusSpring 11:QRT-PCRSpring 11:QRT-PCR: Progress Notes