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20.109 (F07): Phage by design	20.109 (S07): Atomic force microscopy	20.109 (S07): Transmission electron microscopy
20.109 Main Page	20.309:Course Information	20.309:DAQ System
20.309:Lab Report Guidelines	20.309:Learning outcomes	20.309:Safety
20.309: Exam 1 Topics	20.309 Assignment 1: Optics bootcamp	20.309 Main Page
20.309 development to-do list	20.345:Course Information	20.345:Final project proposal
20.345:Key Factors Table	20.345:Literature search	20.345:Main page
20.345: Wiki guidelines	A.Williams: Objectives and Literature Review	AFM
ANOID Project	Additional Resources	Aligning the optical trap
Alumni Page	Aperture and field stops	Assignment 1, Part 1: Pre-lab questions
Assignment 1, Part 2: Optics bootcamp	Assignment 1, Part 3: Building your transillumination microscope	Assignment 1, Part 3: Microscope design
Assignment 1, Part 4: Building your transilluminated microscope	Assignment 1, Part 4: Measuring magnification and bead size	Assignment 10, Part 1: Measuring the osmotic shock response of yeast
Assignment 10 Overview	Assignment 11: Tell us about your lab visit	Assignment 1: Microscope design
Assignment 1: Optics bootcamp	Assignment 1: Pre-lab questions	Assignment 1: Transilluminated microscope
Assignment 1: Transillumination microscopy	Assignment 1 Overview: Transillumination microscopy	Assignment 2: epi illuminator for fluorescence microscopy
Assignment 2: fluorescence microscopy	Assignment 2 Part 1: Noise in images	Assignment 2 Part 2: Fluorescence microscopy
Assignment 2 Part 3: Build an epi-illuminator for your microscope	Assignment 2 Part 4: Fluorescent imaging of actin	Assignment 3, Part 1: visualizing actin with fluorescence contrast
Assignment 3, Part 2: experimental design with fluorescence	Assignment 3: visualizing actin using fluorescence contrast	Assignment 3: visualizing actin with fluorescence contrast
Assignment 3 Overview	Assignment 4: finding and measuring things	Assignment 4 part 1: Make a fake image
Assignment 4 part 2: Measure resolution	Assignment 4 part 3: Track microspheres over time	Assignment 5, Part 1: MSD difference tracking and microscope stability
Assignment 5, Part 1: viscosity and diffusivity in glycerol-water mixtures	Assignment 5, Part 2: live cell particle tracking of endocytosed beads	Assignment 5: Spring 2020
Assignment 5: cellular microrheology	Assignment 5 Overview	Assignment 5 navigation
Assignment 6, Part 1: Pre-lab questions	Assignment 6, Part 1: build a two-color microscope	Assignment 6, Part 2: Electronics bootcamp
Assignment 6, Part 2: electronics written problems	Assignment 6, Part 3: Identifying unknown filter circuits	Assignment 6 Overview
Assignment 6 Overview: two color microscope	Assignment 7, Part 1: op amp golden rules questions	Assignment 7, Part 2: measure temperature and fluorescence
Assignment 7, Part 3: testing your instrument and measuring a DNA melting curve	Assignment 7: Amplifiers and feedback	Assignment 7 Overview
Assignment 8, Part 0: convolution practice	Assignment 8, Part 1: convolution	Assignment 8, Part 1: fabricate a microfluidic device
Assignment 8, Part 2: build a two-color microscope	Assignment 8, Part 2: fabricate a microfluidic device	Assignment 8, Part 2: lock-in amplifier and temperature control
Assignment 8, Part 3: add flow control and test your device	Assignment 8 Overview	Assignment 8 Overview: flow channel & two-color microscope
Assignment 9, Part 1: Analyze two-color yeast images	Assignment 9, Part 1: model function	Assignment 9, Part 2: Simulating DNA melting data and testing the model function
Assignment 9, Part 3: Fitting your data	Assignment 9 Overview	Assignment 9 Overview: Analyzing yeast images
BEECH(F23)	BEECH(F23):Build Communication Toolkit	BEECH(F23):Build Community
BEECH(F23):Build Knowledge	BEECH(F23):Build Your Project	BEECH(F23):People
BEECH(F23): 2023-2024 schedule	BEECH Main Page	BE Classroom Computer Documentation
BE TA Training(Su16):Homepage	BE TA Training (Su17)	BE TA Training (Su18)
BE TA Training (Su19)	Beam Expander Example	Beech
Bode plots	Bode plots and frequency response	Bryan Hernandez/20.109/Lab notebook/Module 1/Day 2
Bryan Hernandez/20.109/Lab notebook/Module 1/Day 3	Bryan Hernandez/20.109/Lab notebook/Module 1/Day 4	Bryan Hernandez/20.109/Lab notebook/Module 1/Day 5
Bryan Hernandez/20.109/Lab notebook/Module 1/Day 6	Bryan Hernandez/20.109/Lab notebook/Module 2/Day 2	CM March14
CM March28	CRISPRi module, Part II: Increasing ethanol yield in E. coli MG1655	Calculating MSD and Diffusion Coefficients
Capacitors and inductors	Cartridge Manipulation	Cell Printing
Cell Printing Experimentation	Cell Reservations	Cellular microrheology
Complex Number Review	Compound Microscope Example	Confocal Wiki
Converting Gaussian fit to Rayleigh resolution	Course Journal -- Nathan S Lachenmyer	Coursework
Creating 20.109(S17):Scan slides to identify FKBP12 binders (Day5)	DAQ Ribbon Cable	DNA Melter Improvements
DNA Melting	DNA Melting: DNA Sequences	DNA Melting: Model function and parameter estimation by nonlinear regression
DNA Melting: Processing DNA Melting Data	DNA Melting: Simulating DNA Melting - Basics	DNA Melting: Simulating DNA Melting - Intermediate Topics
DNA Melting: Using the Basic DNAMelter GUI	DNA Melting: Using the LockIn DNAMelter GUI	DNA Melting: Using the Matlab DNAMelter GUI
DNA Melting II: Using the Matlab DNALockIn GUI	DNA Melting Part 1: Measuring Temperature and Fluorescence	DNA Melting Part 1: Simulating DNA Melting - Basics
DNA Melting Part 2: Lock-in Amplifier and Temperature Control	DNA Melting Part 2: Measuring Temperature and Fluorescence	DNA Melting Part 3: Simulating DNA Melting - Intermediate Topcs
DNA Melting Part 3: Simulating DNA Melting - Intermediate Topics	DNA Melting Part 4: Lock-in Amplifier and Temperature Control	DNA Melting Report Requirements
DNA Melting Report Requirements for Part 1	DNA Melting Report Requirements for Part 2	DNA Melting Thermodynamics
DNA melting: Identifying the unknown sample	DNA melting lab wiki pages	Data Sheets
Deconvolved Image	Develop Research proposal ideas and presentations	Device Creation
ESTORM	Electronics Mini-Lab	Electronics Module
Electronics Primer	Electronics boot camp I: passive circuits and transfer functions	Electronics boot camp lab part 1
Electronics bootcamp II: feedback systems	Electronics primer	Electronics written problems
Electronics written problems II	Emmanuel Quiroz	Equipment on loan
Error analysis	Estimating second order system parameters from noise power spectra using nonlinear regression	Exam 2 study guide
FPGA Design Environment	Fall 2010: DNA melting report outline	Fall 2010: Microscopy report outline
Fall 2010: Problem Set 3	Fall 2010 Syllabus	Fall 2012: Journal Presentations
Final Project: Spatial Light Modulator Galore	Final Project -- Nathan S Lachenmyer	Final Project Proposal Williams
Final Projects	Finding and measuring things	Flat-field correction
Fluorescence Imaging of Actin Cytoskeleton	Geometrical Optics	Geometrical optics and ray tracing
Hattie Chung	Identifying the unknown DNA sample	Impedance Analysis
In silico cloning of pdCas9 construct	Inkjet Technologies	Input and output impedance
Intro Electronics Lab Report	Introduction	Key Project Elements
Key estimates	Lab 1 Report -- Nathan S Lachenmyer	Lab 2 Report -- Nathan S Lachenmyer
Lab Manual:Atomic Force Microscopy (AFM)	Lab Manual:Intro to electronics	Lab Manual:Introduction to electronics
Lab Manual:Measuring DNA Melting Curves	Lab Manual:Optical Microscopy	Lab Manual:Optical Trapping
Lab Manual:Processing DNA Melting Data	Lab Manual: Atomic Force Microscopy (AFM)	Lab Manual: Limits of Detection
Lab Manual: Measuring DNA Melting Curves	Lab Manual: Optical Microscopy	Lab Manual: SLA 3D-Printed Microfluidic Device Master Mold
Lab Report Guidelines	Lab orientation	Laser cutter safe operating procedure
Lecture Notes:Modeling real systems with ideal elements	Limits of Detection:Report Requirements	Limits of Detection: Data Sessions
Limits of Detection: Lab Manual	Locating objects in a fluorescent microscopic image	MATLAB: Estimating resolution from a PSF slide image
MATLAB: Estimating viscoelastic spectrum using Mason's method	MATLAB: Intensity-weighted centroid noise formula	MRI lab: FPGA controller documentation
MSD of Sum and Difference Trajectories	Main Page	Manta G032 camera measurements
March14	Matlab:Division operators	Matlab:Image Processing for Fluorescent Microscopy
Matlab:Matlab Fundamentals	Matlab:Simulating DNA Melting	Matlab:Simulating DNA melting
Matlab: Scalebars	Matlab: Simulating Brownian motion	Measuring biological forces mini-lab
Measuring optical magnification	Methods	Microrheology Measurements via Particle Tracking
Microscope Objective Lenses	Microscopy report general guidelines	Microscopy report outline
More info on BJC2100 Attempt	Nonlinear regression	Objective
Optical Microscopy: Brownian motion and microscope stability	Optical Microscopy: Brownian motion and microscopy stability	Optical Microscopy: Construction of a microscope
Optical Microscopy: Fluorescence Microscopy	Optical Microscopy: Part 1 Report Outline	Optical Microscopy: Part 2 Report Outline
Optical Microscopy: Part 3 Report Outline	Optical Microscopy: Part 4 Report Outline	Optical Microscopy Data Sheets
Optical Microscopy Part 1: Bright Field Microscopy	Optical Microscopy Part 1: Brightfield Microscopy	Optical Microscopy Part 1b: Geometrical Optics and Ray Tracing
Optical Microscopy Part 1b: Ray Tracing	Optical Microscopy Part 1c: Physical Optics and Limits of Detection	Optical Microscopy Part 1d: Noise Sources in Light Detection
Optical Microscopy Part 2: Fluorescence Microscopy	Optical Microscopy Part 2b: High Resolution Microscopy Techniques	Optical Microscopy Part 3: Particle Tracking
Optical Microscopy Part 3: Particle Tracking Applications	Optical Microscopy Part 3: Resolution, Stability, and Particle Tracking	Optical Microscopy Part 3: Resolution and Stability
Optical Microscopy Part 3a: Particle Tracking	Optical Microscopy Part 3a: Particle Tracking in Glycerin Samples	Optical Microscopy Part 3b: Microrheology Measurements in Fibroblast Cells
Optical Microscopy Part 3b: Microrheology Measurements in Live Fibroblast Cells	Optical Microscopy Part 3c: Fluorescence Imaging of Actin Cytoskeleton	Optical Microscopy Part 3c: Protocols for cell culture, cell fixing and cell imaging
Optical Microscopy Part 4: Microrheology Measurements in Fibroblast Cells	Optical Microscopy Part 4: Particle Tracking	Optical Microscopy Week 1: Bright Field Microscopy
Optical Microscopy Week 1: Brightfield Microscopy	Optical Microscopy Week 1: Build a brightfield microscope	Optical Microscopy Week 2: Fluorescence Microscopy
Optical Microscopy Week 3: Experiments	Optical Microscopy Week 3: Particle Tracking	Optical Microscopy Week 4: Microrheology Measurements in Fibroblast Cells
Optical Trap Code	Optical Trap Graphs	Optical aberrations
Optical detectors, noise, and the limit of detection	Optical microscopy lab wiki pages	Optical resolution
Optical trap	Optics Bootcamp	Papers
Papers to read	Part 3 Combined Report Outline	Particle Tracking Exercise
Photobleaching Model	Physical optics and resolution	Power spectral density
Probability and statistics	Problem Set 1	Problem Set 2
Problem Set 2 Fall 2010	Procedure: Diffusion in biological gels	Procedure: Particle tracking
Procedure: Peptide-DNA Tethering Assay	Project ideas	Protocols
Protocols for cell culture	Protocols for cell culture, fixing and imaging	Protocols for making microscopy samples
Python:DNA melting data analysis	Python:Simulating DNA Melting	QRT-PCR
QRT-PCR:Get Started	QRT-PCR:Heated Lid	QRT-PCR:LabView-versions
Real electronics	Recording, displaying and saving images in MATLAB	Reference List
Relay Lens Example	Resource List:Electronics	Resource List:Suppliers
Resource list:DNA melting and PCR	Resource list:Electronics	Resource list:Magnetic Resonance Imaging
Resource list:Optical trapping	Resource list:Optics	Resource list:Suppliers
Resource list: DNA melting and PCR	Resource list: Electronics	Resource list: Fiber optics
Resource list: Image Enhancement	Resource list: Image processing	Resource list: Magnetic Resonance Imaging
Resource list: Matlab	Resource list: Microscopy	Resource list: Optical trapping
Resource list: Optics	Resource list: Particle tracking	Resource list: Suppliers
Results	Review of probability concepts	SToNCalculator.m
Sandbox	Save the curve to a USB memory stick	Shot noise and centroid finding

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