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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	Simulating diffusing microspheres in MATLAB	Spring09/Todo
Spring09:Todo list	Spring 11:CellPrinter	Spring 11:Chemotaxis Assay
Spring 11:Confocal Microscope	Spring 11:Directed Evolution	Spring 11:Directed Evolution/KAF95
Spring 11:Directed Evolution/Perfusion Chambers	Spring 11:Directed Evolution/Week of 3-14-2011 Status	Spring 11:Directed Evolution/Week of 3-21-2011 Status
Spring 11:Directed Evolution/Week of 3-28-2011 Status	Spring 11:Directed Evolution/Week of 4-04-2011 Status	Spring 11:Directed Evolution/Week of 4-11-2011 Status
Spring 11:Directed Evolution/Week of 4-18-2011 Status	Spring 11:Directed Evolution/Week of 4-25-2011 Status	Spring 11:Directed Evolution/Week of 5-02-2011 Status
Spring 11:Directed Evolution/Week of 5-09-2011 Status	Spring 11:QRT-PCR	Spring 11:QRT-PCR: Progress Notes
Spring 11:QRT-PCR weekly reports	Spring 11:SMR	Spring 11:eSTORM
Spring 11 ChemotaxisAssayWeeklyReports	Spring 11 Chemotaxis Assay Weekly Reports	Spring 2011:3D PSF lab
Spring 2011:3D PSF lab:Kristin	Spring 2011:CellFinder	Spring 2011:Optical Trapping Lab
Spring 2012:LFM	Spring 2012:LFM Documentation	Spring 2012:LFM Extra
Spring 2012:LFM Literature	Spring 2012:LFM Proposal	Spring 2012:LFM Report
Spring 2012:Leanna Morinishi	Spring 2012:Leanna Morinishi Journal	Spring 2012:Leanna Morinishi LFM
Spring 2012:Leanna Morinishi Lab 1	Spring 2012:Leanna Morinishi Lab 2	Spring 2012:Leanna Morinishi Lit Search
Spring 2012:PSF lab	Spring 2012:Snot	Spring 2012:Vincent Lee Journal
Spring 2012:Vincent Lee Lab 1	Spring 2012:Vincent Lee Lab 2	Spring 2012: Ajoke Jumoke Williams
Spring 2012: Jonathan Gootenberg	Spring 2012: Jonathan Gootenberg FinProject	Spring 2012: Jonathan Gootenberg Journal
Spring 2012: Jonathan Gootenberg Lab 2	Spring 2012: Jonathan Gootenberg STORM	Spring 2012: Real Time qPCR
Spring 2012: Vincent Lee	Spring 2012: Williams Key Factors Table	Spring 2012 Bioinstrumentation Project Lab
Spring 2012 Bioinstrumentation Project Lab.	Spring 2020 Assignment 10	Spring 2020 Assignment 6

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