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{{Template:20.309}} | {{Template:20.309}} | ||
+ | __NOTOC__ | ||
Bioinstrumentation scholars: you are welcome to edit and improve this course wiki. Correct, helpful, exquisitely-expressed changes will increase your class participation grade. Alterations not meeting those critera may have the opposite effect. | Bioinstrumentation scholars: you are welcome to edit and improve this course wiki. Correct, helpful, exquisitely-expressed changes will increase your class participation grade. Alterations not meeting those critera may have the opposite effect. | ||
If you would like to contribute to this site, please [[Special:RequestAccount|request an account]]. | If you would like to contribute to this site, please [[Special:RequestAccount|request an account]]. | ||
+ | == 20.309 course information== | ||
+ | * [[20.309:Course Information| 20.309 course information]] | ||
+ | * [[20.309:Safety| lab safety]] | ||
+ | * Reserve a lab station here: [http://measurebiology.org/reservations/Web/schedule.php Bioinstrumentation Lab reservation system] | ||
+ | |||
+ | == 20.309 master schedule== | ||
<div style="padding: 10px; width: 740px; border: 5px solid #000FFF;"> | <div style="padding: 10px; width: 740px; border: 5px solid #000FFF;"> | ||
− | + | ===Module 1: Optics & Microscopy=== | |
− | + | ||
− | == | + | |
− | + | ||
− | + | ||
{| border=1px | {| border=1px | ||
|style="width: 10%;"|'''Important dates''' | |style="width: 10%;"|'''Important dates''' | ||
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* [[Assignment 1, Part 1: Pre-lab questions|Part 1: Pre-lab questions]] | * [[Assignment 1, Part 1: Pre-lab questions|Part 1: Pre-lab questions]] | ||
* [[Assignment 1, Part 2: Optics bootcamp|Part 2: Optics bootcamp]] | * [[Assignment 1, Part 2: Optics bootcamp|Part 2: Optics bootcamp]] | ||
− | * [[Assignment 1, Part 3: | + | * [[Assignment 1, Part 3: Building your transillumination microscope|Part 3: Build a microscope]] |
− | * [[Assignment 1, Part 4: Building your transilluminated microscope|Part 4: | + | * [[Assignment 1, Part 4: Building your transilluminated microscope|Part 4: Measure stuff]] |
| | | | ||
− | |||
− | |||
* [https://stellar.mit.edu/S/course/20/fa13/20.309/materials.html Lectures 1 through 9 of the 20.309 class] | * [https://stellar.mit.edu/S/course/20/fa13/20.309/materials.html Lectures 1 through 9 of the 20.309 class] | ||
* From [http://www.microscopyu.com Nikon MicroscopyU] | * From [http://www.microscopyu.com Nikon MicroscopyU] | ||
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** [http://www.microscopyu.com/articles/formulas/formulasresolution.html Resolution] | ** [http://www.microscopyu.com/articles/formulas/formulasresolution.html Resolution] | ||
* [[Understanding log plots]] | * [[Understanding log plots]] | ||
− | |||
|- | |- | ||
| <font color=#04B45F>9/24/17</font color> | | <font color=#04B45F>9/24/17</font color> | ||
| Assignment 2 | | Assignment 2 | ||
| [[Assignment 2: fluorescence microscopy| Assignment 2 Overview]] | | [[Assignment 2: fluorescence microscopy| Assignment 2 Overview]] | ||
− | * [[Assignment 2: | + | * [[Assignment 2 Part 1: Noise in images|Part 1: Noise in images]] |
− | * [[Assignment 2: | + | * [[Assignment 2 Part 2: Fluorescence microscopy|Part 2: Fluorescence microscopy]] |
+ | * [[Assignment 2 Part 3: Build an epi-illuminator for your microscope|Part 3: Build an epi-illuminator for your microscope]] | ||
| | | | ||
+ | * [[Geometrical optics and ray tracing]] | ||
+ | * [[Physical optics and resolution]] | ||
+ | * [[Optical aberrations]] | ||
+ | * [[Aperture and field stops]] | ||
+ | * [[Optical detectors, noise, and the limit of detection]] | ||
+ | * [[Manta G032 camera measurements]] | ||
|- | |- | ||
| <font color=#04B45F>9/28/17</font color> | | <font color=#04B45F>9/28/17</font color> | ||
Line 54: | Line 61: | ||
* [[Assignment 3, Part 2: experimental design with fluorescence| Part 2: choosing filters]] | * [[Assignment 3, Part 2: experimental design with fluorescence| Part 2: choosing filters]] | ||
| | | | ||
+ | *[[Flat-field correction|Flat-field correction of non-uniform illumination]] | ||
+ | *[[Matlab: Scalebars]] | ||
|- | |- | ||
| <font color=#04B45F>10/8/17</font color> | | <font color=#04B45F>10/8/17</font color> | ||
| Assignment 4 | | Assignment 4 | ||
− | | | + | |{{Template:Assignment 4 navigation}} |
| | | | ||
+ | * [[Physical optics and resolution]] | ||
|- | |- | ||
| <font color=#04B45F>10/15/17</font color> | | <font color=#04B45F>10/15/17</font color> | ||
| Assignment 5 | | Assignment 5 | ||
| [[Assignment 5 Overview|Assignment 5 Overview]] | | [[Assignment 5 Overview|Assignment 5 Overview]] | ||
− | * [[Assignment 5, Part 1: viscosity and diffusivity in glycerol-water mixtures|Part 1: | + | * [[Assignment 5, Part 1: viscosity and diffusivity in glycerol-water mixtures|Part 1: Estimating the diffusion coefficient by tracking suspended microspheres]] |
− | * [[Assignment 5, Part 2: live cell particle tracking of endocytosed beads| Part 2: | + | * [[Assignment 5, Part 2: live cell particle tracking of endocytosed beads| Part 2: Live cell particle tracking of endocytosed beads]] |
| | | | ||
+ | * [[Converting Gaussian fit to Rayleigh resolution]] | ||
+ | * [[MATLAB: Estimating resolution from a PSF slide image]] | ||
+ | * [[Matlab: Scalebars]] | ||
+ | * [[Calculating MSD and Diffusion Coefficients]] | ||
|- | |- | ||
| <font color=#04B45F>10/19/17</font color> | | <font color=#04B45F>10/19/17</font color> | ||
− | | Exam 1 (at 7:30pm in | + | | Exam 1 (at 7:30pm in 4-163) |
| | | | ||
| | | | ||
|- | |- | ||
+ | |} | ||
+ | <br /> | ||
+ | |||
+ | ===Module 2: Signals and Systems=== | ||
+ | {| border=1px | ||
+ | |style="width: 10%;"|'''Important dates''' | ||
+ | |style="width: 15%;"|'''Assignment due''' | ||
+ | |style="width: 30%;"|'''Assignment page links''' | ||
+ | |style="width: 45%;"|'''Useful resources''' | ||
+ | |-- | ||
| <font color=#04B45F>10/29/17</font color> | | <font color=#04B45F>10/29/17</font color> | ||
| Assignment 6 | | Assignment 6 | ||
| [[Assignment 6 Overview]] | | [[Assignment 6 Overview]] | ||
− | * [[Assignment 6, Part 1: Pre-lab questions|Part 1: Pre-lab questions]] | + | * [[Assignment 6, Part 1: Pre-lab questions|Part 1: Pre-lab questions]] |
− | * [[Assignment 6, Part 2: Electronics bootcamp|Part 2: Build circuits and measure them | + | * [[Assignment 6, Part 2: Electronics bootcamp|Part 2: Build circuits and measure them]] |
− | + | ||
| | | | ||
+ | * [[Electronics primer]] | ||
+ | * [https://www.khanacademy.org/science/electrical-engineering/ee-circuit-analysis-topic Khan Academy Material, esp. "Ideal Circuit Elements" and "Voltage Divider"] | ||
+ | * [[Real electronics]] | ||
+ | * [[Impedance Analysis|Impedance analysis]] | ||
+ | * [[Bode plots|Transfer functions and Bode plots]] | ||
+ | * [[Complex Number Review|Complex number review]] | ||
+ | * [[Input and output impedance]] | ||
+ | |||
|- | |- | ||
| <font color=#04B45F>11/2/17</font color> | | <font color=#04B45F>11/2/17</font color> | ||
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* [[Assignment 7, Part 1: op amp golden rules questions|Part 1: Op amps]] | * [[Assignment 7, Part 1: op amp golden rules questions|Part 1: Op amps]] | ||
* [[Assignment 7, Part 2: measure temperature and fluorescence| Part 2: measure temperature and fluorescence]] | * [[Assignment 7, Part 2: measure temperature and fluorescence| Part 2: measure temperature and fluorescence]] | ||
+ | * [[Assignment 7, Part 3: testing your instrument and measuring a DNA melting curve| Part 3: test your instrument and measure a preliminary melting curve]] | ||
+ | |||
| | | | ||
+ | * [[DNA Melting Thermodynamics]] | ||
+ | * [[Real electronics]] | ||
+ | * [[Impedance Analysis|Impedance analysis]] | ||
+ | * [[Bode plots|Transfer functions and Bode plots]] | ||
+ | * [[Complex Number Review|Complex number review]] | ||
+ | * [[Input and output impedance]] | ||
|- | |- | ||
| <font color=#04B45F>11/12/17</font color> | | <font color=#04B45F>11/12/17</font color> | ||
Line 97: | Line 136: | ||
* [[Assignment 8, Part 1: convolution|Part 1: convolution and lock-in amplifiers]] | * [[Assignment 8, Part 1: convolution|Part 1: convolution and lock-in amplifiers]] | ||
* [[Assignment 8, Part 2: lock-in amplifier and temperature control| Part 2: modify your instrument]] | * [[Assignment 8, Part 2: lock-in amplifier and temperature control| Part 2: modify your instrument]] | ||
− | |||
| | | | ||
+ | * [http://mfold.rna.albany.edu/?q=DINAMelt/Hybrid2 DINAMelt Web Server] | ||
|- | |- | ||
| <font color=#04B45F>11/19/17</font color> | | <font color=#04B45F>11/19/17</font color> | ||
| Assignment 9 | | Assignment 9 | ||
− | | | + | | [[Assignment 9 Overview]] |
+ | * [[Assignment 9, Part 1: model function|Part 1: writing the model function]] | ||
+ | * [[Assignment 9, Part 2: Simulating DNA melting data and testing the model function|Part 2: test your code with simulated data]] | ||
+ | * [[Assignment 9, Part 3: Fitting your data|Part 3: fitting your data]] | ||
+ | |||
| | | | ||
+ | * [[DNA Melting: Model function and parameter estimation by nonlinear regression]] | ||
+ | * [[DNA Melting Thermodynamics]] | ||
+ | * [[DNA melting: Identifying the unknown sample]] | ||
|- | |- | ||
| <font color=#04B45F>12/3/17</font color> | | <font color=#04B45F>12/3/17</font color> | ||
| Assignment 10 | | Assignment 10 | ||
− | | | + | | [[Assignment 10 Overview|Assignment 10: measure DNA melting curves and identify your unknown sample.]] |
+ | |||
| | | | ||
+ | * [[DNA melting: Identifying the unknown sample]] | ||
+ | * [[DNA Melting: DNA Sequences]] | ||
+ | * [[DNA Melting: Model function and parameter estimation by nonlinear regression]] | ||
|- | |- | ||
| <font color=#04B45F>12/7/17</font color> | | <font color=#04B45F>12/7/17</font color> | ||
− | | Exam 2 (at 7:30pm in | + | | Exam 2 (at 7:30pm in 4-163) |
| | | | ||
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Line 124: | Line 174: | ||
</div> | </div> | ||
− | + | ==Optics and microscopy resources== | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | ==Optics | + | |
− | + | ||
− | + | ||
− | + | ||
===Background reading=== | ===Background reading=== | ||
* [[Geometrical optics and ray tracing]] | * [[Geometrical optics and ray tracing]] | ||
+ | * [[Physical optics and resolution]] | ||
+ | * [[Optical aberrations]] | ||
+ | * [[Aperture and field stops]] | ||
* [[Optical detectors, noise, and the limit of detection]] | * [[Optical detectors, noise, and the limit of detection]] | ||
* [[Manta G032 camera measurements]] | * [[Manta G032 camera measurements]] | ||
* [[Understanding log plots]] | * [[Understanding log plots]] | ||
− | + | ===Code examples and simulations=== | |
− | + | * [[Converting Gaussian fit to Rayleigh resolution]] | |
− | == | + | * [[MATLAB: Estimating resolution from a PSF slide image]] |
− | + | * [[Matlab: Scalebars]] | |
− | * [[ | + | * [[Calculating MSD and Diffusion Coefficients]] |
+ | ==Electronics resources== | ||
===Background reading=== | ===Background reading=== | ||
* [[Electronics primer]] | * [[Electronics primer]] | ||
Line 161: | Line 200: | ||
* [[Input and output impedance]] | * [[Input and output impedance]] | ||
− | + | ===Code examples and simulations=== | |
+ | * [[DNA Melting: Simulating DNA Melting - Basics]] | ||
+ | * [[DNA Melting: Simulating DNA Melting - Intermediate Topics]] | ||
+ | * [[DNA Melting: Model function and parameter estimation by nonlinear regression]] | ||
+ | |||
+ | ===Reference materials=== | ||
+ | * [[DNA Melting Thermodynamics]] | ||
+ | * [[DNA Melting: DNA Sequences]] | ||
+ | * [http://mfold.rna.albany.edu/?q=DINAMelt/Hybrid2 DINAMelt Web Server] | ||
==Limits of detection mini-lab== | ==Limits of detection mini-lab== |
Revision as of 23:41, 13 November 2017
Bioinstrumentation scholars: you are welcome to edit and improve this course wiki. Correct, helpful, exquisitely-expressed changes will increase your class participation grade. Alterations not meeting those critera may have the opposite effect.
If you would like to contribute to this site, please request an account.
20.309 course information
- 20.309 course information
- lab safety
- Reserve a lab station here: Bioinstrumentation Lab reservation system
20.309 master schedule
Module 1: Optics & Microscopy
Important dates | Assignment due | Assignment page links | Useful resources |
9/17/17 | Assignment 1 |
| |
9/24/17 | Assignment 2 | Assignment 2 Overview | |
9/28/17 | Quiz 1 (in lecture) | ||
10/1/17 | Assignment 3 | Assignment 3 Overview | |
10/8/17 | Assignment 4 | ||
10/15/17 | Assignment 5 | Assignment 5 Overview | |
10/19/17 | Exam 1 (at 7:30pm in 4-163) |
Module 2: Signals and Systems
Important dates | Assignment due | Assignment page links | Useful resources |
10/29/17 | Assignment 6 | Assignment 6 Overview | |
11/2/17 | Quiz 2 (in lecture) | ||
11/5/17 | Assignment 7 | Assignment 7 Overview | |
11/12/17 | Assignment 8 | Assignment 8 Overview | |
11/19/17 | Assignment 9 | Assignment 9 Overview | |
12/3/17 | Assignment 10 | Assignment 10: measure DNA melting curves and identify your unknown sample. | |
12/7/17 | Exam 2 (at 7:30pm in 4-163) | ||
12/13/17 | Assignment 11 |
Optics and microscopy resources
Background reading
- Geometrical optics and ray tracing
- Physical optics and resolution
- Optical aberrations
- Aperture and field stops
- Optical detectors, noise, and the limit of detection
- Manta G032 camera measurements
- Understanding log plots
Code examples and simulations
- Converting Gaussian fit to Rayleigh resolution
- MATLAB: Estimating resolution from a PSF slide image
- Matlab: Scalebars
- Calculating MSD and Diffusion Coefficients
Electronics resources
Background reading
- Electronics primer
- Khan Academy Material, esp. "Ideal Circuit Elements" and "Voltage Divider"
- Real electronics
- Impedance analysis
- Transfer functions and Bode plots
- Complex number review
- Input and output impedance
Code examples and simulations
- DNA Melting: Simulating DNA Melting - Basics
- DNA Melting: Simulating DNA Melting - Intermediate Topics
- DNA Melting: Model function and parameter estimation by nonlinear regression
Reference materials
Limits of detection mini-lab
- Lab Manual: Limits of Detection
- Lab Manual: Atomic Force Microscopy (AFM)
- Limits of Detection: Data Sessions