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{{Template:20.309}}
 
{{Template:20.309}}
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__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.
  
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If you would like to contribute to this site, please [[Special:RequestAccount|request an account]].
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If you would like to contribute to this site, please [[Special:RequestAccount|request an account]]. ()
  
 +
== 20.309 course information==
  
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* [https://accessibility.mit.edu/ Accessibility]
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* [[20.309:Course Information| 20.309 course information]]
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* [[20.309:Safety| lab safety]]
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* Reserve a lab station here: [http://measurebiology.org/reservations/Web/schedule.php Bioinstrumentation Lab reservation system]
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 +
== 20.309 master schedule==
  
 
<div style="padding: 10px; width: 740px; border: 5px solid #000FFF;">
 
<div style="padding: 10px; width: 740px; border: 5px solid #000FFF;">
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===Module 1: Optics & Microscopy===
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== 20.309 Master Schedule==
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{| border=1px
 
{| border=1px
 
|style="width: 10%;"|'''Important dates'''  
 
|style="width: 10%;"|'''Important dates'''  
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|style="width: 45%;"|'''Useful resources'''
 
|style="width: 45%;"|'''Useful resources'''
 
|--  
 
|--  
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|  <font color=#04B45F>9/17/17</font color>
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|  <font color=#04B45F>2/16/20</font color>
 
| Assignment 1
 
| Assignment 1
 
|  
 
|  
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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]]
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* [[Assignment 1, Part 3: Microscope design|Part 3: Microscope design]]
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* [[Assignment 1, Part 3: Building your transillumination microscope|Part 3: Build a microscope]]
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* [[Assignment 1, Part 4: Building your transilluminated microscope|Part 4: Building your microscope]]
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* [[Assignment 1, Part 4: Building your transilluminated microscope|Part 4: Measure stuff]]
 
|  
 
|  
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* [[Geometrical optics and ray tracing]]
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* [https://stellar.mit.edu/S/course/20/sp20/20.309/materials.html Lectures 1 through 9 of the 20.309 class]
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* [[Physical optics and resolution]]
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* [http://www.microscopyu.com/articles/formulas/formulasri.html Snell's law]
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* [https://stellar.mit.edu/S/course/20/fa13/20.309/materials.html Lectures 1 through 9 of the 20.309 class]
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* From [http://www.microscopyu.com Nikon MicroscopyU]
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** [http://www.microscopyu.com/articles/formulas/formulasconjugate.html Conjugate planes in optical microscopy] (includes transmitted and reflected (epi) illumination)
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** [http://www.microscopyu.com/articles/formulas/formulasri.html Snell's law]
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** [http://www.microscopyu.com/articles/formulas/formulasresolution.html Resolution]
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*  [[Understanding log plots]]
 
*  [[Understanding log plots]]
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|-
 
|-
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| <font color=#04B45F>9/24/17</font color>
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| <font color=#04B45F>2/23/20</font color>
 
| Assignment 2
 
| Assignment 2
 
| [[Assignment 2: fluorescence microscopy| Assignment 2 Overview]]
 
| [[Assignment 2: fluorescence microscopy| Assignment 2 Overview]]
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* [[Assignment 2: epi illuminator for fluorescence microscopy|Part 1:epi illumination]]
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* [[Assignment 2 Part 1: Noise in images|Part 1: Noise in images]]
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* [[Assignment 2: resolution and noise|Part 2: resolution and noise]]
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* [[Assignment 2 Part 2: Fluorescence microscopy|Part 2: Fluorescence microscopy]]
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* [[Assignment 2 Part 3: Build an epi-illuminator for your microscope|Part 3: Build an epi-illuminator for your microscope]]
 
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|
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* [[Geometrical optics and ray tracing]]
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* [[Physical optics and resolution]]
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* [[Optical aberrations]]
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* [[Aperture and field stops]]
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* [[Optical detectors, noise, and the limit of detection]]
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* [[Manta G032 camera measurements]]
 
|-
 
|-
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| <font color=#04B45F>9/28/17</font color>
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| <font color=#04B45F>2/25/20</font color>
 
| Quiz 1 (in lecture)
 
| Quiz 1 (in lecture)
 
| ||
 
| ||
 
|-
 
|-
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|  <font color=#04B45F>10/1/17</font color>
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|  <font color=#04B45F>3/1/20</font color>
 
| Assignment 3
 
| Assignment 3
 
| [[Assignment 3 Overview|Assignment 3 Overview]]
 
| [[Assignment 3 Overview|Assignment 3 Overview]]
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* [[Assignment 3, Part 2: experimental design with fluorescence| Part 2: choosing filters]]  
 
* [[Assignment 3, Part 2: experimental design with fluorescence| Part 2: choosing filters]]  
 
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|
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*[[Flat-field correction|Flat-field correction of non-uniform illumination]]
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*[[Matlab: Scalebars]]
 
|-
 
|-
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|  <font color=#04B45F>10/8/17</font color>
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|  <font color=#04B45F>3/8/20</font color>
 
| Assignment 4
 
| Assignment 4
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|  
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|{{Template:Assignment 4 navigation}}
 
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|
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* [http://www.microscopyu.com/articles/formulas/formulasresolution.html Resolution]
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* [[Physical optics and resolution]]
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* [[Converting Gaussian fit to Rayleigh resolution]]
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* [[MATLAB: Estimating resolution from a PSF slide image]]
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* [[Matlab: Scalebars]]
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* [[Calculating MSD and Diffusion Coefficients]]
 
|-
 
|-
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|  <font color=#04B45F>10/15/17</font color>
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|  <font color=#04B45F>4/3/20</font color>
 
| Assignment 5
 
| Assignment 5
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| [[Assignment 5 Overview|Assignment 5 Overview]]
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| [[Assignment 5: Spring 2020|Assignment 5 Overview (Spring 2020)]]
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* [[Assignment 5, Part 1: viscosity and diffusivity in glycerol-water mixtures|Part 1:]] Estimating the diffusion coefficient by tracking suspended microspheres;
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* [[Assignment 5, Part 1: MSD difference tracking and microscope stability|Part 1: MSD difference tracking and microscope stability]]  
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* [[Assignment 5, Part 2: live cell particle tracking of endocytosed beads| Part 2:]] Live cell particle tracking of endocytosed beads.
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* [[Assignment 5, Part 2: live cell particle tracking of endocytosed beads| Part 2: Live cell particle tracking of endocytosed beads]]
 
|
 
|
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* [[Matlab: Scalebars]]
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* [[Calculating MSD and Diffusion Coefficients]]
 
|-
 
|-
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|  <font color=#04B45F>10/19/17</font color>
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|  <font color=#04B45F>4/7/20</font color>
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| Exam 1 (at 7:30pm in room ____)
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| Exam 1  
 
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|-
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|  <font color=#04B45F>10/29/17</font color>
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|}
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<br />
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===Module 2: electronics, signals and systems===
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{| border=1px
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|style="width: 10%;"|'''Important dates'''
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|style="width: 15%;"|'''Assignment due'''
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|style="width: 30%;"|'''Assignment page links'''
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|style="width: 45%;"|'''Useful resources'''
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|--
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|  <font color=#04B45F>4/13/20</font color>
 
| Assignment 6
 
| Assignment 6
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| [[Assignment 6 Overview]]
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| [[Spring 2020 Assignment 6]]
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* [[Assignment 6, Part 1: Pre-lab questions|Part 1: Pre-lab questions]];
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* (Previous semesters' assignment 6 for reference)
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* [[Assignment 6, Part 2: Electronics bootcamp|Part 2: Build circuits and measure them]];
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* [[Assignment 6 Overview: two color microscope|Assignment 6 overview]]
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* [[Assignment 6, Part 3: Transimpedance amplifier|Part 3: Amplify photodiode signal]]
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* [[Assignment 6, Part 1: build a two-color microscope]]
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* [[Assignment 6, Part 2: electronics written problems]]
 
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|
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* [[Electronics primer]]
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* [https://www.khanacademy.org/science/electrical-engineering/ee-circuit-analysis-topic Khan Academy Material, esp. "Ideal Circuit Elements" and "Voltage Divider"]
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* [[Impedance Analysis|Impedance analysis]]
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* [[Input and output impedance]]
 
|-
 
|-
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|  <font color=#04B45F>11/2/17</font color>
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|  <font color=#04B45F>4/20/20</font color>
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| Quiz 2 (in lecture)
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| Assignment 7
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| [[Spring 2020 Assignment 7]]
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* (Previous semesters' assignment 7 for reference)
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* [[Electronics boot camp I: passive circuits and transfer functions|Assignment 7 overview]]
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* [[Electronics written problems II|Assignment 7, Part 1: more electronics written problems]]
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* [[Electronics boot camp lab part 1|Assignment 7, Part 2: Electronics bootcamp I]]
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|  
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* [[Impedance Analysis|Impedance analysis]]
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* [[Bode plots|Transfer functions and Bode plots]]
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* [[Complex Number Review|Complex number review]]
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* [[Input and output impedance]]
 
|-
 
|-
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|  <font color=#04B45F>11/5/17</font color>
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|  <font color=#04B45F>4/21/20</font color>
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| Assignment 7
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| Quiz 2 (60 min)
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| [[Assignment 7 Overview]]
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|  
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* [[Assignment 7, Part 1: op amp golden rules questions|Part 1: Op amps]]
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* [[Assignment 7, Part 2: measure temperature and fluorescence| Part 2: measure temperature and fluorescence]]
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|-
 
|-
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|  <font color=#04B45F>11/12/17</font color>
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|  <font color=#04B45F>4/27/20</font color>
 
| Assignment 8
 
| Assignment 8
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| [[Spring 2020 Assignment 8]]
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|
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*(Previous semester's assignment 8 for reference)
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*[[Assignment 8 Overview: flow channel & two-color microscope|Assignment 8 Overview]]
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* [[Electronics bootcamp II: feedback systems|Part 1: feedback systems]]
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* [[Assignment 8, Part 2: fabricate a microfluidic device| Part 2: fabricate a microfluidic device]]
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* [[Assignment 8, Part 3: add flow control and test your device| Part 3: add flow control and test your device]]
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|[http://science.sciencemag.org/content/319/5862/482 *The* yeast paper: Mettelal ''et al.'', ''Science'' (2008)]
 
|-
 
|-
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|  <font color=#04B45F>11/19/17</font color>
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|  <font color=#04B45F>5/4/20</font color>
 
| Assignment 9
 
| Assignment 9
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|  
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| [[Spring 2020 Assignment 9]]
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*(Previous semester's assignment 9 for reference)
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* [[Assignment 9 Overview: Analyzing yeast images]]
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* [[Assignment 8, Part 0: convolution practice| Part 0: convolution practice]]
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* [[Assignment 9, Part 1: Analyze two-color yeast images| Part 1: Analyze two-color yeast images]]
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* [[Assignment 10, Part 1: Measuring the osmotic shock response of yeast| A10: Measure the osmotic shock response of yeast]]
 
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|
 
|-
 
|-
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|  <font color=#04B45F>12/3/17</font color>
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|  <font color=#04B45F>5/8/20</font color>
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| Assignment 10
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| Exam 2 (90 min)
 
|  
 
|  
 
|
 
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|-
 
|-
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|  <font color=#04B45F>12/7/17</font color>
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|  <font color=#04B45F>5/12/20</font color>
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| Exam 2 (at 7:30pm in room _____)
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| Assignment 10
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|  
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| [[Spring 2020 Assignment 10]]
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*(Previous semester's assignment 10 was combined with assignment 9)
 
|
 
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|-
 
|-
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|  <font color=#04B45F>12/13/17</font color>
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|  cancelled
 
| Assignment 11
 
| Assignment 11
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| [[Assignment 11: Tell us about your lab visit]]
 
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|  
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|-
 
|-
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|}
 
|}
 
</div>
 
</div>
  
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==Optics and microscopy resources==
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__TOC__
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== 20.309 course information==
+
−
 
+
−
* [[20.309:Course Information]]
+
−
* [[20.309:Lab Report Guidelines]]
+
−
* [[20.309:Safety]]
+
−
 
+
−
Reserve a lab station here: [http://measurebiology.org/reservations/Web/schedule.php Bioinstrumentation Lab reservation system]
+
−
 
+
−
==Optics bootcamp==
+
−
===Lab manual===
+
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* [[Optics Bootcamp]]
+
−
 
+
 
===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]]
  
−
{{:Optical microscopy lab wiki pages}}
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===Code examples and simulations===
−
 
+
* [[Converting Gaussian fit to Rayleigh resolution]]
−
==Electronics bootcamp==
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* [[MATLAB: Estimating resolution from a PSF slide image]]
−
===Lab manual===
+
* [[Matlab: Scalebars]]
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* [[Electronics Mini-Lab|Electronics bootcamp]]
+
* [[Calculating MSD and Diffusion Coefficients]]
  
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==Electronics resources==
 
===Background reading===
 
===Background reading===
 
* [[Electronics primer]]
 
* [[Electronics primer]]
 
* [https://www.khanacademy.org/science/electrical-engineering/ee-circuit-analysis-topic Khan Academy Material, esp. "Ideal Circuit Elements" and "Voltage Divider"]
 
* [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]]
 
* [[Impedance Analysis|Impedance analysis]]
 
* [[Bode plots|Transfer functions and Bode plots]]
 
* [[Bode plots|Transfer functions and Bode plots]]
 
* [[Complex Number Review|Complex number review]]
 
* [[Complex Number Review|Complex number review]]
 
* [[Input and output impedance]]
 
* [[Input and output impedance]]
−
 
−
{{:DNA melting lab wiki pages}}
 
  
 
==Limits of detection mini-lab==
 
==Limits of detection mini-lab==

Latest revision as of 20:47, 16 October 2020

20.309: Biological Instrumentation and Measurement

ImageBar 774.jpg


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 master schedule

Module 1: Optics & Microscopy

Important dates Assignment due Assignment page links Useful resources
2/16/20 Assignment 1

Assignment 1 Overview

2/23/20 Assignment 2 Assignment 2 Overview
2/25/20 Quiz 1 (in lecture)
3/1/20 Assignment 3 Assignment 3 Overview
3/8/20 Assignment 4
4/3/20 Assignment 5 Assignment 5 Overview (Spring 2020)
4/7/20 Exam 1


Module 2: electronics, signals and systems

Important dates Assignment due Assignment page links Useful resources
4/13/20 Assignment 6 Spring 2020 Assignment 6
4/20/20 Assignment 7 Spring 2020 Assignment 7
4/21/20 Quiz 2 (60 min)
4/27/20 Assignment 8 Spring 2020 Assignment 8 *The* yeast paper: Mettelal et al., Science (2008)
5/4/20 Assignment 9 Spring 2020 Assignment 9
5/8/20 Exam 2 (90 min)
5/12/20 Assignment 10 Spring 2020 Assignment 10
  • (Previous semester's assignment 10 was combined with assignment 9)
cancelled Assignment 11 Assignment 11: Tell us about your lab visit

Optics and microscopy resources

Background reading

Code examples and simulations

Electronics resources

Background reading

Limits of detection mini-lab

MRI mini-lab

(Kept for historical reasons.)
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