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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]].
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If you would like to contribute to this site, please [[Special:RequestAccount|request an account]]. ()
  
 
== 20.309 course information==
 
== 20.309 course information==
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|style="width: 45%;"|'''Useful resources'''
 
|style="width: 45%;"|'''Useful resources'''
 
|--  
 
|--  
|  <font color=#04B45F>9/16/18</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 4: Building your transilluminated microscope|Part 4: Measure stuff]]
 
* [[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/sp20/20.309/materials.html Lectures 1 through 9 of the 20.309 class]
* From [http://www.microscopyu.com Nikon MicroscopyU]
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* [http://www.microscopyu.com/articles/formulas/formulasri.html Snell's law]
** [http://www.microscopyu.com/articles/formulas/formulasconjugate.html Conjugate planes in optical microscopy] (includes transmitted and reflected (epi) illumination)
+
** [http://www.microscopyu.com/articles/formulas/formulasri.html Snell's law]
+
** [http://www.microscopyu.com/articles/formulas/formulasresolution.html Resolution]
+
 
*  [[Understanding log plots]]
 
*  [[Understanding log plots]]
 
|-
 
|-
| <font color=#04B45F>9/23/18</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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* [[Manta G032 camera measurements]]
 
* [[Manta G032 camera measurements]]
 
|-
 
|-
| <font color=#04B45F>9/27/18</font color>
+
| <font color=#04B45F>2/25/20</font color>
 
| Quiz 1 (in lecture)
 
| Quiz 1 (in lecture)
 
| ||
 
| ||
 
|-
 
|-
|  <font color=#04B45F>9/30/18</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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*[[Matlab: Scalebars]]
 
*[[Matlab: Scalebars]]
 
|-
 
|-
|  <font color=#04B45F>10/7/18</font color>
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|  <font color=#04B45F>3/8/20</font color>
 
| Assignment 4
 
| Assignment 4
 
|{{Template:Assignment 4 navigation}}
 
|{{Template:Assignment 4 navigation}}
 
|
 
|
 +
* [http://www.microscopyu.com/articles/formulas/formulasresolution.html Resolution]
 
* [[Physical optics and resolution]]
 
* [[Physical optics and resolution]]
 
* [[Converting Gaussian fit to Rayleigh resolution]]
 
* [[Converting Gaussian fit to Rayleigh resolution]]
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* [[Calculating MSD and Diffusion Coefficients]]
 
* [[Calculating MSD and Diffusion Coefficients]]
 
|-
 
|-
|  <font color=#04B45F>10/14/18</font color>
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|  <font color=#04B45F>4/3/20</font color>
 
| Assignment 5
 
| Assignment 5
| [[Assignment 5 Overview|Assignment 5 Overview]]
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| [[Assignment 5: Spring 2020|Assignment 5 Overview (Spring 2020)]]
 
* [[Assignment 5, Part 1: MSD difference tracking and microscope stability|Part 1: MSD difference tracking and microscope stability]]  
 
* [[Assignment 5, Part 1: MSD difference tracking and microscope stability|Part 1: MSD difference tracking and microscope stability]]  
 
* [[Assignment 5, Part 2: live cell particle tracking of endocytosed beads| Part 2: Live cell particle tracking of endocytosed beads]]
 
* [[Assignment 5, Part 2: live cell particle tracking of endocytosed beads| Part 2: Live cell particle tracking of endocytosed beads]]
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* [[Calculating MSD and Diffusion Coefficients]]
 
* [[Calculating MSD and Diffusion Coefficients]]
 
|-
 
|-
|  <font color=#04B45F>10/18/18</font color>
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|  <font color=#04B45F>4/7/20</font color>
| Exam 1 (at 7:30pm in 35-225)
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| Exam 1  
 
|  
 
|  
 
|
 
|
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|style="width: 45%;"|'''Useful resources'''
 
|style="width: 45%;"|'''Useful resources'''
 
|--  
 
|--  
|  <font color=#04B45F>10/28/18</font color>
+
|  <font color=#04B45F>4/13/20</font color>
 
| Assignment 6
 
| Assignment 6
| [[Electronics boot camp I: passive circuits and transfer functions|Assignment 6 overview]]
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| [[Spring 2020 Assignment 6]]
* [[Electronics written problems]]
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* (Previous semesters' assignment 6 for reference)
* [[Electronics boot camp lab part 1]]
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* [[Assignment 6 Overview: two color microscope|Assignment 6 overview]]
 +
* [[Assignment 6, Part 1: build a two-color microscope]]
 +
* [[Assignment 6, Part 2: electronics written problems]]
 
|
 
|
 
* [[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]]
 
* [[Complex Number Review|Complex number review]]
 
 
* [[Input and output impedance]]
 
* [[Input and output impedance]]
 
|-
 
|-
|  <font color=#04B45F>11/4/18</font color>
+
|  <font color=#04B45F>4/20/20</font color>
 
| Assignment 7
 
| Assignment 7
| [[Electronics bootcamp II: feedback systems]]
+
| [[Spring 2020 Assignment 7]]
 +
* (Previous semesters' assignment 7 for reference)
 +
* [[Electronics boot camp I: passive circuits and transfer functions|Assignment 7 overview]]
 +
* [[Electronics written problems II|Assignment 7, Part 1: more electronics written problems]]
 +
* [[Electronics boot camp lab part 1|Assignment 7, Part 2: Electronics bootcamp I]]
 +
 
 
|  
 
|  
* [[Real electronics]]
 
 
* [[Impedance Analysis|Impedance analysis]]
 
* [[Impedance Analysis|Impedance analysis]]
 
* [[Bode plots|Transfer functions and Bode plots]]
 
* [[Bode plots|Transfer functions and Bode plots]]
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* [[Input and output impedance]]
 
* [[Input and output impedance]]
 
|-
 
|-
|  <font color=#04B45F>11/9/18</font color>
+
|  <font color=#04B45F>4/21/20</font color>
| Quiz 2 (in lecture)
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| Quiz 2 (60 min)
 
|  
 
|  
 
|
 
|
 
|-
 
|-
|  <font color=#04B45F>11/11/18</font color>
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|  <font color=#04B45F>4/27/20</font color>
 
| Assignment 8
 
| Assignment 8
| [[Assignment 8 Overview: flow channel & two-color microscope]]
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| [[Spring 2020 Assignment 8]]
* [[Assignment 8, Part 0: convolution practice]]
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*(Previous semester's assignment 8 for reference)
* [[Assignment 8, Part 1: fabricate a microfluidic device]]
+
*[[Assignment 8 Overview: flow channel & two-color microscope|Assignment 8 Overview]]
* [[Assignment 8, Part 2: build a two-color microscope]]
+
* [[Electronics bootcamp II: feedback systems|Part 1: feedback systems]]
* [[Assignment 8, Part 3: add flow control and test your device]]
+
* [[Assignment 8, Part 2: fabricate a microfluidic device| Part 2: fabricate a microfluidic device]]
 +
* [[Assignment 8, Part 3: add flow control and test your device| Part 3: add flow control and test your device]]
 
|[http://science.sciencemag.org/content/319/5862/482 *The* yeast paper: Mettelal ''et al.'', ''Science'' (2008)]
 
|[http://science.sciencemag.org/content/319/5862/482 *The* yeast paper: Mettelal ''et al.'', ''Science'' (2008)]
 
|-
 
|-
|  <font color=#04B45F>11/18/18</font color>
+
|  <font color=#04B45F>5/4/20</font color>
 
| Assignment 9
 
| Assignment 9
| [[Assignment 9 Overview: Analyzing yeast images]]
+
| [[Spring 2020 Assignment 9]]
* [[Assignment 9, Part 1: Analyze two-color yeast images]]
+
*(Previous semester's assignment 9 for reference)
 +
* [[Assignment 9 Overview: Analyzing yeast images]]
 +
* [[Assignment 8, Part 0: convolution practice| Part 0: convolution practice]]
 +
* [[Assignment 9, Part 1: Analyze two-color yeast images| Part 1: Analyze two-color yeast images]]
 +
* [[Assignment 10, Part 1: Measuring the osmotic shock response of yeast| A10: Measure the osmotic shock response of yeast]]
 
|
 
|
 
|-
 
|-
|  <font color=#04B45F>12/2/18</font color>
+
|  <font color=#04B45F>5/8/20</font color>
| Assignment 10
+
| Exam 2 (90 min)
| [[Assignment 10, Part 1: Measuring the osmotic shock response of yeast]]
+
|  
 
|
 
|
 
|-
 
|-
|  <font color=#04B45F>12/6/18</font color>
+
|  <font color=#04B45F>5/12/20</font color>
| Exam 2 (at 7:30pm in 35-225)
+
| Assignment 10
|  
+
| [[Spring 2020 Assignment 10]]
 +
*(Previous semester's assignment 10 was combined with assignment 9)
 
|
 
|
 
|-
 
|-
<font color=#04B45F>12/11/18</font color>
+
cancelled
 
| Assignment 11
 
| Assignment 11
 
| [[Assignment 11: Tell us about your lab visit]]
 
| [[Assignment 11: Tell us about your lab visit]]
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* [[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]]
 
===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 21:07, 5 September 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.)