Difference between revisions of "20.309 Main Page"

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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]]. ()
  
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== 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 This week and next==
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{| border=1px
 
{| border=1px
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|style="width: 15%;"|'''Week'''
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|style="width: 10%;"|'''Important dates'''  
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|style="width: 15%;"|'''Summary'''
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|style="width: 15%;"|'''Assignment due'''
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|style="width: 18%;"|'''Assignments due'''
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|style="width: 30%;"|'''Assignment page links'''
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|style="width: 17%;"|'''Lab Manual'''
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|style="width: 45%;"|'''Useful resources'''
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|style="width: 35%;"|'''Resources'''
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|--  
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|--
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| <font color=#04B45F>2/16/20</font color>
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| Week 9: Apr. 2 - 8
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| Assignment 1
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| Get started with circuits in the electronics bootcamp and with PSet3
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| [[Electronics Mini-Lab|Electronics bootcamp]]
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[[Assignment 1 Overview: Transillumination microscopy| Assignment 1 Overview]]
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* [[Assignment 1, Part 1: Pre-lab questions|Part 1: Pre-lab questions]]
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* [[Assignment 1, Part 2: Optics bootcamp|Part 2: Optics bootcamp]]
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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: Measure stuff]]
 
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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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* [http://www.microscopyu.com/articles/formulas/formulasri.html Snell's law]
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*  [[Understanding log plots]]
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|-
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| <font color=#04B45F>2/23/20</font color>
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| Assignment 2
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| [[Assignment 2: fluorescence microscopy| Assignment 2 Overview]]
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* [[Assignment 2 Part 1: Noise in images|Part 1: Noise in images]]
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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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|-
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| <font color=#04B45F>2/25/20</font color>
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| Quiz 1 (in lecture)
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| ||
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|-
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|  <font color=#04B45F>3/1/20</font color>
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| Assignment 3
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| [[Assignment 3 Overview|Assignment 3 Overview]]
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* [[Assignment 3, Part 1: visualizing actin with fluorescence contrast|Part 1: fluorescence imaging]]
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* [[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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|-
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|  <font color=#04B45F>3/8/20</font color>
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| Assignment 4
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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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|-
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|  <font color=#04B45F>4/3/20</font color>
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| Assignment 5
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| [[Assignment 5: Spring 2020|Assignment 5 Overview (Spring 2020)]]
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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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|
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* [[Matlab: Scalebars]]
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* [[Calculating MSD and Diffusion Coefficients]]
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|-
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|  <font color=#04B45F>4/7/20</font color>
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| Exam 1
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|-
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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>
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| Assignment 6
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| [[Spring 2020 Assignment 6]]
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* (Previous semesters' assignment 6 for reference)
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* [[Assignment 6 Overview: two color microscope|Assignment 6 overview]]
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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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|
 
* [[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"]
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* [[Real electronics]]
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* [[Impedance Analysis|Impedance analysis]]
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* [[Input and output impedance]]
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|-
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|  <font color=#04B45F>4/20/20</font color>
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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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* [[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]]
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|--
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|-
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| Week 10: Apr. 9 - 15
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| <font color=#04B45F>4/21/20</font color>
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| Finish up the electronics bootcamp and PSet 3, get started on DNA Melting 1
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| Quiz 2 (60 min)
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| <font color=#04B45F> Monday Apr. 10th: Electronics Bootcamp
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Friday Apr. 14th: PSet 3</font color>
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| [[Electronics Mini-Lab|Electronics bootcamp]]
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[[DNA Melting Part 1: Measuring Temperature and Fluorescence]]
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Overview
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|-
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* [[Lab Manual:Measuring DNA Melting Curves]]
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|  <font color=#04B45F>4/27/20</font color>
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Code examples and simulations
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| Assignment 8
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* [[DNA Melting: Simulating DNA Melting - Basics]]
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| [[Spring 2020 Assignment 8]]
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* [[DNA Melting: Simulating DNA Melting - Intermediate Topics]]
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*(Previous semester's assignment 8 for reference)
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* [[DNA Melting: Model function and parameter estimation by nonlinear regression]]
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*[[Assignment 8 Overview: flow channel & two-color microscope|Assignment 8 Overview]]
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Reference materials
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* [[Electronics bootcamp II: feedback systems|Part 1: feedback systems]]
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* [[DNA Melting Thermodynamics]]
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* [[Assignment 8, Part 2: fabricate a microfluidic device| Part 2: fabricate a microfluidic device]]
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* [[DNA Melting: DNA Sequences]]
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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://mfold.rna.albany.edu/?q=DINAMelt/Hybrid2 DINAMelt Web Server]
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|[http://science.sciencemag.org/content/319/5862/482 *The* yeast paper: Mettelal ''et al.'', ''Science'' (2008)]
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Background reading
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|-
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* [[Electronics Primer]]
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|  <font color=#04B45F>5/4/20</font color>
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| Assignment 9
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<!-- * [[Real electronics]] -->
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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>5/8/20</font color>
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| Exam 2 (90 min)
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|
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|
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|-
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|  <font color=#04B45F>5/12/20</font color>
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| Assignment 10
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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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|-
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|  cancelled
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| Assignment 11
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| [[Assignment 11: Tell us about your lab visit]]
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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==
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−
 
+
−
* [[20.309:Course Information]]
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* [[20.309:Lab Report Guidelines]]
+
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* [[20.309:Safety]]
+
−
 
+
−
Reserve a lab station here: [http://measurebiology.org/reservations/Web/schedule.php Bioinstrumentation Lab reservation system]
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−
 
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==Optics bootcamp==
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===Lab manual===
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* [[Optics Bootcamp]]
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===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]]
  
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{{:Optical microscopy lab wiki pages}}
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===Code examples and simulations===
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* [[Converting Gaussian fit to Rayleigh resolution]]
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==Electronics bootcamp==
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* [[MATLAB: Estimating resolution from a PSF slide image]]
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===Lab manual===
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* [[Matlab: Scalebars]]
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* [[Electronics Mini-Lab|Electronics bootcamp]]
+
* [[Calculating MSD and Diffusion Coefficients]]
  
 +
==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"]
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* [[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]]
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{{: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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