Difference between revisions of "20.309 Main Page"

From Course Wiki
Jump to: navigation, search
(→‎20.309 This week and next)
 
(132 intermediate revisions by 4 users not shown)
Line 1: Line 1:
 
{{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]]. ()
−
 
+
−
 
+
−
 
+
−
<div style="padding: 10px; width: 740px; border: 5px solid #000FFF;">
+
  
 +
== 20.309 course information==
  
 +
* [https://accessibility.mit.edu/ Accessibility]
 +
* [[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 This week and next ==
+
== 20.309 master schedule==
−
 
+
−
 
+
−
== 20.309 This week and next in the 20.309 lab ==
+
−
 
+
−
 
+
  
 +
<div style="padding: 10px; width: 740px; border: 5px solid #000FFF;">
 +
===Module 1: Optics & Microscopy===
 
{| border=1px
 
{| border=1px
−
|style="width: 15%;"|'''Week'''
+
|style="width: 10%;"|'''Important dates'''  
−
|style="width: 15%;"|'''Summary'''
+
|style="width: 15%;"|'''Assignment due'''
−
|style="width: 18%;"|'''Assignments due'''
+
|style="width: 30%;"|'''Assignment page links'''
−
|style="width: 17%;"|'''Lab Manual'''
+
|style="width: 45%;"|'''Useful resources'''
−
|style="width: 35%;"|'''Resources'''
+
|--  
−
|--
+
| <font color=#04B45F>2/16/20</font color>
−
| rowspan="2"| Week 3: Feb. 19 - 25
+
| Assignment 1
−
| rowspan="2"|Finish Microscopy 1, start PSet1 and Microscopy 2
+
|
−
| rowspan="2"|<font color=#04B45F>Monday Feb. 20: Microscopy 1 </font color>
+
[[Assignment 1 Overview: Transillumination microscopy| Assignment 1 Overview]]
−
| [[Optical Microscopy Part 1: Brightfield Microscopy|Microscopy 1]] continued (Sun-Mon)
+
* [[Assignment 1, Part 1: Pre-lab questions|Part 1: Pre-lab questions]]
−
| Overview
+
* [[Assignment 1, Part 2: Optics bootcamp|Part 2: Optics bootcamp]]
−
* [[Lab Manual: Optical Microscopy]]
+
* [[Assignment 1, Part 3: Building your transillumination microscope|Part 3: Build a microscope]]
−
Code examples and simulations
+
* [[Assignment 1, Part 4: Building your transilluminated microscope|Part 4: Measure stuff]]
−
* [[Converting Gaussian fit to Rayleigh resolution]]
+
|  
−
* [[MATLAB: Estimating resolution from a PSF slide image]]
+
* [https://stellar.mit.edu/S/course/20/sp20/20.309/materials.html Lectures 1 through 9 of the 20.309 class]
−
* [[Matlab: Scalebars]]
+
* [http://www.microscopyu.com/articles/formulas/formulasri.html Snell's law]
−
Background reading
+
*  [[Understanding log plots]]
 +
|-
 +
| <font color=#04B45F>2/23/20</font color>
 +
| Assignment 2
 +
| [[Assignment 2: fluorescence microscopy| Assignment 2 Overview]]
 +
* [[Assignment 2 Part 1: Noise in images|Part 1: Noise in images]]
 +
* [[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]]
 
* [[Geometrical optics and ray tracing]]
 
* [[Physical optics and resolution]]
 
* [[Physical optics and resolution]]
Line 42: Line 49:
 
* [[Manta G032 camera measurements]]
 
* [[Manta G032 camera measurements]]
 
|-
 
|-
−
| [[Optical Microscopy Part 2: Fluorescence Microscopy|Microscopy 2]] (Tues-Sat)
+
| <font color=#04B45F>2/25/20</font color>
 +
| Quiz 1 (in lecture)
 +
| ||
 +
|-
 +
|  <font color=#04B45F>3/1/20</font color>
 +
| Assignment 3
 +
| [[Assignment 3 Overview|Assignment 3 Overview]]
 +
* [[Assignment 3, Part 1: visualizing actin with fluorescence contrast|Part 1: fluorescence imaging]]
 +
* [[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>3/8/20</font color>
 +
| Assignment 4
 +
|{{Template:Assignment 4 navigation}}
 +
|
 +
* [http://www.microscopyu.com/articles/formulas/formulasresolution.html Resolution]
 +
* [[Physical optics and resolution]]
 +
* [[Converting Gaussian fit to Rayleigh resolution]]
 +
* [[MATLAB: Estimating resolution from a PSF slide image]]
 +
* [[Matlab: Scalebars]]
 +
* [[Calculating MSD and Diffusion Coefficients]]
 +
|-
 +
|  <font color=#04B45F>4/3/20</font color>
 +
| Assignment 5
 +
| [[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 2: live cell particle tracking of endocytosed beads| Part 2: Live cell particle tracking of endocytosed beads]]
 +
|
 +
* [[Matlab: Scalebars]]
 +
* [[Calculating MSD and Diffusion Coefficients]]
 +
|-
 +
|  <font color=#04B45F>4/7/20</font color>
 +
| Exam 1
 
|  
 
|  
−
|--
 
−
| Week 4: Feb. 26 - Mar. 4
 
−
| Work on PSet 1 and continue Microscopy 2
 
−
| <font color=#04B45F>
 
−
*Sunday Feb. 26: PSet 1
 
−
*Friday Mar. 3: Microscopy 2 due</font color>
 
−
| [[Optical Microscopy Part 2: Fluorescence Microscopy|Microscopy 2]]
 
 
|
 
|
 +
|-
 
|}
 
|}
−
</div>
+
<br />
  
 +
===Module 2: electronics, 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>4/13/20</font color>
 +
| Assignment 6
 +
| [[Spring 2020 Assignment 6]]
 +
* (Previous semesters' assignment 6 for reference)
 +
* [[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]]
 +
* [https://www.khanacademy.org/science/electrical-engineering/ee-circuit-analysis-topic Khan Academy Material, esp. "Ideal Circuit Elements" and "Voltage Divider"]
 +
* [[Impedance Analysis|Impedance analysis]]
 +
* [[Input and output impedance]]
 +
|-
 +
|  <font color=#04B45F>4/20/20</font color>
 +
| Assignment 7
 +
| [[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]]
  
 +
|
 +
* [[Impedance Analysis|Impedance analysis]]
 +
* [[Bode plots|Transfer functions and Bode plots]]
 +
* [[Complex Number Review|Complex number review]]
 +
* [[Input and output impedance]]
 +
|-
 +
|  <font color=#04B45F>4/21/20</font color>
 +
| Quiz 2 (60 min)
 +
|
 +
|
 +
|-
 +
|  <font color=#04B45F>4/27/20</font color>
 +
| Assignment 8
 +
| [[Spring 2020 Assignment 8]]
 +
*(Previous semester's assignment 8 for reference)
 +
*[[Assignment 8 Overview: flow channel & two-color microscope|Assignment 8 Overview]]
 +
* [[Electronics bootcamp II: feedback systems|Part 1: feedback systems]]
 +
* [[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)]
 +
|-
 +
|  <font color=#04B45F>5/4/20</font color>
 +
| Assignment 9
 +
| [[Spring 2020 Assignment 9]]
 +
*(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>5/8/20</font color>
 +
| Exam 2 (90 min)
 +
|
 +
|
 +
|-
 +
|  <font color=#04B45F>5/12/20</font color>
 +
| 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]]
 +
|
 +
|-
 +
|}
 +
</div>
  
−
 
+
==Optics and microscopy resources==
−
 
+
−
 
+
−
__TOC__
+
−
 
+
−
== 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===
+
−
* [[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]]
  
−
{{:Optical microscopy lab wiki pages}}
+
===Code examples and simulations===
−
 
+
* [[Converting Gaussian fit to Rayleigh resolution]]
−
==Electronics bootcamp==
+
* [[MATLAB: Estimating resolution from a PSF slide image]]
−
===Lab manual===
+
* [[Matlab: Scalebars]]
−
* [[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"]
−
* [[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.)
Retrieved from "http://measurebiology.org/w/index.php?title=20.309_Main_Page&oldid=45842"