Difference between revisions of "Assignment 3 Overview"

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(Assignment details)
(Assignment details)
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# [[Assignment 3, Part 2: experimental design with fluorescence| Part 2:]] Explore interesting calculations and considerations to guide your experimental design with fluorescence.
 
# [[Assignment 3, Part 2: experimental design with fluorescence| Part 2:]] Explore interesting calculations and considerations to guide your experimental design with fluorescence.
  
Turn in all of your work on Stellar in a single PDF file named <lastname><firstname>Assignment3.pdf.
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{{Template:Assignment Turn In|message= all of your work (comprehensive list below) on Stellar in a single PDF file named <lastname><firstname>Assignment3.pdf.}}
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Turn in:
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# A figure with images of the 3.26 &mu;m fluorescent microsphere samples, and the stained cell samples with and without Cyto-D.
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#* For each sample, create 1 figure with 5 panels.
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#* The panels of the figure should be: A) unprocessed image; B) reference image; C) dark image; D) flat-field corrected image; and E) histogram.
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#* In the caption, specify the exposure and gain settings. Each image should have a scale bar. State the dimension of the scale bar in the caption.
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#* For panel E, plot histograms of the unprocessed, dark, reference, and corrected image on the same set of axes. Plot <tt>log10( count )</tt> on the vertical axis and intensity on the horizontal axis. Use a line plot instead of a bar chart for the histogram.
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# Image profile
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#* For one reference, dark and cell image set, plot an intensity profile across the same diagonal. You may also use a bead image, along with it's unique reference and dark images. The intensity of your three images should be on the same scale, i.e., 0 to 65,535 or 0 to 1. Place all three profiles on a single set of axes for comparison. (Use the <tt>improfile</tt> command in MATLAB.)
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#Discussion
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#* How did your beam expander design affect your images?
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#* What differences did you observe between the cells with and without CytoD?
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# Answers to all questions in [[Assignment 3, Part 2: experimental design with fluorescence|Assignment 3, Part 2]].
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On to [[Assignment 4 Overview| Assignment 4]]<br>
 
On to [[Assignment 4 Overview| Assignment 4]]<br>

Revision as of 13:03, 24 August 2017

20.309: Biological Instrumentation and Measurement

ImageBar 774.jpg


Assignment details

This assignment has 2 parts:

  1. Part 1: Use the epifluorescence microscope you built to image fixed biological samples, and use the flat-field correction code you wrote for Assignment 2 to address non-uniform illumination;
  2. Part 2: Explore interesting calculations and considerations to guide your experimental design with fluorescence.


Pencil.png

all of your work (comprehensive list below) on Stellar in a single PDF file named <lastname><firstname>Assignment3.pdf.


Turn in:

  1. A figure with images of the 3.26 μm fluorescent microsphere samples, and the stained cell samples with and without Cyto-D.
    • For each sample, create 1 figure with 5 panels.
    • The panels of the figure should be: A) unprocessed image; B) reference image; C) dark image; D) flat-field corrected image; and E) histogram.
    • In the caption, specify the exposure and gain settings. Each image should have a scale bar. State the dimension of the scale bar in the caption.
    • For panel E, plot histograms of the unprocessed, dark, reference, and corrected image on the same set of axes. Plot log10( count ) on the vertical axis and intensity on the horizontal axis. Use a line plot instead of a bar chart for the histogram.
  2. Image profile
    • For one reference, dark and cell image set, plot an intensity profile across the same diagonal. You may also use a bead image, along with it's unique reference and dark images. The intensity of your three images should be on the same scale, i.e., 0 to 65,535 or 0 to 1. Place all three profiles on a single set of axes for comparison. (Use the improfile command in MATLAB.)
  3. Discussion
    • How did your beam expander design affect your images?
    • What differences did you observe between the cells with and without CytoD?
  4. Answers to all questions in Assignment 3, Part 2.


On to Assignment 4
Back to Assignment 2

Background reading