Difference between revisions of "Assignment 3 Overview"
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{{Template:Assignment Turn In|message= Here is a comprehensive list of what you need to turn in: | {{Template:Assignment Turn In|message= Here is a comprehensive list of what you need to turn in: | ||
− | + | # A figure with images of the stained cell samples with and without Cyto-D. ('''as a team''') | |
− | # A figure with images of the stained cell samples with and without Cyto-D. | + | |
#* For each sample, create 1 figure with 5 panels. | #* 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. | #* 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. | #* 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 <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. | #* 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. | ||
− | # Image profile | + | # Image profile ('''as a team''') |
#* 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.) | #* 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.) | ||
#Discussion ('''individually''') | #Discussion ('''individually''') | ||
#* How did your beam expander design affect your images? | #* How did your beam expander design affect your images? | ||
#* What differences did you observe between the cells with and without CytoD? | #* What differences did you observe between the cells with and without CytoD? | ||
− | # Answers to all questions in [[Assignment 3, Part 2: experimental design with fluorescence|Assignment 3, Part 2]]. | + | # Answers to all questions in [[Assignment 3, Part 2: experimental design with fluorescence|Assignment 3, Part 2]]. ('''individually''') |
− | + | }} | |
{{Template:Assignment 3 navigation}} | {{Template:Assignment 3 navigation}} |
Revision as of 00:11, 25 January 2018
Assignment details
This assignment has 2 parts:
- 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;
- Part 2: Explore interesting calculations and considerations to guide your experimental design with fluorescence.
Submit your work on Stellar in a single PDF file with the naming convention <Lastname><Firstname>Assignment3.pdf. Here is a checklist of all things you have to turn in:
Here is a comprehensive list of what you need to turn in:
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