Difference between revisions of "Assignment 2: fluorescence microscopy"
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# Is the Poisson distribution a good approximation of shot noise? | # Is the Poisson distribution a good approximation of shot noise? | ||
#* What percentage of the results fall with one, two, and three standard deviations? | #* What percentage of the results fall with one, two, and three standard deviations? | ||
− | #* Produce a log-log plot of standard deviation of the number of photons emitted as a function of the average number of photons emitted for probability of photon emission equal to the values: 10-6, 10-5, 10-4, 10-3, and 10-2. | + | #* Produce a log-log plot of standard deviation of the number of photons emitted as a function of the average number of photons emitted for probability of photon emission equal to the values: 10<sup>-6</sup>, 10<sup>-5</sup>, 10<sup>-4</sup>, 10<sup>-3</sup>, and 10<sup>-2</sup>. |
#* Hints: Use a nested loop. Use the poissrnd function instead of the line containing rand. Speed things up by getting rid of the plotting inside the loop and only run 100 simulations for each probability. | #* Hints: Use a nested loop. Use the poissrnd function instead of the line containing rand. Speed things up by getting rid of the plotting inside the loop and only run 100 simulations for each probability. | ||
#* What is the relationship between the number of photons detected and the noise (standard deviation)? | #* What is the relationship between the number of photons detected and the noise (standard deviation)? | ||
#* Turn in the code you used to generate the plots | #* Turn in the code you used to generate the plots | ||
− | # On one set of axes, plot the variance vs. mean for exposure times of 10-4, 10-3, 10-2, 10-1, | + | # On one set of axes, plot the variance vs. mean for exposure times of 10<sup>-4</sup>, 10<sup>-3</sup>, 10<sup>-2</sup>, 10<sup>-1</sup>, and 10<sup>0</sup> seconds. |
# Using the camera measurements provided: | # Using the camera measurements provided: | ||
## Plot the raw data from the static scene measurements and the model best fit on one set of axes. | ## Plot the raw data from the static scene measurements and the model best fit on one set of axes. | ||
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Parts 2 & 3 | Parts 2 & 3 | ||
− | # Draw a block diagram of the LED epi- | + | # Draw a block diagram of the LED epi-illumination path. Indicate the focal lengths of all lenses, the correct lens orientation, and all important distances between components. |
# Lenses L3 and L4 make an image of the LED. Assuming the initial size of the LED is 1.3 mm, what is the size of the LED image made by lens L3? | # Lenses L3 and L4 make an image of the LED. Assuming the initial size of the LED is 1.3 mm, what is the size of the LED image made by lens L3? | ||
# For each bead sample, include the original, reference, and flat-field corrected images in your lab report. In the caption note the exposure and gain settings used for each image. | # For each bead sample, include the original, reference, and flat-field corrected images in your lab report. In the caption note the exposure and gain settings used for each image. |
Latest revision as of 18:23, 14 February 2020
This assignment has 3 parts.
- Part 1: Noise in images
- Part 2: Fluorescence microscopy
- Part 3: Build an epi-illuminator for your microscope
Submit your work on Stellar in a single PDF file with the naming convention <Lastname><Firstname>Assignment2.pdf.
- Overview
- Part 1: Noise in images
- Part 2: Fluorescence microscopy
- Part 3: Build an epi-illuminator for your microscope
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