Difference between revisions of "Assignment 2: fluorescence microscopy"
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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: | ||
Part 1 | Part 1 | ||
− | # | + | # Turn in your plot of simulation results |
− | # 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 | + | #* Find the interval [ <math>\mu - s</math>, <math>\mu + s</math> ] that contains about 68% of the simulation results. |
− | #* Use a nested loop. | + | #* Turn in the code you used to find the interval. |
− | + | # On the same plot, plot the PDF of a normal distribution with the same mean and standard deviation as the simulation results. Multiply the PDF by a constant so that it has the same vertical scale as the histogram. | |
− | # What is the relationship between the number of photons detected and the noise (standard deviation)? | + | # Is the Poisson distribution a good approximation of shot noise? |
− | # | + | #* 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. | |
− | # On one set of axes, plot the | + | #* 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)? | |
+ | #* 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, 100 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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## Determine the read noise standard deviation. | ## Determine the read noise standard deviation. | ||
## Under what circumstances is each of the three noise terms is dominant? | ## Under what circumstances is each of the three noise terms is dominant? | ||
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Parts 2 & 3 | Parts 2 & 3 |
Revision as of 21:47, 25 September 2018
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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