Part 3 Combined Report Outline

1. Resolution
   1. Procedure
      • Document the samples you used and how you captured images (camera settings, software used, etc…)
   2. Data
   • Include an image of the PSF sample indicating which beads were used for resolution measurement..
   • Include the intensity histogram of your image (created by imhist)
   3. Analysis and Results
   • Report the resolution you measured. Make sure to include N and a measure of uncertainty.
   • Show sample Gaussian fits.
   • Explain the Matlab algorithm used for data analysis.
   4. Discussion
   • Compare the measured value to the theoretical value.
   • Include a thorough discussion of error sources. Do not comment on insignificant sources of error. To determine which error sources are significant, and which are not, you must think carefully about the uncertainty related to each error source and estimate its magnitude and sign. Include these estimates in your report along with your estimate of the combined, total uncertainty. It may be helpful to list out the error sources in a table, including a category for the error source, type of error (random, systematic, fundamental, technical, etc.), the magnitude of the error, and a description and way to minimize each one.
2. Stability
   1. Procedure
      • Document the samples you used and how you captured images (camera settings, frame rate, total number of frames, exposure, software used, etc…)
   2. Data
   • Show an example frame from the stability movie.
   • Include the MSD vs. tau plot from your stability video, containing at least 2 sum trajectories and 2 difference trajectories on a log-log scale
   3. Discussion
   • What are the benefits and drawbacks of differential tracking?
   • Include a thorough discussion of error sources.

3. Viscosity
   1. Procedure
      • Document the samples you prepared and used and how you captured images (camera settings including frame acquisition rate, number of frames, number of particles in the region of interest, choice of sample plane, etc)
   2. Data
   • Include a snapshot of the 0.84 μm fluorescent beads monitored.
   • Plot two or more example bead trajectories for each of the glycerin samples. (Hint: If you subtract the initial position from each trajectory, then you can plot multiple trajectories on a single set of axes.)
   3. Analysis and Results
   • Plot the average MSD vs τ results for all glycerin samples (A, B, C, and D); use log-log axes. Use the minimum number of axes that can convey your results clearly.
   • Include a table of the diffusion coefficient, viscosity and glycerin/water ratio for each of the samples (A, B, C, and D).
   • Provide a bullet point outline of all calculations and data processing steps.
   4. Discussion
   • How do your viscosity calculations compare to your expectations? (This chart is a useful reference.)
   • Include a thorough discussion of error sources and the approaches to minimize them. It may be helpful to list out the error sources in a table, including a category for the error source, type of error (random, systematic, fundamental, technical, etc.), the magnitude of the error, and a description and way to minimize each one.

4. Particle Tracking in Cells
   1. Procedure
      • Document the samples you prepared and used and how you captured images (camera settings including frame acquisition rate, number of frames, number of particles in the region of interest, choice of sample plane, etc)
   2. Data
   • Include a snapshot of the 0.84 μm fluorescent beads monitored.
   • Plot two or more example bead trajectories for each of the samples. (Hint: If you subtract the initial position from each trajectory, then you can plot multiple trajectories on a single set of axes.)
   3. Analysis and Results
   • Combine your data with others from the class to increase your sample size.
   • Plot the average MSD (from the difference trajectories) for untreated and Cyto D treated cells on a single set of log-log axes.
   4. Discussion
   • What kind of motion do you see described by your MSD vs τ results?
   • What differences do you see between the untreated and Cyto D treated MSD curves?
   • Please suggest an interpretation of the behavior of your cells based on your data.
   • Include a discussion of your error sources.