Optical Microscopy: Part 4 Report Outline

7. 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 an example bead trajectory in the X-Y plane.
   • Plot the beads' MSD vs time interval (τ) data on log-log axes.
   3. Analysis and Results
   • Provide a bullet point outline of all calculations and data processing steps.
   • Explain how you can use the mean squared displacement data to extract D, the diffusion coefficient of a purely viscous fluid. What equation relates D and η, the fluid's viscosity?
   • Estimate diffusion coefficient and viscosity for each water-glycerin mixture sample (A, B, C and D).
   • Comment on results, specifically how they are influenced by microscope stability and resolution.
   4. Discussion
   • How do your viscosity calculations compare to your expectations? (This chart is a useful reference.)
   • Comment extensively on sources of error and approaches to minimize them, both utilized and proposed. Categorize the sources of error as systematic, random, or just mistakes (so-called "illegitimate" errors).
8. Bacteria behavior
   1. Data Analysis
      • Analyze the centroid data provided by Kwangmin Son (posted as ParticleCentroid.mat in the Optical Microscopy section of the 20.309 Spring 2014 Stellar website), whose format is:
        • MSD(ii,1).TimeLoc(:,1); % time in seconds
        • MSD(ii,1).TimeLoc(:,2); % x location in microns
        • MSD(ii,1).TimeLoc(:,3); % y location in microns
      • Plot the mean squared displacement MSD of the bacteria as a function of lag time τ.
      • Specify the transition between diffusive and ballistic behavior on the horizontal τ axis.
9. Conclusion
   • Take a step back to reflect on the Optical Microscopy module of 20.309: what did you accomplish and learn through your work?