Difference between revisions of "Optical Microscopy: Part 4 Report Outline"

Revision as of 13:40, 6 March 2014

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. Protocols
      • Describe how sample was prepared and epi-fluorescence microscopy and microfluidics apparatus readied for your live bacteria tracking experiments.
   2. Data
      • Show significant frames of your videos of Vibrio alginolyticus swimming in the central channel.
        • Before the introduction of gas through the outer channels, compare bacteria population in representative frames of movie_rest_bottom vs. movie_rest_middle vs. movie_rest_top.
        • As the gas supply was turned on, how did the bacteria population evolve in the vicinity of the "top" (red flag, air or 20% oxygen) channel? Compare early vs. middle vs. late frames of movie_gradient_top.
        • Did the presence of an oxygen gradient across the central channel alter the bacteria population in the vicinity of the "top" channel? Compare frames of movie_rest_top vs movie_gradient_top.
   3. Model
      • Based on the simple classic model of the diffusion-convection equation and presuming oxygen is an attractant to Vibrio alginolyticus, what distribution B(x) do you expect at steady state for the bacteria in suspension in a microchannel with boundary conditions "air = 20% oxygen" on one side and "nitrogen = 0% oxygen" on the other side? Express your result B(x)as a function of μ, the diffusivity of the bacteria, V_c, their drift or convection velocity, and x, the space coordinate across the microchannel width. (This review article will be both inspiring and helpful.)
      • Count the bacteria present in representative frames of movie_gradient_top, movie_gradient_middle and movie_gradient_bottom. Does the actual bacteria population corroborate your theoretical model?
   4. Results and Discussion
      • Plot on the same set of axes MSD versus time interval τ for Vibrio alginolyticus pre-, during- and post- aerotactic gradient application (from movie_rest_top, movie_transient_top and movie_gradient_top).
      • What do the MSD plot features teach you regarding the bacteria response to oxygen?