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

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<ol start="7">
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<ol start="5">
 
   </li>  <li>Viscosity  
 
   </li>  <li>Viscosity  
 
     <ol>
 
     <ol>
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         <ul>
 
         <ul>
 
           <li>Include a snapshot of the 0.84 &mu;m fluorescent beads monitored.</li>
 
           <li>Include a snapshot of the 0.84 &mu;m fluorescent beads monitored.</li>
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           <li>Plot an example bead trajectory in the X-Y plane.</li>
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           <li>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.)</li>
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          <li>Plot the beads' MSD vs time interval (&tau;) data on log-log axes.</li>
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         </ul>
 
         </ul>
 
       <li>Analysis and Results</li>
 
       <li>Analysis and Results</li>
 
         <ul>
 
         <ul>
 +
          <li>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.</li>
 +
          <li>Include a table of the diffusion coefficient, viscosity and glycerin/water ratio for each of the samples (A, B, C, and D).</li>
 
           <li>Provide a bullet point outline of all calculations and data processing steps.</li>
 
           <li>Provide a bullet point outline of all calculations and data processing steps.</li>
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          <li>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 &eta;, the fluid's viscosity?</li>
 
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          <li>Estimate diffusion coefficient and viscosity for each water-glycerin mixture sample (A, B, C and D).</li>
 
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          <li>Comment on results, specifically how they are influenced by microscope stability and resolution.</li>
 
 
         </ul>
 
         </ul>
 
       <li>Discussion</li>
 
       <li>Discussion</li>
 
         <ul>
 
         <ul>
 
           <li>How do your viscosity calculations compare to your expectations? (This [https://dl.dropboxusercontent.com/u/12957607/Viscosity%20of%20Aqueous%20Glycerine%20Solutions.pdf chart] is a useful reference.)</li>
 
           <li>How do your viscosity calculations compare to your expectations? (This [https://dl.dropboxusercontent.com/u/12957607/Viscosity%20of%20Aqueous%20Glycerine%20Solutions.pdf chart] is a useful reference.)</li>
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           <li>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).</li>
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           <li>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.</li>
 
         </ul>
 
         </ul>
 
     </ol>
 
     </ol>
 
   </li>
 
   </li>
 
   </li>   
 
   </li>   
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</ol>
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   <li>Bacteria behavior
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<ol start="6">
 +
   </li>  <li>Particle Tracking in Cells
 
     <ol>
 
     <ol>
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       <li>Protocols
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       <li>Procedure
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         <ul>
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         <ul><li>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)</li></ul>
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        <li>Describe how sample was prepared and epi-fluorescence microscopy and microfluidics apparatus readied for your live bacteria tracking experiments.</li>
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−
        </ul>
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       </li>
 
       </li>
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       <li>Data
+
       <li>Data</li>
 
         <ul>
 
         <ul>
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        <li>Show significant frames of your videos of ''Vibrio alginolyticus'' swimming in the central channel.
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           <li>Include a snapshot of the 0.84 &mu;m fluorescent beads monitored.</li>
−
          <ul>
+
           <li>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.)</li>
−
           <li>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'''.</li>
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−
           <li>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'''.</li>
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−
          <li>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'''.</li>
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−
          </ul>
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−
        </li>
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         </ul>
 
         </ul>
−
       </li>
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       <li>Analysis and Results</li>
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      <li>Model
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         <ul>
 
         <ul>
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        <li>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 &mu;, the diffusivity of the bacteria, ''V<sub>c</sub>'', their drift or convection velocity, and ''x'', the space coordinate across the microchannel width. ([http://pubs.rsc.org/en/content/articlepdf/2012/lc/c2lc21006a This review article] will be both inspiring and helpful.)</li>
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          <li>Combine your data with others from the class to increase your sample size.</li>
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        <li>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?</li>
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          <li>Plot the average MSD for untreated and Cyto D treated cells on a single set of log-log axes.</li>
 
         </ul>
 
         </ul>
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       </li>
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       <li>Discussion</li>
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      <li>Results and Discussion
+
 
         <ul>
 
         <ul>
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        <li>Plot on the same set of axes MSD versus time interval &tau; for ''Vibrio alginolyticus'' pre-, during- and post- aerotactic gradient application (from '''movie_rest_top''', '''movie_transient_top''' and '''movie_gradient_top''').
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          <li>What kind of motion do you see described by your MSD vs τ results?</li>
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           <ul><li>As always, summarize the data analysis steps in your write-up, and provide all Matlab code in appendix.</li></ul>
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           <li>What differences do you see between the untreated and Cyto D treated MSD curves? </li>
−
        </li>
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          <li>Please suggest an interpretation of the behavior of your cells based on your data.</li>
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        <li>What do the MSD plot features teach you regarding the bacteria response to oxygen?</li>
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          <li>Include a discussion of your error sources.</li>
 
         </ul>
 
         </ul>
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      </li>
 
 
     </ol>
 
     </ol>
 +
  </li>
 
   </li>   
 
   </li>   
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</ol>
 
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<ol>Conclusion
 
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  <li>Take a step back to reflect on the Optical Microscopy module of 20.309: what did you accomplish and learn through your work?</li>
 
 
</ol>
 
</ol>

Latest revision as of 19:44, 14 March 2016

  1. 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.
  1. 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 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.
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