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>
−
           <li>Plot an example bead trajectory in the X-Y plane.</li>
+
           <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>
−
          <li>Plot the beads' MSD vs time interval (&tau;) data on log-log axes.</li>
+
 
         </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>
−
          <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>
 
−
          <li>Estimate diffusion coefficient and viscosity for each water-glycerin mixture sample (A, B, C and D).</li>
 
−
          <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>
−
           <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>
+
           <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>   
−
 
+
</ol>
−
   </li>  <li>Bacteria behavior
+
<ol start="6">
 +
   </li>  <li>Particle Tracking in Cells
 
     <ol>
 
     <ol>
−
       <li>Model
+
       <li>Procedure
 +
        <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>
 +
      </li>
 +
      <li>Data</li>
 
         <ul>
 
         <ul>
−
        <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.</li>
+
          <li>Include a snapshot of the 0.84 &mu;m fluorescent beads monitored.</li>
−
        <li>Count the bacteria present in a few example pictures taken at various ''x''-locations in the microchannel (from small ''x'' values near the air-PDMS wall to large ''x'' values closer to the nitrogen-PDMS wall). Does the actual bacteria population agree with your theoretical model?</li>
+
          <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>
 +
        </ul>
 +
      <li>Analysis and Results</li>
 +
        <ul>
 +
          <li>Combine your data with others from the class to increase your sample size.</li>
 +
          <li>Plot the average MSD for untreated and Cyto D treated cells on a single set of log-log axes.</li>
 +
        </ul>
 +
      <li>Discussion</li>
 +
        <ul>
 +
          <li>What kind of motion do you see described by your MSD vs τ results?</li>
 +
          <li>What differences do you see between the untreated and Cyto D treated MSD curves? </li>
 +
          <li>Please suggest an interpretation of the behavior of your cells based on your data.</li>
 +
          <li>Include a discussion of your error sources.</li>
 
         </ul>
 
         </ul>
−
      </li>
 
 
     </ol>
 
     </ol>
 +
  </li>
 
   </li>   
 
   </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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