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

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<ol start="8">
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<ol start="5">
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   </li>  <li>Viscosity and viscoelasticity
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   </li>  <li>Viscosity  
 
     <ol>
 
     <ol>
 
       <li>Procedure
 
       <li>Procedure
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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 and an example differential 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 ''differential'' MSD vs time interval (&tau;) data on log-log axes, for beads tracked in glycerol:water mixtures and on a separate figure for beads tracked in polyacrylamide gels.</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>
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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>
 
 
         </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 on viscoelasticity results, specifically on the divergence in viscoelastic behavior of the PAGs at various total acrylamide concentrations, and the existence of an elastic plateau characteristic of solid-like material for some cross-linking percentages but not others.</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>
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          <li>Could this passive microrheology approach be used to study cellular biomechanics?  Under what assumptions could the intracellular viscoelasticity be quantified by monitoring beads embedded in the cytoskeleton?</li>
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−
          <li>How are your results affected by microscope stability and resolution?</li>
+
−
          <li>Comment extensively on significant 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). 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 the combine, total uncertainty.</li>
+
 
         </ul>
 
         </ul>
 
     </ol>
 
     </ol>
 
   </li>
 
   </li>
 
   </li>   
 
   </li>   
−
 
+
</ol>
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   <li>Conclusion
+
<ol start="6">
−
  <ul>
+
   </li> <li>Particle Tracking in Cells
−
    <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>
−
  </ul>
+
      <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>
 +
          <li>Include a snapshot of the 0.84 &mu;m fluorescent beads monitored.</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>
 +
    </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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