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

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   </li>   
 
   </li>   
  
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[[Image: 20.309 140314 BacteriaTracksAerotaxis.png|right|thumb|200px|Bacteria trajectories showing aerotaxis in microchannel where oxygen gradient was established (O<sub>2</sub> source at left)]]
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</li> <li>Viscoelasticity
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  <li>Bacteria behavior
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     <ol>
 
     <ol>
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       <li>Data Analysis
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      <li>Procedure
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        <ul><li>Document the samples you 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>
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       <li>Data</li>
 
         <ul>
 
         <ul>
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        <li>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:
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          <li>Include a snapshot of the 0.84 &mu;m fluorescent beads monitored.</li>
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           <ul>
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           <li>Plot an example bead trajectory in the X-Y plane.</li>
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          <li>MSD(ii,1).TimeLoc(:,1); % time in seconds</li>
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          <li>Plot the beads' MSD vs time interval (&tau;) data on log-log axes.</li>
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          <li>MSD(ii,1).TimeLoc(:,2); % x location in microns</li>
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          <li>Plot the PAG storage moduli G'(&omega;) vs. frequency &omega; on log-log axes for all three samples E, F, and G.</li>
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          <li>MSD(ii,1).TimeLoc(:,3); % y location in microns</li>
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        </ul>
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          <li>with the 'ii' index indicating an individual bacterium's track number (there were 1507 bacteria traces monitored in total).</li>
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      <li>Analysis and Results</li>
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           </ul>
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        <ul>
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        </li>
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          <li>Provide a bullet point outline of all calculations and data processing steps.</li>
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        <li>Plot the mean squared displacement MSD of the bacteria as a function of lag time &tau;.</li>
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          <li>Explain how you can use the mean squared displacement data to extract G'(&omega;).</li>
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        <li>Specify the transition between diffusive and ballistic behavior on the horizontal &tau; axis.</li>
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           <li>Comment on 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>
 +
        </ul>
 +
      <li>Discussion</li>
 +
        <ul>
 +
          <li>Do you observe long-range diffusion for the beads in any of the three PAG networks?  If not, what can you deduce from this absence?</li>
 +
          <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>
 
         </ul>
 
         </ul>
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      </li>
 
 
     </ol>
 
     </ol>
 +
  </li>
 
   </li>   
 
   </li>   
 +
 
   <li>Conclusion
 
   <li>Conclusion
 
   <ul>
 
   <ul>

Revision as of 19:12, 17 September 2014

  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 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).
  2. Viscoelasticity
    1. Procedure
      • Document the samples you 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.
      • Plot the PAG storage moduli G'(ω) vs. frequency ω on log-log axes for all three samples E, F, and G.
    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 G'(ω).
      • Comment on 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.
    4. Discussion
      • Do you observe long-range diffusion for the beads in any of the three PAG networks? If not, what can you deduce from this absence?
      • 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?
  3. Conclusion
    • Take a step back to reflect on the Optical Microscopy module of 20.309: what did you accomplish and learn through your work?
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