Difference between revisions of "Optical Microscopy: Part 2 Report Outline"

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* Update the apparatus section of your report to reflect the changes you made in part 2.
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# Microscope documentation
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<br />
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## Include an updated block diagram of your microscope.
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# Images
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<ol start="4">
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## Include a figure with an images of the 3.26 &mu;m fluorescent microsphere samples, and the stained cell samples with and without Cyto-D.
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  <li>Fluorescence imaging and flat-field correction
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##* For each sample, create 1 figure with 5 panels.
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    <ol>
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##* The panels of the figure should be: A) unprocessed image; B) reference image; C) dark image; D) flat-field corrected image; and E) histogram.  
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      <li>Procedure
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##* In the caption, specify the exposure and gain settings. Each image should have a scale bar. State the dimension of the scale bar in the caption.
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        <ul><li>Document the samples you used and how you captured images (camera settings, software used, etc…)</li></ul>
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##* For panel E, plot histograms of the unprocessed, dark, reference, and corrected image on the same set of axes. Plot <tt>log10( count )</tt> on the vertical axis and intensity on the horizontal axis. Use a line plot instead of a bar chart for the histogram.
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      </li>
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## Image profile
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      <li>Data</li>
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##* For one reference, dark and cell image set, plot an intensity profile across the same diagonal. You may also use a bead image, along with it's unique reference and dark images. The intensity of your three images should be on the same scale, i.e., 0 to 65,535 or 0 to 1. Place all three profiles on a single set of axes for comparison. (Use the <tt>improfile</tt> command in MATLAB.)
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        <ul>
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# Discussion
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          <li>Include raw images of 0.84 um and 3.2 um fluorescent bead samples, the stained cell samples (with and without Cyto-D), the reference image captured before each bead or cell sample images, as well as the dark image (if available) captured before each bead or sample image.</li>
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## How did your beam expander design affect your images?
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        </ul>
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## What differences did you observe between the cells with and without CytoD?
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      <li>Analysis and Results</li>
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        <ul>
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          <li>For one reference, dark and bead or cell sample image set, plot an intensity profile across the diagonals. Place all three profiles on a single set of axes. (Use the <tt>improfile</tt> command in MATLAB.)</li>
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          <li>Use the reference and dark images to correct the raw bead and cell sample images for nonuniform illumination and include the corrected image.</li>
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          <li>For the bead samples on the one hand, and for the cell samples on the other hand, include histograms of the sample, reference, dark, and corrected images on a single plot of '''log10'''(count) vs intensity. (You may plot the mere envelop of the histogram, for clarity purposes.)  </li>
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          <li>Document the steps you used to process the image.</li>
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        </ul>
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      <li>Discussion</li>
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        <ul><li>How did your beam expander design affect your images?</li></ul>
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    </ol>
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  </li>
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</li>  <li>Disrupting and imaging the actin network
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    <ol>
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      <li>Procedure
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        <ul><li>Document sample preparation, including difficulties, and recording conditions (particularly exposure time and gain selected in the camera settings)</li></ul>
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      </li>
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      <li>Data</li>
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        <ul>
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          <li>Include images of mouse embryonic fibroblasts + and - CytoD.</li>
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        </ul>
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      <li>Analysis and Results</li>
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        <ul>
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          <li>What contrast do you unveil between the + and - CytoD conditions?</li>
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        </ul>
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      <li>Discussion</li>
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        <ul>
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          <li>Can you quantify the morphological and physiological effect of CytoD treatment?  What parameters would you choose to measure and report?</li>
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        </ul>
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    </ol>
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  </li>
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  </li>
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</ol>
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Latest revision as of 18:29, 30 September 2015

  1. Microscope documentation
    1. Include an updated block diagram of your microscope.
  2. Images
    1. Include a figure with an images of the 3.26 μm fluorescent microsphere samples, and the stained cell samples with and without Cyto-D.
      • For each sample, create 1 figure with 5 panels.
      • The panels of the figure should be: A) unprocessed image; B) reference image; C) dark image; D) flat-field corrected image; and E) histogram.
      • In the caption, specify the exposure and gain settings. Each image should have a scale bar. State the dimension of the scale bar in the caption.
      • For panel E, plot histograms of the unprocessed, dark, reference, and corrected image on the same set of axes. Plot log10( count ) on the vertical axis and intensity on the horizontal axis. Use a line plot instead of a bar chart for the histogram.
    2. Image profile
      • For one reference, dark and cell image set, plot an intensity profile across the same diagonal. You may also use a bead image, along with it's unique reference and dark images. The intensity of your three images should be on the same scale, i.e., 0 to 65,535 or 0 to 1. Place all three profiles on a single set of axes for comparison. (Use the improfile command in MATLAB.)
  3. Discussion
    1. How did your beam expander design affect your images?
    2. What differences did you observe between the cells with and without CytoD?
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