Microscopy report outline

General guidelines

• This is a group report — one paper per group.
• Use of bulleted lists and tables is highly encouraged; long paragraphs are not necessary.
• Include a summary of the algorithm used for all calculations and analyses performed, including MATLAB (or other language) code. Put the code in an appendix.
• Don’t forget scale bars on images, titles, units, nd labels on plots.
• The report should be in PDF format, submitted electronically in advance of the deadline to Stellar

Section 1: Microscope Documentation and Design

• Block diagram of the microscope, including all optical elements and relevant distances. It is unnecessary to document the details of the mechanical construction.
• Design calculations and considerations
• Photograph of your setup (optional, but nice)

Section 2: Microscope Characterization

• Basic optics: include a table with the following values for the 10X, 40X, and 100X objectives:
  • Theoretical resolution
  • Actual magnification by multiple measures (Air Force Target, Ronchi Ruling, microspheres)1
  • Actual field of view (FOV)1
  • Example pictures from each objective (fluorescence mode)
• Estimate of actual resolution of the 40X Objective
  • Images used for computation (with fit, if you like – see plotgaussfit command)
  • Estimate of FWHM by Gaussian fitting
  • Bullet point outline of data analysis methodology
  • Comments on estimated versus theoretical value
• Stability
  • X-Y plots of sum and difference tracks for “stationary” particles.
  • MSD versus time interval for sum and difference tracks
  • Bullet point outline of data analysis methodology
  • Comments on observed vs. expected data trend

Section 3: Fluorescence Microscopy

• Unprocessed Images of fluorescent bead and onion samples and associated reference images
• Corrected images
• Image or surface plot (see surf command in Matlab) of correction applied
• Histograms of original and corrected images
• Segmented onion image
• Corrected, fluorescent image overlayed on bright field onion image
• Bullet point outline of image processing methodology

Section 4: Particle Tracking

• X-Y plots of tracks for all 5 samples
• MSD versus time interval plots for 5 samples
• Estimate of diffusion coefficient and solvent viscosity for each sample
• Comments on results
• Bullet point outline of all calculation and data processing steps

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