Microscopy report outline

General guidelines

• Submit one paper per group.
• Bulleted list or outline format is encouraged
• Report numerical results properly
  • Indicate the units of measurement
  • Include the sample size and an appropriate measure of variability, such as a range, standard deviation, or standard error
  • Use the abbreviation "s.d." for standard deviation and "s.e.m." for standard error after the "±"
  • For example: 1.21 ± 0.03 GW (±s.d., n=42)
• Explain how you analyzed the data
  • Summarize the algorithm used for all calculations and analyses
  • Provide an outline of each MATLAB (or other language) function or script you used
  • Put the complete code in an appendix
  • Indicate the source of any code you did not write yourself
• Discuss your results
  • Compare your results to theoretical predictions, reported values from literature, or other students' results
  • Explain any factors that may have affected your results
  • Describe what you would do differently if you had the opportunity to do the experiment again.
• Provide a detailed, correct, and comprehensive discussion of error sources for each measurement
  • Is the resulting error random or systematic?
  • If the error is systematic, can you determine the sign of the effect and its approximate magnitude?
  • How could the error be reduced?
• Present data properly
  • Images should include a scale bar
  • Plots should have a clear title; axes should be labeled with units; use a plot legend when appropriate

• See the Lab report general guidelines.
• The report should be in PDF format, submitted electronically to Stellar in advance of the deadline

Section 1: Microscope Documentation and Design

• Microscope block diagram, 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)
• Measured resolution of 40X (or 100X) objective¹
  • Images used for resolution estimation (preferably with fit – see plotgaussfit command)
  • Estimate of FWHM by Gaussian fitting¹
  • 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 tracks¹
  • 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 sample¹
• Comments on results
• Sources of error
• Bullet point outline of all calculation and data processing steps

¹Remember to include uncertainty and a discussion of error sources for all numerical results.