Difference between revisions of "Microscopy report outline"
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** Include a table with the following values for the 10X, 40X, and 100X objectives: | ** Include a table with the following values for the 10X, 40X, and 100X objectives: | ||
*** Theoretical resolution | *** Theoretical resolution | ||
− | *** Actual magnification by multiple measures (Air Force Target, Ronchi Ruling | + | *** Actual magnification by multiple measures (Air Force Target, Ronchi Ruling)<sup>1</sup> |
− | *** | + | *** Calculate the actual field of view (FOV)<sup>1</sup> |
− | ** | + | ** Measure an appropriate size of microspheres for each of the objectives and comment on the mean and uncertainty of your measurements |
+ | ** Provide a few example transilluminated pictures from each objective (there is no need to provide all) | ||
==Part 2: Fluorescence microscopy== | ==Part 2: Fluorescence microscopy== |
Revision as of 03:32, 15 September 2012
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
Part 1: Microscope construction and bright field characterization
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)
Microscope characterization
- Magnification and field of view
- 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)1
- Calculate the actual field of view (FOV)1
- Measure an appropriate size of microspheres for each of the objectives and comment on the mean and uncertainty of your measurements
- Provide a few example transilluminated pictures from each objective (there is no need to provide all)
- Include a table with the following values for the 10X, 40X, and 100X objectives:
Part 2: Fluorescence microscopy
- Unprocessed Images of fluorescent bead associated reference images
- Corrected images
- Image or surface plot (see surf command in Matlab) of correction applied
- Histograms of original and corrected images
Parts 3+: Particle tracking and other experiments
- Bullet point outline of image processing methodology
- 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 fixed particles.
- MSD versus time interval for sum and difference tracks1
- Bullet point outline of data analysis methodology
- Comments on observed vs. expected data trend
- X-Y plots of tracks for all samples
- MSD versus time interval plots for measured samples
- Estimate of diffusion coefficient, viscosity and other mechanical properties for each sample
- Comments on results, specifically microscope stability, resolution,
- Comment extensively on sources of error and approaches to minimize them, both utilized and proposed
- Bullet point outline of all calculation and data processing steps
1Remember to include uncertainty and a discussion of error sources for all numerical results.