Difference between revisions of "Microscopy report outline"
From Course Wiki
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| Line 13: | Line 13: | ||
*Design calculations and considerations | *Design calculations and considerations | ||
*Photograph of your setup (optional, but nice) | *Photograph of your setup (optional, but nice) | ||
| + | |||
==Section 2: Microscope Characterization== | ==Section 2: Microscope Characterization== | ||
*Basic optics: include a table with the following values for the 10X, 40X, and 100X objectives: | *Basic optics: 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, microspheres)<sup>1</<sup> | **Actual magnification by multiple measures (Air Force Target, Ronchi Ruling, microspheres)<sup>1</<sup> | ||
| − | **Actual field of view (FOV)<sup>1</ | + | **Actual field of view (FOV)<sup>1</sup> |
**Example pictures from each objective (fluorescence mode) | **Example pictures from each objective (fluorescence mode) | ||
| − | *Estimate of actual resolution of the 40X Objective | + | *Estimate of actual resolution of the 40X Objective<sup>1</sup> |
**Images used for computation (with fit, if you like – see plotgaussfit command) | **Images used for computation (with fit, if you like – see plotgaussfit command) | ||
| − | **Estimate of FWHM by Gaussian fitting<sup>1</ | + | **Estimate of FWHM by Gaussian fitting<sup>1</sup> |
**Bullet point outline of data analysis methodology | **Bullet point outline of data analysis methodology | ||
**Comments on estimated versus theoretical value | **Comments on estimated versus theoretical value | ||
*Stability | *Stability | ||
**X-Y plots of sum and difference tracks for “stationary” particles. | **X-Y plots of sum and difference tracks for “stationary” particles. | ||
| − | **MSD versus time interval for sum and difference tracks<sup>1</ | + | **MSD versus time interval for sum and difference tracks<sup>1</sup> |
**Bullet point outline of data analysis methodology | **Bullet point outline of data analysis methodology | ||
**Comments on observed vs. expected data trend | **Comments on observed vs. expected data trend | ||
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==Section 3: Fluorescence Microscopy== | ==Section 3: Fluorescence Microscopy== | ||
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*X-Y plots of tracks for all 5 samples | *X-Y plots of tracks for all 5 samples | ||
*MSD versus time interval plots for 5 samples | *MSD versus time interval plots for 5 samples | ||
| − | *Estimate of diffusion coefficient and solvent viscosity for each sample | + | *Estimate of diffusion coefficient and solvent viscosity for each sample<sup>1</sup> |
*Comments on results | *Comments on results | ||
*Bullet point outline of all calculation and data processing steps | *Bullet point outline of all calculation and data processing steps | ||
| + | |||
| + | <br /> | ||
| + | <sup>1</sup>Remember to include uncertainty and a discussion of error sources for all numerical results. | ||
{{Template:20.309 bottom}} | {{Template:20.309 bottom}} | ||
Revision as of 01:57, 10 October 2010
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, and labels on plots.
- Take a look at 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
- 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 Objective1
- Images used for computation (with fit, if you like – 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
- Bullet point outline of all calculation and data processing steps
1Remember to include uncertainty and a discussion of error sources for all numerical results.
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