Difference between revisions of "Assignment 5, Part 1: viscosity and diffusivity in glycerol-water mixtures"
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[[Image: 20.309_130924_GlycerolChamber.png|right|thumb|200px|Imaging chamber for fluorescent microspheres diffusing in water:glycerol mixtures]] | [[Image: 20.309_130924_GlycerolChamber.png|right|thumb|200px|Imaging chamber for fluorescent microspheres diffusing in water:glycerol mixtures]] | ||
− | 1. Track some 0. | + | 1. Track some 0.86μm Pink Spherotech polystyrene beads in water-glycerin mixtures (Samples A and B contain 30% and 50% glycerin, respectively). |
:''Notes'': Fluorescent microspheres have been mixed for you by the instructors into water-glycerin solutions A and B. (a) Vortex the stock Falcon tube, and then (b) transfer the bead suspension into its imaging chamber (consisting of a microscope slide, double-sided tape delimiting a 2-mm channel, and a 22mm x 40mm No. 1.5 coverslip, and sealed at both ends nail polish). | :''Notes'': Fluorescent microspheres have been mixed for you by the instructors into water-glycerin solutions A and B. (a) Vortex the stock Falcon tube, and then (b) transfer the bead suspension into its imaging chamber (consisting of a microscope slide, double-sided tape delimiting a 2-mm channel, and a 22mm x 40mm No. 1.5 coverslip, and sealed at both ends nail polish). | ||
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:''Tip 1'': Do not choose to monitor particles that remain stably in focus: these are likely to be 'sitting on the coverslip' and their motion will not be representative of diffusion in the viscous water-glycerol fluid. | :''Tip 1'': Do not choose to monitor particles that remain stably in focus: these are likely to be 'sitting on the coverslip' and their motion will not be representative of diffusion in the viscous water-glycerol fluid. | ||
− | :''Tip 2'': | + | :''Tip 2'': Either limit the ROI to a region with only 3 or 4 particles for a long movie (~30-60s) or use the full FOV for a short time (~10s). Long movies with the whole field of view is a sure way to make MATLAB complain. |
2. Record movies of beads diffusing in the two glycerol solutions and use your newly developed code to estimate the diffusion coefficient of each sample. | 2. Record movies of beads diffusing in the two glycerol solutions and use your newly developed code to estimate the diffusion coefficient of each sample. | ||
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{{Template:Assignment Turn In|message=Turn in for the viscosity part: | {{Template:Assignment Turn In|message=Turn in for the viscosity part: | ||
− | # Include a snapshot of the 0. | + | # Include a snapshot of the 0.86 μm fluorescent beads monitored. |
# Document the samples you prepared and how you captured images (camera settings including frame acquisition rate, number of frames, number of particles in the region of interest, choice of sample plane, etc) | # Document the samples you prepared and how you captured images (camera settings including frame acquisition rate, number of frames, number of particles in the region of interest, choice of sample plane, etc) | ||
# Plot two or more example bead trajectories for each of the glycerin samples. (Hint: If you subtract the initial position from each trajectory, then you can plot multiple trajectories on a single set of axes.) | # Plot two or more example bead trajectories for each of the glycerin samples. (Hint: If you subtract the initial position from each trajectory, then you can plot multiple trajectories on a single set of axes.) |
Revision as of 20:26, 1 October 2018
This is Part 1 of Assignment 5.
Estimating the diffusion coefficient by tracking suspended microspheres
1. Track some 0.86μm Pink Spherotech polystyrene beads in water-glycerin mixtures (Samples A and B contain 30% and 50% glycerin, respectively).
- Notes: Fluorescent microspheres have been mixed for you by the instructors into water-glycerin solutions A and B. (a) Vortex the stock Falcon tube, and then (b) transfer the bead suspension into its imaging chamber (consisting of a microscope slide, double-sided tape delimiting a 2-mm channel, and a 22mm x 40mm No. 1.5 coverslip, and sealed at both ends nail polish).
- Tip 1: Do not choose to monitor particles that remain stably in focus: these are likely to be 'sitting on the coverslip' and their motion will not be representative of diffusion in the viscous water-glycerol fluid.
- Tip 2: Either limit the ROI to a region with only 3 or 4 particles for a long movie (~30-60s) or use the full FOV for a short time (~10s). Long movies with the whole field of view is a sure way to make MATLAB complain.
2. Record movies of beads diffusing in the two glycerol solutions and use your newly developed code to estimate the diffusion coefficient of each sample.
- Consider how many particles you should track and for how long. What is the uncertainty in your estimate?
- Calculate the viscosity of the solution and estimate the glycerin/water weight ratio of each solution. (Hint: what is the relationship between diffusion coefficient and viscosity? You may find that this chart is a useful reference.)
Turn in for the viscosity part:
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- Overview
- Part 1: MSD difference tracking and microscope stability
- Part 2: Live cell particle tracking of endocytosed beads
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