Difference between revisions of "Assignment 5, Part 1: viscosity and diffusivity in glycerolwater mixtures"
From Course Wiki
(→Estimating the diffusion coefficient by tracking suspended microspheres) 
Juliesutton (Talk  contribs) (→Estimating the diffusion coefficient by tracking suspended microspheres) 

Line 27:  Line 27:  
# Include a table of the diffusion coefficient, viscosity and measured glycerin/water ratio for each of the samples (A and B)  # Include a table of the diffusion coefficient, viscosity and measured glycerin/water ratio for each of the samples (A and B)  
# Is the viscosity you measured close to the theoretical value predicted by [http://www.met.reading.ac.uk/~sws04cdw/viscosity_calc.html this website]?  # Is the viscosity you measured close to the theoretical value predicted by [http://www.met.reading.ac.uk/~sws04cdw/viscosity_calc.html this website]?  
−  #  +  # Discuss the error sources present in your measurement of the MSD of diffusing particles. It may be helpful to list out the error sources in a table, including a category for the error source, type of error (random, systematic, fundamental, technical, etc.), and a description and way to minimize each one. We will quantify the magnitude of these errors in the next assignment. 
}}  }}  
</onlyinclude>  </onlyinclude>  
{{Template:Assignment 5 navigation}}  {{Template:Assignment 5 navigation}}  
{{Template:20.309 bottom}}  {{Template:20.309 bottom}} 
Revision as of 14:46, 3 October 2019
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 waterglycerin mixtures (Samples A and B contain 80% and 85% glycerin, respectively).
 Notes: Fluorescent microspheres have been mixed for you by the instructors into waterglycerin 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, doublesided tape delimiting a 2mm channel, and a 22mm x 40mm No. 1.5 coverslip, and sealed at both ends nail polish).
 Tip 1: Ensure that the focal plane you choose to image is not near the coverslip or the slide. If some particles don't move or hardly move at all, it is likely that they are stuck to the coverslip. Adjust the focus so that you are viewing a plane near the middle of the sample. (A good way to do this is to focus on the top and bottom of the sample chamber and then split the difference.)
 Tip 2: Each full frame of the full camera field of view takes up almost 2.5 MB of memory, so movies can get large very fast. Try to limit image data variables to a reasonable size by keeping the length of the movie short or limiting the Region of Interest (ROI) to a fraction of the full field of view.( A fullfield, three minute move takes up about 4 GB, which is certain to push MATLAB over the edge.)
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 factors determine the uncertainty and accuracy of your estimate?
Turn in for the viscosity part:

 Overview
 Part 1: MSD difference tracking and microscope stability
 Part 2: Live cell particle tracking of endocytosed beads
Back to 20.309 Main Page