20.309: Biological Instrumentation and Measurement
Assignment details
This assignment has 2 parts:
 Part 1: Implementing difference tracking and measuring the stability of your microscope;
 Part 2: Live cell particle tracking of endocytosed beads.
Submit your work in on Stellar in a single PDF file with the naming convention <Lastname><Firstname>Assignment5.pdf.

Here is a checklist of all things you have to turn in:
For Part 1:
For a slide of fixed beads:
 Plot the MSD versus time interval of
 the sum trajectories, and
 the difference trajectories.
For Part 2:
 Procedure
 Document the samples you prepared and used 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)
 Data
 Include a snapshot of the 0.84 μm fluorescent beads monitored.
 Plot two or more example bead trajectories for each of the samples. (Hint: If you subtract the initial position from each trajectory, then you can plot multiple trajectories on a single set of axes.)
 Analysis and Results
 Plot the MSD vs time (from the difference trajectories) for untreated and Cyto D treated cells on a single set of loglog axes. Plot the individual MSDs from each pair of beads in each movie. Use a single color for all the untreated cells, and a different color for all the treated cells. Do not include MSDs of particles not endocytosed by the cells.
 Combine your data with others from the class to increase your sample size.
 Discussion
 What kind of motion do you see described by your MSD vs τ results?
 What differences do you see between the untreated and Cyto D treated MSD curves?
 Please suggest an interpretation of the behavior of your cells based on your data.
 Include a thorough discussion of error sources and your approaches to minimize them. As in Assignment 4, list out the error sources in a table, including a category for the error source, type of error (random, systematic, fundamental, technical, etc.), the magnitude of the error, and a description and way to minimize each one. Your MSD measurements of the still beads (from Part 1 of this assignment) will be useful for estimating the magnitude of several significant error sources.
Include any MATLAB code you've written as an appendix to your assignment.

Code examples and simulations
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