You will evaluate your 3T3 cells on the different stiffnesses of PDMS today. You must passage your T25 flask today in preparation for your independent experiment over the next two weeks (if you plan on using cells). Make sure you have at least 2 new T25 (one per person) flask started today so that you will have enough cells for you experiment to begin next week.
There are many methods for analyzing cell morphology. One of the measures that could be used for this purpose is circularity which is a dimensionless number that describes the degree of compactness of a shape. A common measure would be the ratio of the area of the shape to the area of a circle having the same perimeter. You could utilize ImageJ software which has the circularity feature to calculate circularity. Note that this is only one possible way of looking at it, and you are definitely encouraged to come up with other ways of looking at the experimental results and analyzing them. ImageJ is a free program available from the NIH. Download the appropriate version for your operating system: http://rsbweb.nih.gov/ij/download.html. After installing, open the program. A tool bar should appear. Drag an image that you captured onto the tool bar to open it.
In the Analyze tab choose Set Measurements. Circularity MAY be one of the options, in which case check Circularity and uncheck all other measurements. If it is not available, the equation for circularity is $C = 4\pi (\textrm{area}/\textrm{perimeter}^2)$. Check area and perimeter while leaving all other measurements unchecked. Click Ok. Now select the Freehand selections tool. For the next task you will likely want to Maximize the image to give you the best accuracy. Make a freehand selection of a cell by clicking and dragging the mouse around the perimeter of a cell. When finished select Measure under the Analyze tab or type Control-M. A window should appear containing your measurements (Circularity or Area and Perimeter). Copy measurements for each cell and, if necessary, compute the circularity. Using basic statistics (mean, standard deviation, Student’s t-test) compare the cell morphology on the three substrates.
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