plot the coordinates of migrating cells over time and calculate the overall angle to vertical

I am shooting movies of cells migrating in chicken embryos from a central mid line and I need to plot each fluorescent cell (hundreds) (GFP) at each time point in Matlab. These co-ordinates will over time provide an overall trajectory to the vertical midline or a reset 0 deg angle and the cell direction angles recorded to provide an average angle direction for all the cells. several movies need to be analysed this way with varying treatments so that differences in the angle will be noted. Hope you can guide me to the appropriate training. thanks Tim

Answer 1

[Lauren]

I'm not sure I quite understand what you're looking for. Are you looking for a way to process the movie frames so that the cell positions are found automatically? If so, I would take a look at normxcorr2 and feed it an image of one cell. Your correlation will spike where the cell image matches and you can track the cell positions over time and then subsequently calculate your average angle. You might need to do some filtering/processing of the image beforehand to improve your correlation but it hopefully provides you with a starting point.