Suppose that I want to calculate the transport across a certain transect (green line) from the outputs of an ocean numerical model. The model has the $u$ values at the center of the grids (crosses) and the $v$ values at the corners (circles), as it uses a C-grid.
Should I use the velocity values closest to the transect? Should I average the values at the corners? Interpolate?
Side question: does anyone know some Matlab toolbox to analyze numerical model outputs?