simulation results for (a–d) a yeast cell with a large vacuole inside (Visualization 1) and (e–h) a yeast cell with a large vacuole and a multitude of smaller vacuoles (Visualization 2). (a, g) Visualization of a slice in the yz plane from the 3D RI profiles; (b, f) Cut along the red dotted line in subfigures (a, e), highlighting the RI profile into the vacuole; (c, e) Visualization of a slice in the xy plane from the 3D RI profiles; (d, h) Isolevel visualizations. EM = External membrane, C = Cytoplasm, N = Nucleus, V = Vacuole. For each cell, the isolevels’ thresholds for the visualization are set with respect to the maximum value of the simulated RI profile.