Parameter values and initial conditions of the 3d model.

The parameter values for the 3d model listed here correspond to the “GCaMP” model. The parameter values for the “No-GCaMP” 3d model are the same except that GCaMP6s concentration equals 0 nM. In the “GCaMP6f” model variant, Gcamp_f = 1.05 × 10⁷ M⁻¹.s⁻¹ and Gcamp_b = 3.93s⁻¹. Parameter values in the 3d model have been adjusted to optimize the match with experimental data as described in the Methods section. Note that the values for calcium and IP₃ binding or unbinding to IP₃R, i.e. the a_i’s and b_j’s parameters below, are smaller in our model than in the literature, probably because our model is not cooperative. For GCaMP6s and GCaMP6f, we used the diffusion coefficient of calmodulin. The initial number of Ca²⁺ ions was adjusted so that the measured basal GCaMP6s-Ca concentration was around 300nM [86, 124].