Table 2. 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].

Parameter	Description	Value in 3d GCaMP model	Reference
V	Cell volume	2.81 × 10−17 L	[128]
IP3 dynamics
IP0	Initial IP3 number/conc	3 molec. i.e 177 nM	[85]
DIP3	IP3 diffusion	280 μm2.s−1	[107]
Nplc	PLCδ number/conc.	1696 molec. i.e 100 μM	[129]
δ	PLCδ max rate	1 s−1	-
β	IP3 decay	1.2 × 10−4 s−1	-
Ca2+ dynamics
Ca0	Initial Ca2+ number/conc.	5 molec. i.e 295 nM	[86]
DCa	Ca2+ diffusion	13 μm2.s−1	[107]
μ	Ca2+ flux through open IP3R	6 × 103 s−1	-
γ	cytosolic Ca2+ influx	1.5 × 10−7 s−1	-
α	Ca2+ decay rate	30 s−1	-
GCaMP6s
CGCa	GCaMP6s conc.	169 molec. i.e 10 μM	[130, 131]
DGCaMP	GCaMP6s diffusion	50 μm2.s−1	[132]
Gcampf	GCaMP6s Ca binding rate	7.78 × 106 M−1.s−1	[72]
Gcampb	GCaMP6s-Ca dissociation rate	1.12 s−1	[72]
IP3R
$N_{{\text{IP}}_{\text{3}}\text{R}}$	IP3R number	50 molec.	[89]
$d_{{\text{IP}}_{\text{3}}\text{R}}$	IP3R interact. distance	1 mesh triangle	-
IP3R binding
a1	First Ca	1.2 × 106 M−1.s−1	-
a2	IP3	4.1 × 107 M−1.s−1	-
a3	Second Ca	1.6 × 104 M−1.s−1	-
IP3R dissociation
b1	First Ca	50 s−1	-
b2	IP3	400 s−1	-
b3	Second Ca	100 s−1	-