Table 1:

Parameters used for in-silico simulation of neural activity in layer II/III of mouse primary visual area V1. Values for each parameter were either directly found in the literature or estimated from published data (entries with a †). The third column indicates whether these parameters were set directly in NAOMi, or were fit indirectly by setting other simulation parameters. In the latter cases, the measured values from a simulated NAOMi volume are shown for comparison, indicating that the simulated anatomy matches measured anatomical statistics.

Parameter	Lit. Val.	Fit type	NAOMi Val.	Unit	Refs
Anatomical parameters:
Neural density	9.20E+04	Direct	–	mm−3	[60]
Fraction vasculature	0.01–0.04	Indirect	0.032	–	[60, 77, 78]
Fraction cell bodies	0.12	Indirect	0.135	–	[60]
Fraction neuropil	0.84	Indirect	0.833	–	[60]
Fraction dendrites*	0.294	Indirect	0.223	–	[60]
Fraction other (fluorescing)*	0.401	Indirect	0.33	–	[60]
Fraction other (not fluorescing)*	0.293	Indirect	0.28	–	[60, 79]
Vessel radius (capillary)	2.00E+00	Direct	–	µm	[58]
Vessel radius (penetrating)	10 (9,11)	Direct	–	µm	[58]
Vascular density	1–3	Indirect	2	%	[77, 60, 58, 78]
Penetrating vessel density	30†	Direct	–	mm−2	[58]
Somatic volume*	1.80E+03†	Indirect	1.80E+03	µm3	[80]
Nuclear volume*	800†	Indirect	800	µm3	[80]
Cytoplasm volume*	1000†	Indirect	1000	µm3	[80]
Basal dendrite diameter	0.7	Direct	–	µm	[81]
Basal dendrite length	100–160†	Indirect	105	µm	[61, 62, 63]
Apical dendrite diameter	1–2	Direct	–	µm	[82]
Axonal diameter	0.3	Direct	–	µm	[60]
Fluorescence parameters:
GCaMP6f binding affinity Kd	290	Direct	–	nMol	[72]
Baseline Ca2+ concentration	50.00	Direct	–	nMol	[70]
Ca2+ binding ratio ks	100,110	Direct	110	AU	[69, 83, 84, 85]
Ca2+ diffusion constant γ	1800	Data fit	292.3	s−1	[69, 83, 86]
Ca2+ axon diffusion constant γ	2800	Direct	–	s−1	[69, 83, 84]
GCaMP6f Hill eqn. exponent nh	2.7	Direct	–	AU	[72]
GCaMP6f Hill eqn. amplitude	25.2	Direct	–	F	[72]
Indicator concentration	10–200	Direct	10	µM	[70, 87, 88]

^*Adjusted for shrinkage: 31% [89]

^†Value estimated from data in the literature