Modeling of Neuronal Growth In Vitro: Comparison of Simulation Tools NETMORPH and CX3D

EURASIP Journal on Bioinformatics and Systems Biology

Table 1 The list of the relevant model parameters. Model parameters are listed in the third column. The references used to obtain these parameters are given in the last column. Reference [3] points to the parameters that can be found directly in NETMORPH tutorial paper, while [3]* points to the reconstructed neurons from the same paper, which parameters can be found on the simulator web site. The notation "simulators" points to the value selected as a result of simulator constraints. The parameters for apical and basal dendrites differ only for and they are shown together in the table (the for the apical dendrites is given between the brackets). The initial elongation rates , marked with +, are varied in the simulations.

	Parameter	Value	Unit	Selection criteria
	Number of neurons	100		Simulators
	Proportion pyr.	80		[14]
	Proportion nonpyr.	20		[14]
	Density of neurons	100	cells/mm²	Simulators, [14, 18, 19, 22]
	Soma diameter	10	μ m	[21]
Axon		45	μ m/day	[3]
		0.16		[3]
		17.38		[3]
		14	days	[3]
		0.39		[3]
		0		[3]
Basal (apical) dendrite		9.635 (19.27)	μ m/day	[3]* ([3]*, [15])
		0		[3]*
		2.52		[3]*
		3.006	days	[3]*
		0.73		[3]*
		0.5		[3]*
Nonpyr. dendrite		9.635	μ m/day	[3]*, [17]
		0		[3]*, [17]
		2.6475		[3]*, [17]
		4.706	days	[3]*, [17]
		0.594		[3]*, [17]
		−0.259		[3]*, [17]
Synapses NETMORPH	Distance pyr.-pyr.	1	μ m	[3]
	Distance pyr.-nonpyr.	0.1	μ m	[3]
	Distance nonpyr.-pyr.	1	μ m	[3]
	Distance nonpyr.-nonpyr.	0.1	μ m	[3]
Synapse CX3D	Spine length	3	μ m	[4], [23]
	Bouton length	2	μ m	[4]