Table 2 Quantitative metric outputs of neuron segmentation and network reconstruction tools

Software Tool	Local Metrics						Global Metrics							Other
Software Tool	Neurite length per cell or cluster	Number of neurites per cell or cluster	Area of somata per cell or cluster	Hierarchal classification of neurite branches^a	Spatial/ morphological analysis of neurite branches	Sholl analysis^b	Number of somata	Total length/ area of neurites	Total somata area	Number of branch/end/ attachment points	Average pixel intensity of neurons	Neuron polarity^c	Graph metrics	Other
AutoNeuriteJ	✓	✓		✓			✓					✓
GAIN	✓	✓	✓	✓			✓
MorphoNeuroNet							✓	✓	✓	✓				Somata shape
NeurITES	✓	✓	✓	✓	✓
Neurient														Angular alignment of neurites
Neurite Analyser		✓	✓		✓		✓	✓		✓				Number of neurites
NeuriteIQ							✓	✓	✓	✓	✓
NeuriteQuant					✓		✓		✓	✓
NeuriteSegmentation								✓						Distance of axon from somata
NeuriteTracer							✓	✓
Neuron Image Analyser	✓													Neurite orientation
NeuronAnalyzer2D	✓	✓	✓	✓						✓				Average neurite width, number of protrusions in growth cone
Neuroncyto II	✓	✓	✓	✓			✓	✓
NeuronMetrics	✓	✓			✓					✓		✓		Neuron territory
NEMO	✓		✓		✓	✓	✓				✓			Fractal analysis, angular measurement
NeuronRead							✓	✓	✓					Somata shape and perimeter
NeuroTreeTracer											✓
NeurphologyJ							✓	✓	✓	✓
SynD						✓		✓	✓		✓			Synapse analysis, soma axis
WIS-Neuromath	✓	✓	✓	✓	✓		✓	✓			✓
Cytonet													✓
DeepTEGINN													✓
ExplantAnalyzer						✓		✓		✓		✓	✓	Convex hull enclosing neurites, neurite orientation

^aHierarchical classification of neurite branches includes primary/secondary/tertiary or short/long or axon/dendrite classifications.
^bSholl analysis quantifies the complexity and arborization of neurites extending from parent somata.
^cNeuron polarity metrics characterize axodendritic properties of neurites.

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