Table 1 Input and output specifications of neuron segmentation and network reconstruction tools

Software Tool	Required Inputs		Software Capabilities				Neurite Segmentation		Somata Segmentation		Network Graph Reconstruction
Software Tool	Microscopy image type	Nuclei and neuron image pair	Signal: noise enhancement^a	Repair of fragmentary neurite signal^b	Batch processing mode	Processing of overlapping neurites	For total population	For individual cells	For total population	For individual cells
AutoNeuriteJ	Fluorescence	✓						✓		✓
GAIN	Fluorescence	✓		✓	✓	✓	✓	✓	✓	✓
MorphoNeuroNet	Fluorescence	✓	✓		✓	✓	✓		✓	✓
NeurITES	Brightfield		✓	✓	c		✓		✓
Neurient	Fluorescence		✓			✓	✓
Neurite Analyser	Fluorescence	✓		✓	✓	✓	✓		✓
NeuriteIQ	Fluorescence		✓	✓	✓	✓			✓
NeuriteQuant	Fluorescence				✓	✓	✓		✓
NeuriteSegmentation	Brightfield				✓	✓	✓		✓
NeuriteTracer	Fluorescence	✓	✓		✓		✓		✓
Neuron Image Analyzer	Fluorescence or brightfield		✓			✓	✓	✓	✓	✓
NeuronAnalyzer2D	Fluorescence	✓		✓	✓			✓		✓
Neuroncyto II	Fluorescence	✓	✓		✓	✓	✓	✓	✓	✓
NeuronMetrics	Fluorescence		✓	✓	✓		✓
NEMO	Fluorescence or brightfield				✓	✓	✓		✓
NeuronRead	Fluorescence or brightfield		✓			✓	✓		✓
NeuroTreeTracer	Fluorescence		✓			✓	✓	✓	✓	✓
NeurphologyJ	Fluorescence		✓		✓	✓	✓		✓
SynD	Fluorescence			✓	✓	✓	✓		✓
WIS-Neuromath	Fluorescence			✓	✓	✓		✓	✓
Cytonet	Fluorescence				✓				✓		✓
DeepTEGINN	Fluorescence or brightfield		✓	✓			✓		✓		✓
ExplantAnalyzer	Fluorescence	✓	✓	✓	✓	✓	✓		✓		✓

^aSignal:noise enhancement identifies tools that employ specialized background subtraction techniques beyond blurring or size filtering.
^bRepair of fragmentary neurite signal identifies tools that employ operations or algorithms to bridge neurite gaps that have resulted from uneven staining, trans-planar localization of cells, etc.
^cNeurITES performs batch processing on time-series images.

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