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Table 2 Typical open-source platforms for data processing

From: Smart imaging to empower brain-wide neuroscience at single-cell levels

Software Featured functions URL
ImageJ [180] Multi-purposed tool for image visualization and analysis; rich user-developed plugins
BioImageXD [181] 2D and 3D analysis; immersive visualization of multidimensional data
Icy [182] Visualize, annotate, and quantify 2D and 3D bioimaging data
FarSight Display results derived from segmentation, tracking, feature extraction; build connections between these results and the raw data
FluoRender [183] Data visualization and analysis; support multi-channel volume data and polygon mesh data rendering
BisQue [177] Server-based platform for image sharing, analysis, visualization, and organization
Trees toolbox [172] Edit, visualize and analyze neuronal trees; neuron reconstruction; generation of synthetic neuron morphologies
GTree [138] System for brain-wide neuron tracing and error-screening
Lychnis [17] 3D neuron tracing, interactive visualization and annotation
Vaa3D [174] Registration; real-time visualization and analysis of large-scale multidimensional data; (brain-wide) neuron reconstruction; content extraction and annotation directly in 3D; rich user-developed plugins;
Natverse [173] Local/remote data import, visualization, data transformation/registration, clustering and graph-theoretic analysis of neuronal branching
SNT [184] Neuron tracing, proof-editing, and visualization; Morphological quantification and modeling