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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 https://imagej.nih.gov/ij/
BioImageXD [181] 2D and 3D analysis; immersive visualization of multidimensional data http://www.bioimagexd.net/
Icy [182] Visualize, annotate, and quantify 2D and 3D bioimaging data http://icy.bioimageanalysis.org/
FarSight Display results derived from segmentation, tracking, feature extraction; build connections between these results and the raw data http://farsight-toolkit.org/
FluoRender [183] Data visualization and analysis; support multi-channel volume data and polygon mesh data rendering https://github.com/SCIInstitute/fluorender/releases
BisQue [177] Server-based platform for image sharing, analysis, visualization, and organization https://bioimage.ucsb.edu/bisque
Trees toolbox [172] Edit, visualize and analyze neuronal trees; neuron reconstruction; generation of synthetic neuron morphologies http://www.treestoolbox.org
GTree [138] System for brain-wide neuron tracing and error-screening https://github.com/GTreeSoftware/GTree
Lychnis [17] 3D neuron tracing, interactive visualization and annotation https://doi.org/10.1038/S41587-021-00986-5
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; http://www.vaa3d.org/
Natverse [173] Local/remote data import, visualization, data transformation/registration, clustering and graph-theoretic analysis of neuronal branching https://natverse.org/
SNT [184] Neuron tracing, proof-editing, and visualization; Morphological quantification and modeling https://github.com/morphonets/SNT