Table 2 Typical open-source platforms for data processing

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