Welcome To Morphonets!
Morphonets is an open, community-driven effort to provide tools for tracing, visualization, quantification, and modeling of neuroanatomical data, from Fiji/ImageJ to Python and napari. Our tools stand on the shoulders of SciJava and its Python sibling scyjava. Our immediate focus is cellular neuroscience, but the software we develop has been successfully applied to other areas of the biosciences.
Projects
Morphonets has incorporated several projects that were previously scattered across the Fiji ecosystem of plugins. Currently, the following major projects are being developed under the Morphonets umbrella:
The open-source framework for quantification of neuronal anatomy: semi- and fully automated tracing, proofreading, 2D, 3D and large-volume visualization, morphometry, Sholl and other comparative analyses, and graph analysis.
The big data cousin of SNT: tracing and analysis of terabyte-scale volumes, including remote OME-Zarr and N5 datasets, with interactive 3D visualization powered by BigDataViewer and BigVolumeViewer.
Run SNT from Python: reconstructions, measurements and images move directly between SNT and the scientific Python stack (e.g., NumPy, SciPy, scikit-learn, NetworkX, napari), with no separate Fiji workflow.
A napari plugin that bridges napari and SNT: it sends polylines drawn in napari to SNT and receives SNT reconstructions back as napari layers.
An image-based modeling framework for neurodevelopment simulations powered by Cx3D and sciview.
Sholl analysis directly from images, with no tracing required, or from reconstructions. Originally a stand-alone project, now incorporated into SNT.
Learning Resources
A self-paced series of runnable notebooks that teaches neuroanatomy in Python using real data, from a single reconstruction to atlas-scale analysis and ML-ready ground truth. Assumes basic Python only.
More than 70 ready-to-run scripts in Groovy and Python covering analysis, batch processing, tracing, rendering, and big data. Open them from the Script Editor (Templates > Neuroanatomy) and adapt them to your data.
Video tutorials for getting started with SNT and its main workflows.
Questions, tips, and discussions about SNT from users and developers.
Getting Involved
Anyone can contribute! Contact us on GitHub or the Image.sc Forum