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Leibnitz is the calculator you've always wanted (even if you didn't know it!), short of handwriting recognition.
FAQ: https://github.com/jafl/jx_application_framework/tree/master/programs/leibnitz#readme
ChangeLog: http://leibnitz.sourceforge.net/ChangeLog.html
The flNeuronTool allows users to reconstruct and proofread neuronal morphologies in light microscopy images. The system incorporates automatic tracing and manual editing of neuron reconstruction into a cooperative 3D interactive visualization-assisted environment, which is a powerful tool for analysis of complex neuronal images.
This is a short program built with Processing that displays information as a tree. It was originally created for a Software Architecture class. See the 1-minute presentation here: http://www.youtube.com/watch?v=zorUX8ZSZWQ
Hydra3D is a 3-dimensional XML visualization and editing tool for UNIX variants and Windows. Documents are displayed as interactive 3Dtree structures. Hydra3D uses QT for windowing, OpenGL for three-dimensional display, Xerces and Xalan for XML process