filament

neuTube is a collection of neuron reconstruction tools from fluorescence microscope images. It has an interactive system with a 3D viewer, which can be clicked in 3D and perform neuron tracing automatically and semi-automatically. It can automatically recognize branching points as junctions. Traced neurons can be exported to swc format, which could be imported by various software packages. neuTube has Win and Mac OS standalone executable builds and may also be installed by manual compilation. In addition, neuTube can be used as a plugin in Vaa3D.

This macro segments blood vessels in a 3D stack. It is suited for well-contrasted images (low background) and works better if the width of the vessels of interest is reasonably uniform.

Sample image: 1

sample image: 2

Neuron studio is a software package to reconstruct neurons from 3D confocal images. Reconstruction can be done manually, semi-manually or fully automatic. The images as well as the detected objects are rendered in 3D. A spine detection and classification function is also included. Results can be exported as a text file with coords of the spines. It seems that active development has stopped in 2009. NeuronStudio is being developed at the Computational Neurobiology and Imaging Center (CNIC), a research laboratory at the Neuroscience Department of the Mount Sinai School of Medicine in New York.

NeuronStudio can be used with default parameters or user-defined parameters (Fully or semi-automated).

This plugin performs Strahler analysis on topographic skeletons (2D/3D). Strahler numbering is a numerical procedure that summarizes the branching complexity of mathematical trees.