skeleton

MiNA is a simplified workflow for analyzing mitochondrial morphology using fluorescence images or 3D stacks in Fiji. The workflow makes use of ImageJ Ops, 3D Viewer, Skeletonize (2D/3D), Analyze Skeleton, and Ridge Detection. In short, the tool estimates mitochondrial footprint (or volume) from a binarized copy of the image as well as the lengths of mitochondrial structures using a topological skeleton. The values are reported in a table and overlays (or a 3D rendering) are generated to assess the accuracy of the analysis.

Web based viewer developped for google for very big data: 

Neuroglancer is a WebGL-based viewer for volumetric data. It is capable of displaying arbitrary (non axis-aligned) cross-sectional views of volumetric data, as well as 3-D meshes and line-segment based models (skeletons). The segmentation has to be done before loading the dataset, it is not done Inside the viewer.

This is not an official Google product.

It has among other the nice feature of beeing able to generate url for sharing a specific view.

Note that the only supported browser for now are 

• Chrome >= 51
• Firefox >= 46

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).