Paintera is a general visualization tool for 3D volumetric data and proof-reading in segmentation/reconstruction with a primary focus on neuron reconstruction from electron micrographs in connectomics. It features/supports:
Views of orthogonal 2D cross-sections of the data at arbitrary angles and zoom levels
Mipmaps for efficient display of arbitrarily large data at arbitrary scale levels
3D visualization as polygon meshes
Meshes for each mipmap level
Mesh generation on-the-fly via marching cubes to incorporate painted labels and agglomerations in 3D visualization. Marching Cubes is parallelized over small blocks. Only relevant blocks are considered (huge speed-up for sparse label data).
Paintera is implemented in Java and makes extensive use of the UI framework JavaFX
Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline—modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation.