CONNECTOMICS SOFTWARE

Primary Tools

Ilastik - Autosegmentation
Knossos - Rapid manual skeletonization tracing through cubed volumetric image datasets

Other Tools

Cytoseg - Open source project for automatic segmentation and circuit reconstruction
Elegance - Circuit reconstruction software
Reconstruct - 3D reconstruction software
StackVis - Interactive multiresolution image stack viewer with ability to import data from BrainMaps.org database
TrakEM2 - ImageJ plugin for segmentation and reconstruction

Missing software link? Email us.

Ultrastructural Brain Mapping Consortium

For the supreme cunning of the structure of the gray matter is so intricate that it defies and will continue to defy for many centuries the obstinate curiosity of investigators.

- Santiago
Ramón y Cajal

Ultrastructural Data

Scanning Electron Microscopy
(80 nm pixel size)

Light Microscopy Data

Nissl (from BrainMaps.org)

Myelin (from BrainMaps.org)

Allen Brain Atlas
(from Brain-Map.org)