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News

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.




    Copyright 2012-2013, Ultrastructural Brain Mapping Consortium
    All rights reserved.
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)