Connectome Resources

Software

VIKING Connectome navigation and annotation
VIZ Connectome graph and topology visualization
IRIS Image registration

 

Documentation

MANUAL Serial EM / GATAN Marclab Manual
CAFE Viking 2012 CAFE Viking Guide

 

Data

TRACK The standardized tracking challenge dataset
 

GRIDS

 The RC gridlist
CMP MAP RC1 molecular tags

 

Papers

  • A detailed description of a complete ATEM framework, hardware configuration and data pipeline. Cited in Wired Magazine and other public science digests. A computational framework for ultrastructural mapping of neural circuitry. Anderson JR, Jones BW, Yang J-H, Shaw MV, Watt CB, Koshevoy P, Spaltenstein J, Jurrus E, Kannan UV, Whitaker R, Mastronarde D, Tasdizen T, Marc R 2008 PLoS Biol 7(3): e1000074 [doi:10.1371/journal.pbio.1000074].  PubMed Direct Link PDF  8.6 Mb PDF

 

  • A description of our open-source software for large-scale, automated volume assembly. Automatic mosaicking and volume assembly for high-throughput serial-section transmission electron microscopy. T. Tasdizen, P. Koshevoy, B. Grimm, J. Anderson, B.W. Jones, R.T. Whitaker, R.E. Marc (2010). J Neurosci Methods. PubMed Direct Link PDF

 

  • A description of our open-source software Viking for browsing and analyzing connectomes. This paper also contains public release of a standard test volume for automated process tracking. The Cover article for the January issue of the journal. The Viking viewer for connectomics: scalable multi-user annotation and summarization of large volume data sets. Anderson JR, Mohammed S, Grimm B, Jones BW, Koshevoy P, Tasdizen T, Whitaker R, Marc (2010). J Microsc. PubMed Direct Link PDF

 

  • The first complete synaptic connectome published, with public release of the volume. Dr. Marc was interviewed regarding this work for Douglas Fox’s cover article for the New Scientist, February 2011. Exploring The Retinal Connectome. J.R. Anderson, B.W. Jones, C.B. Watt, M.V. Shaw, J-H. Yang, D. DeMill, J.S. Lauritzen, Y. Lin, Kevin D. Rapp, D. Mastronarde, P. Koshevoy, B. Grimm, T. Tasdizen, R. Whitaker, R.E. Marc (2010). Mol Vis. PubMed Direct Link PDF