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
CAFE Viz 2012 CAFE Viz 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.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 2009 A computational framework for ultrastructural mapping of neural circuitry. PLoS Biol 7(3): e1000074 PubMed PMID 19855814::PubMedCentral PMC2661966
  • A description of our open-source software for large-scale, automated volume assemblyTasdizen T, Koshevoy P,Grimm B, Anderson JR, Jones BW, Whitaker R, Marc RE 2010 Automatic mosaicking and volume assembly for high-throughput serial-section transmission electron microscopy. J Neuroscience Methods: 193:132-44. PubMed PMID 20713087
  • 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.Anderson JR, Mohammed S, Grimm B, Jones BW, Koshevoy P, Tasdizen T, Whitaker R, Marc R 2011 The Viking viewer for connectomics: scalable multi-user annotation and summarization of large volume data sets. J Microscopy: 241:13-28. PubMed PMID 21118201:: PubMedCentral PMCID 3017751
  • 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.Anderson JR, Jones BW, Watt CB, Shaw MV, Yang J.-H., DeMill D, Lauritzen J.S., Lin Y., Rapp KD, Mastronarde D, Koshevoy P, Grimm B, Tasdizen T, Whitaker R, Marc RE 2011 Exploring the retinal connectome. ∞ Molecular Vision 17:355-379 :: PubMed PMID 21311605
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