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Outreach Science Tools Technologies
The Connectome Connectome RC1 Quick Links Connectome Resources
Retinal Disease Metabolic Atlas Protocols Excitation Mapping
Blindness Remodeling Capture Classification
Vision Images Code Imaging
People Papers Core CMP

Software

Connectome navigation and annotation

VIZ

Connectome graph and topology visualization
Image registration


Documentation

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


Data

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 assembly

    Tasdizen 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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