Connectome RC1

Key Images

 

 

 

RC1.mp4

RC1 GraphViz Networks

Networks

RC1 Rod-Cone Crossover

CRXO

RC1 Ganglion cell :: Amacrine cell Coupling

GC :: AC Coupling

 

 

Key Connectome Manuscripts

  • Mining the ON cone BC cohort for new motifs. Practical application of data mining in connectomics. Lauritzen JS, Anderson JR, Jones BW, Watt CB, Mohammed S, Hoang JV, Marc RE 2012 ON cone bipolar cell axonal synapses in the OFF inner plexiform layer of the rabbit retina. J Comp Neurol doi: 10.1002/cne.23244. PubMed PMID 23042441
  • 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
  • A review of theoretical and practical synaptic connectomics. 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 Building retinal connectomes. Current Opinion in Neurobiology 22:568-574 :: PubMed PMID 22498714

Open Source, Open Access and Open Data

The Retinal Connectome RC1 Open Data license :: CC BY NC SA

Retinal Connectome RC1 by The Marc Laboratory, John A. Moran Eye Center, University of Utah
is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.
Permissions beyond the scope of this license may be available at Licenses.

Contact bryan.jones@m.cc.utah.edu for more information about how to acquire the RC1 volume.

Citation:
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

 

The Viking Open Source License :: CC BY NC SA

Viking by The Marc Laboratory, John A. Moran Eye Center, University of Utah
is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.
Permissions beyond the scope of this license may be available at Licenses

Contact bryan.jones@m.cc.utah.edu for more information about how to acquire Viking code.

Citation:
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

 

The Retinal Connectome RC1 Open Access License :: CC BY NC SA

RC1 Data excerpts and images by The Marc Laboratory, John A. Moran Eye Center, University of Utah
are licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.
Permissions beyond the scope of this license may be available at Licenses

Citation:
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

Go to the big ∞ mosaics page

Go to the ∞ tracking challenge page

RC1 Accessory Data

∞ Connectome gridlist

 

 

∞ Fig 1S large array (4000 pixels wide)

 

∞ RC1a map

 

∞ RC1b map