Rat Hippocampus Atlas

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The rat hippocampus atlas is an interactive resource providing detailed descriptions of 18 hippocampal structures, criteria for delineating 63 boundaries between these structures, a histological image repository with delineated boundaries, and bidirectional links between descriptions (Index of structures) and corresponding section images (Image viewer). The system is intended for researchers working in the field, as well as students interested in this brain region.

Access image repository

The image repository consists of ~100 coronal images stained for NeuN, calbindin, and parvalbumin displayed in a triple image viewer that allows interactive zooming and panning of each viewer panel (with a possibility to synchronize the three panels). Annotations can be toggled on / of, and pre-set high-magnification positions for annotated regions are available.

Re-use of data from this repository is allowed provided that reference is given to the following publication: Kjonigsen LJ, Leergaard TB, Witter MP, Bjaalie JG., 2011. Digital atlas of anatomical subdivisions and boundaries of the rat hippocampal region. Frontiers in Neuroinformatics, 2011; 5:2. doi: 10.3389/fninf.2011.00002

Rat Hippocampus Atlas application 2.0

Contributing laboratories

Kavli Institute for Systems Neuroscience & Centre for the Biology of Memory, Medical-Technical Research Centre, Norwegian University of Science and Technology, N - 7489 Trondheim, Norway  (http://www.ntnu.no/cbm/). People: Menno P. Witter

Neural Systems Laboratory (http://www.nesys.uio.no), Centre for Molecular Biology and Neuroscience & Institute of Basic Medical Sciences, Department of Anatomy, University of Oslo, P.O. Box 1105 Blindern, N - 0317 Oslo, Norway. People: Lisa J. Kjønigsen, Dmitri Darine, Jan Olav Kjøde, Ivar A. Moene, Trygve B. Leergaard, Jan G. Bjaalie

External links

The Hippocampal Connectome Project


  • 2015-10 Transfer to new viewer platform. Release of version 2.0 running on Navigator 3.0.6
  • 2011-03 Speed optimization. Release of version 1.2
  • 2011-01 Release of version 1.1 in conjunction with publication
  • 2010-06 Poster, 7th Forum for European Neuroscience 2010, Amsterdam, The Netherlands
  • 2009-11 Poster / demonstration, Society of Neuroscience conference in Chicago, USA
  • 2009-09 Poster / demonstration, 2nd INCF Congress of Neuroinformatics, Plzen, Czech Republic

Funded by:

  • The Human Brain Project through the European Union Seventh Framework Program (FP7/2007-2013) under grant agreement no. 604102 (HBP)
  • The Research Council of Norway (INCF National NodeI, project 214842)