Welcome to the Rat Hippocampus Atlas - Version 2.0 Navigator-3 3.2.6

The rat hippocampus atlas is an interactive resource providing:

  • Detailed descriptions of 18 hippocampal structures

  • Criteria for delineating 63 boundaries between these structures

  • Histological image repository with boundaries delinated according to the described cyto- and chemoarchitectonic criteria

  • Bidirectional links between the structure/boundary descriptions (Index of structures) and the corresponding section images (Image viewer)

The system is intended for researchers working in the field, as well as students interested in this brain region. The atlas is accessed through the structure index or image viewer. See tutorial for details about functionality. These web pages contain Flash applications (see requirements)

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



2012-09 Migration to Navigator-3 platform. Release of version 2.0

2011-03 Speed optimization. Release of version 1.2

2011-01 Modified version, released for review. Release of version 1.1

2010-11 Deployed for review in conjunction with submitted original manuscript

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

Work in progress

  • Histological image repositories with annotated sagittal and horizontal section images

  • 3-D interactive model


  • The Hippocampal Connectome Project
    (van Strien NM, Cappaert NL, Witter MP (2009). The anatomy of memory: an interactive overview of the parahippocampal-hippocampal network. Nat Rev Neurosci.10(4): 272-82)