Rat Hippocampus Atlas

About

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.

The atlas is accessed through the structure index or image viewer. See tutorial for details about functionality.

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

News

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

 

External links

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)

3D

 

Image viewer

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

Image repository :

Name	Species	CuttingDirection	Comments
Hippocampus atlas application (coronal)	RAT	CORONAL	NeuN, parvalbumin and calbindin

 

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/

Neural Systems and Graphics Computing Laboratory 
Institute of Basic Medical Sciences 
Department of Anatomy 
University of Oslo 
P.O. Box 1105 Blindern 
N - 0317 Oslo 
Norway 
http://www.nesys.uio.no

Credits

NeSys and CMBN atlas development team:

Lisa J. Kjonigsen, M.Sc.
Jan Olav Kjode, M.Sc.
Ivar Andre Moene, M.Sc.
Trygve B. Leergaard, M.D., Ph.D.
Jan G. Bjaalie, M.D., Ph.D.

KI-CBM and Witter-group:
Menno P. Witter, Ph.D.