The rat hippocampus atlas is an interactive resource providing a systematic overview of cyto- and chemoarchectonical feastures of the hippocampus proper, fasciola, and associated parahippocampal cortices. This atlas system has been developed to serve the need to integrate detailed descriptions of structures and criteria defining boundaries and atlas images in which the underlying histological features can be explored.
FeaturesTop ↑
Alphabetical and hierarchical overview of 18 hippocampal structures Detailed, illustrated descriptions of 63 boundaries Interactive image repository with ~100 coronal histological images stained for NeuN, calbindin, and parvalbumin Triple image viewer in wich differently stained neighbouring sections can be interactively compared Graphical overlay of substructures based on described boundary criteria Bidirectional links between structure descriptions and image repository
Methods
The atlas is based on histological material from an adult Long Evans rat, stained for NeuN, calbindin, and parvalbumin (for details, see Kjonigsen et al., Frontiers in Neuroinformatics, 2011; 5:2. doi: 10.3389/fninf.2011.00002).
ContactTop ↑
Contributing laboratories: Top ↑
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
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
http://www.nesys.uio.no
CreditsTop ↑
NeSys and CMBN atlas development team:
Lisa J. Kjonigsen, M.Sc.
Dmitri Darine, 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.
DocumentationTop ↑
The Rat Hippocampus Atlas System:
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
Hippocampal boundary definitions, ontology and nomenclature:
Boccara CN, Kjonigsen LJ, Hammer IM, Bjaalie JG, Leergaard TB, Witter MP. 2011. A three-plane architectonic atlas of the rat hippocampal region. Hippocampus, 2015 25:838-57. doi: 10.1002/hipo.22407.
Database architecture:
Moene IA, Subramaniam S, Darine D, Leergaard TB, Bjaalie JG. 2007. Towards a workbench for rodent brain image data: systems architecture and design. Neuroinformatics; 5: 35-58
Technical requirementsTop ↑
Web browser requirements for this site:
- To view the Flash applications you need Adobe Flash Player installed on your computer
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Pop-up blocker must be switched off
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To get a user-friendly experience we recommend you have a broadband connection
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The web-pages perform best in full screen
The web site has been tested for the following browser - platform combinations:
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X = Primary platform and browser combination, extensive testing performed.
X = Basic testing indicate that this platform and browser combination works well.
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References for the index of structuresTop ↑
Back to Index of structures
Amaral DG, Scharfman HE, Lavenex P. 2007. The dentate gyrus: fundamental neuroanatomical organization (dentate gyrus for dummies) Prg Br Res163:3-22.
Blackstad TW. 1956. Commissural connections of the hippocampal region in the rat, with special reference to their mode of termination. J Comp Neurol 105:417-519.
Brodmann K. 1909. Vergleichende Lokalisationslehre der Grosshirnrinde in ihren Prinzipien dargestellt auf Grund des Zellenbauers. Leipzig.
Burwell RD. 2001. Borders and cytoarchitecture of the perirhinal and postrhinal cortices in the rat. J Comp Neurol 437(1):17-41.
Caballero-Bleda M, Witter MP. 1993. Regional and laminar organization of projections from the presubiculum and parasubiculum to the entorhinal cortex: an anterograde tracing study in the rat. J Comp Neurol 328(1):115-129.
Haug FM. 1974. Light microscopical mapping of the hippocampal region, the pyriform cortex and the corticomedial amygdaloid nuclei of the rat with Timm's sulphide silver method. I. Area dentata, hippocampus and subiculum. Z Anat Entwicklungsgesch 145(1):1-27.
Haug FM. 1976. Sulphide silver pattern and cytoarchitectonics of parahippocampal areas in the rat. Special reference to the subdivision of area entorhinalis (area 28) and its demarcation from the pyriform cortex. Adv Anat Embryol Cell Biol 52(4):3-73.
Insausti R, Herrero MT, Witter MP. 1997. Entorhinal cortex of the rat: cytoarchitectonic subdivisions and the origin and distribution of cortical efferents. Hippocampus 7(2):146-183.
Jaffe DB, Gutierrez R. 2007. Mossy fiber synaptic transmission: communication from the dentate gyrus to area CA3. Prg Br Res 163:109-132.
Krettek JE, Price JL. 1977. Projections from the amygdaloid complex and adjacent olfactory structures to the entorhinal cortex and to the subiculum in the rat and cat. J Comp Neurol 172(4):723-752.
Paxinos G, Watson C. 1998. The Rat Brain In Stereotaxic Coordinates: Academic Press.
Ruth RE, Collier TJ, Routtenberg A. 1982. Topography between the entorhinal cortex and the dentate septotemporal axis in rats: I. Medial and intermediate entorhinal projecting cells. J Comp Neurol 209(1):69-78.
Ruth RE, Collier TJ, Routtenberg A. 1988. Topographical relationship between the entorhinal cortex and the septotemporal axis of the dentate gyrus in rats: II. Cells projecting from lateral entorhinal subdivisions. J Comp Neurol 270(4):506-516.
Stephan H. 1975. Allocortex. Handbuch der Mikroskopischen Anatomie des Menschen. Berlin: Springer-Verlag.
Steward O. 1976. Topographic organization of the projections from the entorhinal area to the hippocampal formation of the rat. J Comp Neurol 167(3):285-314.
van Groen T, Wyss JM. 1990. The postsubicular cortex in the rat: characterization of the fourth region of the subicular cortex and its connections. Brain Res 529(1-2):165-177.
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):272-282.
Witter MP, Amaral DG, Paxinos G. 2004. Hippocampal formation. The Rat Nervous System. San Diego, CA: Elsevier Academic Press. p 635-704.
Wyss JM. 1981. An autoradiographic study of the efferent connections of the entorhinal cortex in the rat. J Comp Neurol 199(4):495-512.
Release notes
Version 2.0
- migrated to Navigator-3 platform.
Version 1.2
- optimized the data upload to the viewer.
Version 1.1
- better support for Mozilla Firefox
- some changes in the text
- links are added in the structure descriptions
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