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| − | '''Welcome to the Rat Hippocampus Atlas - Version 1.2'''
| + | == About == |
| | + | <span style="font-family:georgia,serif;">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). <span style="font-family:georgia,serif;">The system is intended for researchers working in the field, as well as students interested in this brain region.</span> |
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| − | *The rat hippocampus atlas is an interactive resource providing:
| + | == Access image repository == |
| − | *Detailed descriptions of 18 hippocampal structures
| + | <span style="font-family:georgia,serif;">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. </span> |
| − | *Criteria for delineating 63 boundaries between these structures
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| − | *Histological image repository with boundaries delinated according to the described cyto- and chemoarchitectonic criteria
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| − | *Bidirectional links between the structure/boundary descriptions (Index of structures) and the corresponding section images (Image viewer)
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| − | 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)
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| − | Re-use of data from this repository is allowed provided that reference is given to the following publication:
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| − | 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
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| − | == News ==
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| − | 2011-03 Speed optimization. Release of version 1.2
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| − | 2011-01 Modified version, released for review. Release of version 1.1
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| − | 2010-11 Deployed for review in conjunction with submitted original manuscript
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| − | 2010-06 Poster, 7th Forum for European Neuroscience 2010, Amsterdam, The Netherlands
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| − | 2009-11 Poster / demonstration, Society of Neuroscience conference in Chicago, USA
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| − | 2009-09 Poster / demonstration, 2nd INCF Congress of Neuroinformatics, Plzen, Czech Republic
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| − | == External links == | |
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| − | The Hippocampal Connectome Project
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| − | (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)
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| − | 3D
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| − | == Image viewer ==
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| − | 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. | |
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| − | <br/>'''Image repository :'''
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| − | '''Name'''
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| − | '''Species'''
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| − | '''CuttingDirection'''
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| − | '''Comments'''
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| − | '''Hippocampus atlas application (coronal) '''
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| − | '''RAT '''
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| − | '''CORONAL '''
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| − | '''NeuN, parvalbumin and calbindin '''
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| − | == Tutorial ==
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| − | The atlas system has two main elements:
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| − | · An illustrated '''text''' describing 18 hippocampal structures and 63 boundaries between these structures. The structure descriptions can be accessed from an alphabetical or hierarchical index.
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| − | · An '''image repository''' of ~100 coronal images showing the cyto- and chemoarchitecture of the hippocampus region. The images are organized in triplets of neighbouring sections stained for calbinding, NeuN, and parvalbumin. The image triples are sorted from anterior to posterior by distance from bregma.
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| − | The structure and boundary definitions and the image viewer open in separate browser windows, and bidirectional links are provided between corresponding structure descriptions and image levels. Tools for querying are not yet implemented. For optimal use it is recommended to view the browser windows in full screen, preferably using a dual screen setup.
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| − | To use the index of structures, scroll through the alphabetical index to a structure name of interest. Links are provided to structure and boundary descriptions as well as to corresponding levels in the image repository. The structure descriptions give a review of key anatomical features, and provides links to descriptions of boundaries with surrounding structures and corresponding levels in the image repository. The boundary descriptions review the characteristic histological criteria used to identify the boundaries in histological sections, together with links to corresponding levels in the image repository.
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| − | (MUST BE REVISED) To use the image viewer first drag the slider under the row of thumbnail images horizontally to select an anterioposterior level of interest (Bregma coordinates are indicated). Click on the thumbnail images to open them in the triple viewer. The image panels show images of sections stained for calbindin (left), NeuN (middle), and parvalbumin (right). Not all image triplets are complete. ''The viewer has the following options for navigating the images:''
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| − | · Zoom, click the + button in the toolbar or press the shift key to zoom in; click the - button or press the ctrl key to zoom out
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| − | · Pan, click the arrows in the tool bar, or left-click and drag the images freely in the viewer
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| − | · Synchronize, to synchronize the three viewer panels to the same position and zoom scale, click the = button in the toolbar
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| − | · Pre-set, to navigate to a predefined view of a given region, select a structure in the Annotation toolbar and click GO
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| − | · Reset, to reset viewer to default, click the reset button in the toolbar
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| − | · Annotation, click the annotation button in the toolbar to toggle annotations on and off. Graphical overlay is only available for the NeuN images in the middle viewer panel. The employed color coding is in correspondence with the interactive connectivity diagram provided by van Strien et al., 2009; Nat Rev Neurosci.10:272-282
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| − | · Scale bar, the ZoomScale bar shows a scale bare for the image panels. The bar is transparent and can be moved to make crude measurements in the images
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| − | To look up structure descriptions and boundary definitions, click on the color-coded structure name abbreviations in the top panel.
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| − | <div>
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| − | Examples of use:
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| − | </div>
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| − | The atlas system is designed to provide both text description and annotated histological details from the rat hippocampus. The atlas has two main elements, which serve as entry points for use:
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| − | · Find a structure of interest using the alphabetical or hierarchical structure index
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| − | · Find a structure or position of interest using the image repository and the provided stereotaxic positions (bregma levels).
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| − | A student of the hippocampal region may for example use the structure index as a starting point to read about the structure, and then explore the histoarchitecture in the image repository. A researcher seeking to define a boundary in experimental histological material, may for example look up a corresponding level in the image repository, and then read about boundary definitions through the index of structures.
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| − | == About the project ==
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| − | 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.
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| − | <div>
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| − | === ===
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| − | === Features ===
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| − | </div>
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| − | *Alphabetical and hierarchical overview of 18 hippocampal structures
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| − | *Detailed, illustrated descriptions of 63 boundaries
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| − | *Interactive image repository with ~100 coronal histological images stained for NeuN, calbindin, and parvalbumin
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| − | *Triple image viewer in wich differently stained neighbouring sections can be interactively compared
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| − | *Graphical overlay of substructures based on described boundary criteria
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| − | *Bidirectional links between structure descriptions and image repository
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| − | <div>
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| − | === ===
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| − | === Methods ===
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| − | </div>
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| − | 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).
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| − | <div>
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| − | === ===
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| − | === Contact ===
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| − | </div>
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| − | Digital brain atlasing:
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| − | [mailto:j.g.bjaalie@medisin.uio.no <b>j.g.bjaalie@medisin.uio.no</b>]
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| − | Technical issues and functionality:
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| − | [mailto:i.a.moene@medisin.uio.no <b>i.a.moene@medisin.uio.no</b>]
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| − | Neuroanatomy of the hippocampus:
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| − | [mailto:menno.witter@ntnu.no <b>menno.witter@ntnu.no</b>]
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| | + | <span style="font-family:georgia,serif;">'''Re-use of data from this repository is allowed provided that reference is given to the following publication:''' </span><span style="font-family:georgia,serif;">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</span> |
| | + | {| class="wikitable" |
| | + | ![http://cmbn-navigator.uio.no/rat_hippocampus_atlas/ Rat Hippocampus Atlas application 2.0] |
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| | + | == <span style="font-family:georgia,serif;">Contributing laboratories</span> == |
| | + | <span style="font-family:georgia,serif;">'''Kavli Institute for Systems Neuroscience & Centre for the Biology of Memory''', </span><span style="font-family:georgia,serif;">Medical-Technical Research Centre, Norwegian University of Science and Technology, N - 7489 Trondheim, Norway </span> (<span style="font-family:georgia,serif;">http://www.ntnu.no/cbm/). '''People:''' Menno P. Witter</span> |
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| − | <div> | + | '''Neural Systems Laboratory''' (<span style="font-family:georgia,serif;">[http://www.nesys.uio.no/ http://www.nesys.uio.no]</span>), 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 |
| − | === Contributing laboratories: === | |
| − | </div>
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| − | Kavli Institute for Systems Neuroscience & Centre for the Biology of Memory
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| − | Medical-Technical Research Centre <br/>Norwegian University of Science and Technology <br/>N - 7489 Trondheim <br/>Norway <br/>[http://www.ntnu.no/cbm/ http://www.ntnu.no/cbm/]<br/><br/>Neural Systems and Graphics Computing Laboratory <br/>Institute of Basic Medical Sciences <br/>Department of Anatomy <br/>University of Oslo <br/>P.O. Box 1105 Blindern <br/>N - 0317 Oslo <br/>Norway <br/>[http://www.nesys.uio.no/ http://www.nesys.uio.no]
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| − | <div>
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| − | === ===
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| − | === Credits ===
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| − | </div>
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| − | NeSys and CMBN atlas development team:
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| − | Lisa J. Kjonigsen, M.Sc.<br/>Jan Olav Kjode, M.Sc.<br/>Ivar Andre Moene, M.Sc.<br/>Trygve B. Leergaard, M.D., Ph.D.<br/>Jan G. Bjaalie, M.D., Ph.D.<br/><br/>KI-CBM and Witter-group:<br/>Menno P. Witter, Ph.D. | |
| − | <div>
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| − | === ===
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| − | === Documentation ===
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| − | </div>
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| − | ''The Rat Hippocampus Atlas System:'' <br/>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 <br/><br/>''Hippocampal boundary definitions, ontology and nomenclature:''<br/>Boccara CN, Kjonigsen LJ, Hammer I, Bjaalie JG, Leergaard TB, Witter M.P. Manuscript in preparation <br/><br/>''Database architecture:''<br/>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
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| − | <div>
| + | == <span style="font-family:georgia,serif;">External links</span> == |
| − | === References for the index of structures === | + | <span style="font-family:georgia,serif;">[http://www.temporal-lobe.com The Hippocampal Connectome Project]</span> |
| − | </div>
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| − | Amaral DG, Scharfman HE, Lavenex P. 2007. The dentate gyrus: fundamental neuroanatomical organization (dentate gyrus for dummies) Prg Br Res163:3-22.<br/><br/>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.<br/><br/>Brodmann K. 1909. Vergleichende Lokalisationslehre der Grosshirnrinde in ihren Prinzipien dargestellt auf Grund des Zellenbauers. Leipzig.<br/><br/>Burwell RD. 2001. Borders and cytoarchitecture of the perirhinal and postrhinal cortices in the rat. J Comp Neurol 437(1):17-41.<br/><br/>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.<br/><br/>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.<br/><br/>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.<br/><br/>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. <br/><br/>Jaffe DB, Gutierrez R. 2007. Mossy fiber synaptic transmission: communication from the dentate gyrus to area CA3. Prg Br Res 163:109-132. <br/><br/>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. <br/><br/>Paxinos G, Watson C. 1998. The Rat Brain In Stereotaxic Coordinates: Academic Press. <br/><br/>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. <br/><br/>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. <br/><br/>Stephan H. 1975. Allocortex. Handbuch der Mikroskopischen Anatomie des Menschen. Berlin: Springer-Verlag.<br/><br/>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.<br/><br/>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.<br/><br/>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.<br/><br/>Witter MP, Amaral DG, Paxinos G. 2004. Hippocampal formation. The Rat Nervous System. San Diego, CA: Elsevier Academic Press. p 635-704. <br/><br/>Wyss JM. 1981. An autoradiographic study of the efferent connections of the entorhinal cortex in the rat. J Comp Neurol 199(4):495-512.
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| − | <div>
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| − | === Release notes === | + | == <span style="font-family:georgia,serif;">History</span> == |
| − | </div> | + | * <span style="font-family:georgia,serif;">2015-10 Transfer to new viewer platform. Release of version 2.0 running on Navigator 3.0.6</span> |
| − | Version 1.2<br/>- optimized the data upload to the viewer.
| + | * <span style="font-family:georgia,serif;">2011-03 Speed optimization. Release of version 1.2</span> |
| | + | * <span style="font-family:georgia,serif;">2011-01 Release of version 1.1 in conjunction with publication </span> |
| | + | * <span style="font-family:georgia,serif;">2010-06 Poster, 7th Forum for European Neuroscience 2010, Amsterdam, The Netherlands</span> |
| | + | * <span style="font-family:georgia,serif;">2009-11 Poster / demonstration, Society of Neuroscience conference in Chicago, USA</span> |
| | + | * <span style="font-family:georgia,serif;">2009-09 Poster / demonstration, 2nd INCF Congress of Neuroinformatics, Plzen, Czech Republic</span> |
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| − | Version 1.1<br/>- better support for Mozilla Firefox <br/>- some changes in the text <br/>- links are added in the structure descriptions
| + | == 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) |
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| + | == Contact == |
| | + | j.g.bjaalie@medisin.uio.no<span style="font-family:georgia,serif;"></span> |
| | + | [[Category:Atlas]] |
