Displaying results 1 - 20 out of 71 total results.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on December 20, 2013. A freely downloadable interactive diagram containing existing knowledge of hippocampal - parahippocampal connections in which any connection can be turned on or off at the level of cortical layers. It includes references for each connection. Project Goals: * To provide an overview of all known anatomical projections of the rat hippocampal - parahippocampal network. * To provide a graphical interface with which users can turn on or off any connections at regional level down to the level of cortical layers. * To make it easy to find references for a particular projection. Almost 1600 connections in the rat hippocampal - parahippocampal region are displayed.
A software package for automatic segmentation of hippocampal subfields in magnetic resonance imges. Given a pair of T1-weighted and T2-weighted images (the latter acquired using a protocol tuned for hippocampus imaging), ASHS will automatically label main subfields of the hippocampus, and some extra-hippocampal structures, using multi-atlas segmentation. The main method is described in the Yushkevich et al. 2011 Neuroimage paper (http://tinyurl.com/cffrp3p). * execution requires: Advanced Normalization Tools, FSL
Open-source turnkey software for automatic hippocampus segmentation. Its primary use is for delineating hippocampus in T1-weighted MRI images. AHEAD is developed by Jung W. Suh, Hongzhi Wang, Sandhitsu Das, Brian Avants, Philip Cook, John Pluta and Paul Yushkevich, and colleagues at the Penn Image Computing and Science Laboratory (PICSL) at the University of Pennsylvania.
An interactive reference atlas providing a systematic overview of cyto- and chemoarchectonical features 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. Features * 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 which differently stained neighboring sections can be interactively compared * Graphical overlay of substructures based on described boundary criteria * Bidirectional links between structure descriptions and image repository The atlas is based on histological material from an adult Long Evans rat, stained for NeuN, calbindin, and parvalbumin. 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. Re-use of data from this repository is allowed provided that reference is given to the publication.
This dataset contains T1-weighted MR images of 50 subjects, 40 of whom are patients with temporal lobe epilepsy and 10 are nonepileptic subjects. Hippocampus labels are provided for 25 subjects for training. The users may submit their segmentation outcomes for the remaining 25 testing images to get a table of segmentation metrics.
Atlas of segmented and normalized high-resolution postmortem MRI of the human hippocampus. Additional data (raw images) is available through the SCM link. It requires knowing how to use CVS.
Data files for a high resolution three dimensional (3D) structure of the rat hippocampus reconstructed from histological sections. The data files (supplementary data for Ropireddy et al., Neurosci., 2012 Mar 15;205:91-111) are being shared on the Windows Live cloud space provided by Microsoft. Downloadable data files include the Nissl histological images, the hippocampus layer tracings that can be visualized alone or superimposed to the corresponding Nissl images, the voxel database coordinates, and the surface rendering VRML files. * Hippocampus Nissl Images: The high resolution histological Nissl images obtained at 16 micrometer inter-slice distance for the Long-Evans rat hippocampus can be downloaded or directly viewed in a browser. This dataset consists of 230 jpeg images that cover the hippocampus from rostral to caudal poles. This image dataset is uploaded in seven parts as rar files. * Hippocampus Layer Tracings: The seven hippocampus layers ''ML, ''GC'', ''HILUS'' in DG and ''LM'', ''RAD'', ''PC'', ''OR'' in CA were segmented (traced) using the Reconstruct tool which can be downloaded from Synapse web. This tool outputs all the tracings for each image in XML format. The XML tracing files for all these seven layers for each of the above Nissl images are zipped into one file and can be downloaded. * Hippocampus VoxelDB: The 3D hippocampus reconstructed is volumetrically transformed into 16 micrometer sized voxels for all the seven layers. Each voxel is reported according to multiple coordinate systems, namely in Cartesian, along the natural hippocampal dimensions, and in reference to the canonical brain planes. The voxel database file is created in ascii format. The single voxel database file was split into three rar archive files. Please note that the three rar archive files should be downloaded and decompressed in a single directory in order to obtain the single voxel data file (Hippocampus-VoxelDB.txt). * 3D Surface Renderings: This is a rar archive file with a single VRML file containing the surface rendering of DG and CA layers. This VRML file can be opened and visualized in any VRML viewer, e.g. the open source software view3dscene. * 3D Hippocampus Movie: This movie contains visualization of the 3D surface renderings of CA (blue) and DG (red) inner and outer boundaries; neuronal embeddings of DG granule and CA pyramidal dendritic arbors; potential synapses between CA3b interneuron axon and pyramidal dendrite, and between CA2 pyramidal axon and CA pyramidal dendrites.
The long-term goals of my research are to understand the relationship between neuronal structure and function, and to elucidate the factors that affect neuronal morphology and function over the lifespan of the mammal. Currently we are examining 1) the effects of synaptic activity on neuronal development; 2) the effects of estrogen on neuronal morphology and on learning and memory; and, 3) the effects of aging on neuronal structure and function. We have focused our efforts on single neurons in the hippocampal formation, a region that is critical for certain forms of learning and memory in rodents and humans. From the portal, you may click on a cell in your region of interest to see the complete database of cells from that region. You may also explore the Neuron Database: * Comparative Electrotonic Analysis of Three Classes of Rat Hippocampal Neurons. (Raw data available) * Quantitative, three-dimensional analysis of granule cell dendrites in the rat dentate gyrus. * Dendritic Growth and Regression in Rat Dentate Granule Cells During Late Postnatal Development.(Raw data available) * A light and electron microscopic analysis of the mossy fibers of the rat dentate gyrus.
2D mouse brain atlas of high quality coronal Nissl- and myelin-stained sections with labels, 3D images of hippocampal formation and limited other brain structures. The data for this digital atlas are based on the Atlas of the Mouse Brain and Spinal Cord, authored by Richard L. Sidman, Jay. B. Angevine and Elizabeth Taber Pierce, published as a hard cover book by Harvard University Press in 1971 and currently out of print. C57BL/6J strain adult specimens were used in creating the atlas.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 29, 2013. Supplemental data for the paper Changes in mitochondrial function resulting from synaptic activity in the rat hippocampal slice, by Vytautas P. Bindokas, Chong C. Lee, William F. Colmers, and Richard J. Miller that appears in the Journal of Neuroscience June 15, 1998. You can view digital movies of changes in fluorescence intensity by clicking on the title of interest.
Software package designed to enable researchers with advanced tools for brain and image mapping. Many of the ANTS registration tools are diffeomorphic*, but deformation (elastic and BSpline) transformations are available. Unique components of ANTS include multivariate similarity metrics, landmark guidance, the ability to use label images to guide the mapping and both greedy and space-time optimal implementations of diffeomorphisms. The symmetric normalization (SyN) strategy is a part of the ANTS toolkit as is directly manipulated free form deformation (DMFFD). *Diffeomorphism: a differentiable map with differentiable inverse. In general, these maps are generated by integrating a time-dependent velocity field. ANTS Applications: * Gray matter morphometry based on the jacobian and/or cortical thickness. * Group and single-subject optimal templates. * Multivariate DT + T1 brain templates and group studies. * Longitudinal brain mapping -- special similarity metric options. * Neonatal and pediatric brain segmentation. * Pediatric brain mapping. * T1 brain mapping guided by tractography and connectivity. * Diffusion tensor registration based on scalar or connectivity data. * Brain mapping in the presence of lesions. * Lung and pulmonary tree registration. * User-guided hippocampus labeling, also of sub-fields. * Group studies and statistical analysis of cortical thickness, white matter volume, diffusion tensor-derived metrics such as fractional anisotropy and mean diffusion.
Anatomical atlases constructed by Computational Anatomy of Johns Hopkins University for analysis of shape vectors. The atlases were generated from segmented hippocampal and amygdala structures in acquired populations of children, adolescents and young adults in neuroimaging studies of major depression disorder (MDD) at Washington University at St Louis.
Virtual database currently indexing multiple connectivity databases including: * The Brain Architecture Management System (BAMS) - http://brancusi.usc.edu/bkms/ * Collations of Connectivity data on the Macaque brain (CoCoMac) - http://cocomac.org * BrainMaps - http://brainmaps.org/ * Connectome Wiki - http://www.connectome.ch * the Hippocampal-Parahippocampal table of Temporal-Lobe.com - http://www.temporal-lobe.com/ * Avian Brain Circuitry Database, http://www.behav.org/abcd/abcd.php These data come primarily from published work or expert opinion. It is likely that some differences in connectivity among brain regions may be due to differing opinion of brain region boundaries in addition to species differences. All data was fit from the source data to statements that have two connected regions, i.e., connection from and connection to with the region abbreviation first followed by the region full name. Thus, an afferent from hippocampus to cortex (in the source data) would be aligned to connection from cortex, connection to hippocampus. The connection strength was aligned from symbols and numbers into the following categories: heavy, moderate, weak, not detected, exists, and unknown. Publications are reported and links to PubMed have been added, where possible. All other information that was available and relevant from each source was concatenated into the notes column. The specifics of the alignment below: * For CoCoMac the projection strength was translated as follows: ** when l2_nif_0000_00022_cocomac_connectivity.density = ''''0'''' then ''''Not detected'''' ** when l2_nif_0000_00022_cocomac_connectivity.density = ''''1'''' then ''''Weak'''' ** when l2_nif_0000_00022_cocomac_connectivity.density = ''''2'''' then ''''Moderate'''' ** when l2_nif_0000_00022_cocomac_connectivity.density = ''''3'''' then ''''Heavy'''' ** when l2_nif_0000_00022_cocomac_connectivity.density = ''''X'''' then ''''Exists'''' * For BAMS database: ** lower (case when a.PROJECTION_STRENGTH like ''''strong'''' then ''''Heavy'''' ** when a.PROJECTION_STRENGTH like ''''very strong'''' then ''''Heavy'''' ** when a.PROJECTION_STRENGTH like ''''light/moderate'''' then ''''Moderate'''' ** when a.PROJECTION_STRENGTH like ''''moderate'''' then ''''Moderate'''' ** when a.PROJECTION_STRENGTH like ''''light'''' then ''''Weak'''' ** when a.PROJECTION_STRENGTH like ''''very light'''' then ''''Weak'''' ** when a.PROJECTION_STRENGTH like ''''moderate/strong'''' then ''''Heavy'''' ** when a.PROJECTION_STRENGTH like ''''not present'''' then ''''Not detected'''' * For BrainMaps: ** when l2_nif_0000_00093_brainmaps_connectivity.strength like ''''++++'''' then ''''Heavy'''' ** when l2_nif_0000_00093_brainmaps_connectivity.strength like ''''+++'''' then ''''Moderate'''' ** else ''''Unknown''''
A comprehensive library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. The tools include registration, atlases, diffusion MRI tools for parameter reconstruction and probabilistic taractography, and a viewer. Most of the tools can be run both from the command line and as GUIs (point-and-click graphical user interfaces). Several complementary brain atlases, integrated into FSLView and Featquery, allow viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. FSL includes the Harvard-Oxford cortical and subcortical structural atlases, Julich histological atlas, JHU DTI-based white-matter atlases, Oxford thalamic connectivity atlas, Talairach atlas, MNI structural atlas, and Cerebellum atlas. FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK.
Multidisciplinary research team devoted to the study of basic neuroscience with a specific interest in the description and generation of dendritic morphology, and in its effect on neuronal electrophysiology. In the long term, they seek to create large-scale, anatomically plausible neural networks to model entire portions of a mammalian brain (such as a hippocampal slice, or a cortical column). Achievements by the CNG include the development of software for the quantitative analysis of dendritic morphology, the implementation of computational models to simulate neuronal structure, and the synthesis of anatomically accurate, large scale neuronal assemblies in virtual reality. Based on biologically plausible rules and biophysical determinants, they have designed stochastic models that can generate realistic virtual neurons. Quantitative morphological analysis indicates that virtual neurons are statistically compatible with the real data that the model parameters are measured from. Virtual neurons can be generated within an appropriate anatomical context if a system level description of the surrounding tissue is included in the model. In order to simulate anatomically realistic neural networks, axons must be grown as well as dendrites. They have developed a navigation strategy for virtual axons in a voxel substrate.
Behavioral and imaging data from about 120 participants aged 18-89. Data were collected as part of a grant to use high-resolution imaging and advanced behavioral tasks to understand how aging affects the hippocampus and how this is related to age-related cognitive decline. The full dataset includes traditional neuropsycholgical measures, hippocampal-specific behavioral measures, whole-brain DTI, high-resolution DTI of the medial temporal lobes, and structural MRI including segmentation of grey/white/CSF, of cortical regions and of hippocampal subfields.
This database contains morphologies of hippocampal pyramidal cells and interneurons (in Neurolucida, NEURON, and pdf formats) as well as data recorded from those cells. Sponsors:This work was supported by grants from the NIH (T32-GM-08061 to T.J.M., F32-NS-10532 to N.L.G., and R01-NS35180 and R01-NS 46064 to N.S. and W.L.K.) and NSF (IGERT fellowship to Y.K.). NS46064 is part of the NSF/NIH Collaborative Research in Computational Neuroscience Program
A database of genes concerning adult neurogenesis mapped to cell types and processes that have been curated from the literature. In its present state, the database is restricted to neurogenesis in the hippocampus. Although the literature contains data from several species, for the sake of uniformity, all genes in the database are reported as the mouse homologue. The resource also contains a comprehensive survey of the literature to annotate the results of all published reports on gene function in adult hippocampal neurogenesis (257 manuscripts covering 228 genes) to the appropriate terms in our ontology The Mammalian Neurogenesis Gene Ontology was designed and curated by Gerd Kempermann and Rupert Overall The database was created by Maciej Paszkowski-Rogacz and Rupert Overall. Each entry corresponds to a discrete effect of a gene as reported in a single study. Thus a study may report multiple effects for one gene, and several studies may report data for the same gene.
A 3D stereoscopic (anaglyph method) full brain functional connectivity atlas created using a parcellation atlas published by Craddock et al. (2012). Using 3D Slicer 3.6.3 and the two hundred Region of Interest (ROI) version of the Craddock atlas, 200 grayscale surface models were created using a z-stat threshold > 2.3, and each surface model was processed with a surface decimation algorithm, smoothed with the Taubin algorithm and without surface normals. For improved visualization of the functional connectivity networks and their relative anatomical position, the surface model of five subcortical anatomical structures (corpus callosum, bilateral caudate, pallidum, putamen, thalamus, amygdala and hippocampus) were included in SAIBN. These surfaces were created with 3D Slicer using the segmentation computed with Freesurfer v. 5.1. The viewer should use red-cyan glasses to see the 3D stereoscopic effect using 3D Slicer (version 3.6.3, http://www.slicer.org/pages/Special:SlicerDownloads).
A database of virtually generated anatomically plausible neurons for several morphological classes, including cerebellar Purkinje cells, hippocampal pyramidal and granule cells, and spinal cord motoneurons. It presently contains 542 cells. In the trade neurons collection the database contains an amaral cell archive, neuron morpho reconstructions, and mouse alpha motoneurons. Their collection of generated neurons include motoneurons, Purkinje cells, and hippocampal pyramidal cells.