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http://cns.iaf.cnrs-gif.fr/alain_geometries.html

Database that provides 3-dim reconstructions of thalamic and neocortical neurons. These cells were reconstructed from 80-micron serial sections using a computerized tracing system, as well as a Neurolucida tracing system. The dendritic morphology and diameters were reconstructed in 3-dim using a X 100 objective and correction for tissue shrinkage was included, leading to a theoretical accuracy of 0.1 microns on dendritic diameters. The morphology and the modeling of these cells is described in the references given for each cell. The NEURON geometry of these cells are also available. Anyone is welcome to use these geometries in models.

Proper citation: Database of Cellular Morphologies (RRID:SCR_001708) Copy   

•   Source: SciCrunch Registry

http://www.neuronland.net/NLMorphologyConverter/NLMorphologyConverter.html

NLMorphologyConverter is a simple command-line program for converting between the various neuron morphology data formats which are used to describe the three-dimensional physical branching structure of biological neurons. The aim is to provide coverage of all formats, old and new, in which data is available online, and/or which are supported by free and commercial software packages (e.g. software for neuron reconstruction, generation, simulation, visualization, and analysis of neuron morphology). Permission is granted for this software to be freely copied. Main Features Currently 21 different morphology file formats fully or partially supported. Automatic detection of input file format. Faithful reproduction of output file formatting. Many command line options for manipulating the imported data Intensively tested using over 10000 publicly available morphology data files. Sponsors. This software is supported by NeuronLand.

Proper citation: Neuronland: NLMorphologyConverter (RRID:SCR_001817) Copy   

•   Source: SciCrunch Registry

http://penglab.janelia.org/proj/v3d/V3D/About_V3D.html

V3D is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. It also provides many unique functions, is Open Source, supports a very simple and powerful plugin interface and thus can be extended & enhanced easily. V3D-Neuron is a powerful 3D neuron reconstruction, visualization, and editing software built on top of V3D. Both V3D and V3D-Neuron have recently been published in Nature Biotechnology (April, 2010), and Highlighted in Nature Methods (May, 2010), and Science News (April, 2010), etc. V3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. This makes V3D suitable for various bioimage informatics applications, and a nice platform to develop new 3D image analysis algorithms for high-throughput processing. In short, V3D streamlines the workflow of visualization-assisted analysis. In the latest V3D development, it can render 5D (spatial-temporal) data directly in 3D volume-rendering mode; it supports convenient and interactive local and global 3D views at different scales. It even has a Matlab file IO toolbox. A user can now write his/her own plugins to take advantage of the V3D platform very easily.

Proper citation: V3D (RRID:SCR_008646) Copy   

•   Source: SciCrunch Registry

http://neurospaces.sourceforge.net/

The GEneral NEural SImulation System (GENESIS) started as a very advanced software package in the late eighties, for biologically accurate neuronal modeling. Besides being used as a neuronal simulator, it was also applied to various domains outside computational neuroscience. The Neurospaces project is a departure from the monolithic software system design of the original GENESIS system. It is a development center for software components of computational neuroscience simulators. There are many advantages of developing independent software components: - Interfacing to an individual component is obviously more simple than interfacing to a do-all monolithic system. The compartmental solver developed for the Neurospaces project can be connected to Matlab fi. - It simplifies the individual components and encourages other developers to get involved. - It allows for separate testing of the components. More than 1000 use case tests been defined for these software components, including integration tests. - Integrating different component, gives different flavours of the same simulator, and enhances the user experienced consistency when doing multilevel simulations. - A component based software system avoids vendor-lockin. Its life-cycle is more smooth than that of a monolithic system, because software components can be upgraded one at a time. The Neurospaces project embodies many software components that all have been developed in full isolation. The core of the most important components is finished. The current development focus has shifted from component integration to the support of specific use case with an emphasis on single neuron modeling. This is a list of software components that have been developed or are under construction. Together, these tools give the core for the upcoming GENESIS 3 GUI. - GShell: a simple replacement for the Genesis 2 SLI. - Heccer: a fast compartmental solver, a backend. - Dash: a second compartmental solver faster than Heccer, for simpler models. - Neurospaces Model Container: provides a solver independent internal and external storage format for models. - Discrete event system: consists of a discrete event distributor and queuer. This is used for abstract modeling of an action potential traveling inside an axon as a ''discrete event''. - SSP: a flexible scheduler written in perl, to run simulations with the Neurospaces model container and Heccer. - The Neurospaces Studio: some tools for graphical browsing and command line usage. - The Genesis Script Language Interface: a scripting component that reads Genesis 2 scripts and feeds them to the Neurospaces model container. - The Geometry Library is a general purpose geometry library, with some essential geometrical operators, not commonly found in other geometrical libraries. - Using the Geometry Library, a Reconstruct Interface has been written. This interface supports the conversion of contours exported by the Reconstruct software to the Neurospaces declarative NDF format. - The Neurospaces project browser for browsing projects and inspecting simulation results. - The Installer package contains the Neurospaces installer and developer tools that have emerged from developing Neurospaces software components. - The Configurator package contains configuration utilities for the other tools. It is not needed for the other tools to work properly. Rather, it allows to set up model database and simulation servers in a convenient way. - There is also a Neurospaces blog and a wiki at googlecode for the Neurospaces project, with information for developers.

Proper citation: GEneral NEural SImulation System: The Neurospaces Project (RRID:SCR_008035) Copy   

•   Source: SciCrunch Registry

http://celltypes.brain-map.org

Database of neuronal cell types based on multimodal characterization of single cells to enable data-driven approaches to classification. It includes data such as electrophysiology recordings, imaging data, morphological reconstructions, and RNA and DNA sequencing data.

Proper citation: Allen Cell Types Database (RRID:SCR_014806) Copy   

•   Source: SciCrunch Registry

http://icg.neurotheory.ox.ac.uk/

A database that provides a comprehensive and quantitative assay of ion channel models currently available in the neuroscientific modeling community. Specifically, it contains analyses of the ion channel models from NEURON. The database quantifies the similarity in kinetics between models using a series of standardized voltage clamp simulation protocols and subsequent cluster analysis. Citation links and duplications of channels, along with similarity of kinetics between channel models, are combined into genealogical trees and dendrograms that are searchable through the ICG web interface. ICG also experimentally recorded current traces and provides tools for uploading new channel models.

Proper citation: IonChannelGenealogy (RRID:SCR_014194) Copy   

•   Source: SciCrunch Registry

https://github.com/ambertk/NeuronRegistryCorpus

Annotated document corpus, containing PubMed identifiers and text spans of documents reviewed for consideration for the Neuron Registry by Kyle H. Ambert, PhD.

Proper citation: Neuron Registry Annotated Corpus (RRID:SCR_002443) Copy   

•   Source: SciCrunch Registry

http://hippocampome.org

A curated knowledge base of the circuitry of the hippocampus of normal adult, or adolescent, rodents at the mesoscopic level of neuronal types. Knowledge concerning dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex is distilled from published evidence and is continuously updated as new information becomes available. Each reported neuronal property is documented with a pointer to, and excerpt from, relevant published evidence, such as citation quotes or illustrations. Please note: This is an alpha-testing site. The content is still being vetted for accuracy and has not yet undergone peer-review. As such, it may contain inaccuracies and should not (yet) be trusted as a scholarly resource. The content does not yet appear uniformly across all combinations of browsers and screen resolutions.

Proper citation: Hippocampome.org (RRID:SCR_009023) Copy   

•   Source: SciCrunch Registry

http://www.oumedicine.com/oklahoma-clinical-and-translational-science-institute/research-resources/ndri/ndri-dorsal-root-ganglia-program

NDRI actively recovers a diverse range of normal and diseased human tissues for biomedical researchers. We have recently implemented a new program to make human dorsal root ganglia (DRG) available for your research studies. The dorsal root ganglia contain cell bodies of afferent (inbound) neurons, and transmit pain and temperature sensations from the body. DRGs from C5 through L5 regions will be available. DRGs will be recovered under operating room conditions with a low post mortem interval to preservation and can be shipped at 4 degrees C, snap-frozen or fixed. Detailed medical-social history information is provided for each donor. If you are interested in obtaining these specimens, please contact me at your earliest convenience. Current NDRI researchers can immediately request these samples. Non-NDRI researchers need to submit a researcher application. * The program provides a reliable source of human DRG neurons that can be utilized for: Electrophysiology analysis, Live cell imaging studies * Low PMI yields high quality samples that are suitable for rigorous molecular applications: Deep sequencing analysis, In situ hybridization, Micro-array analysis * DRGs from C5 through L5 regions will be available. * The tissue fee for this program is 500 dollars per DRG * Customizable-- the researcher determines the DRG location and quantity that is needed for their research.

Proper citation: NDRI Dorsal Root Ganglia Program (RRID:SCR_005043) Copy   

•   Source: SciCrunch Registry

http://catmaid.org/

A toolkit designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface enables synchronized navigation through multiple registered datasets even at vastly different scales such as in comparisons between optical and electron microscopy. The interface is inspired by GoogleMaps, with which it shares basic navigation concepts, enhanced to allow the exploration of 3D biological image data acquired by optical or physical sectioning microscopy techniques. The interface enables seamless sharing of regions of interest through bookmarks and synchronized navigation through multiple registered data sets. With massive biological image data sets it is unrealistic to create a sustainable centralized repository. A unique feature of CATMAID is its partially decentralized architecture where the presented image data can reside on any Internet accessible server and yet can be easily cross-referenced in the central database. In this way no image data are duplicated and the data producers retain full control over their images. CATMAID is intended to serve as data sharing platform for biologists using high-resolution imaging techniques to probe large specimens. Any high-throughput, high-content imaging project such as gene expression pattern screens would benefit from the interface for data sharing and annotation. Features: * Fast terabyte-scale image data browsing * Collaborative microcircuit reconstruction and annotation * Flexible hierarchical semantic annotation * Multiple linked image stack display * Neuron Catalog * SVG and WebGL-based neuronal morphology viewer * Open source software

Proper citation: CATMAID (RRID:SCR_006278) Copy   

•   Source: SciCrunch Registry

http://neuroelectro.org

A database of elecrophysiological properties text-mined from the biomedical literature as a function of neuron type. Specifically, NeuroElectro seeks to extract information about the electrophysiological properties (e.g. resting membrane potentials and membrane time constants) of diverse neuron types from the existing literature and place it into a centralized database. There are 252 neurons currently available, with the naming convention established in NeuroLex.

Proper citation: neuroelectro (RRID:SCR_006274) Copy   

•   Source: SciCrunch Registry

http://www.histology-world.com/photoalbum/index.php?cat=7

This website contains a lot of images and slides of the nervous system. Most images are of the central nervous system histology and peripheral nervous system histology. Computation Neuroscience

Proper citation: Histology World: Nervous System Histology (RRID:SCR_000762) Copy   

•   Source: SciCrunch Registry

https://www.utsouthwestern.edu/education/medical-school/departments/neurology/research/microscopy-facility/

Core suited to advance study of traumatic brain injury, as well as other neurological and psychiatric disorders.Utilizes microscopy strategies to evaluate neuropathology across micro-, meso-, and macro-scales of inquiry. Provides access to microscopes including TissueCyte 1000 multi-photon microscopes,Hamamatsu NanoZoomer 2.0-HT,Zeiss Axioscan.Z1. Offers access to fluorescence stereomicroscope and upright microscope, both with digital cameras, as well as sectioning equipment (cryostat, microtome, and vibrotome). Provide computer available for use running MicroBrightField Stereo Investigator and Neurolucida software packages for offline stereological analysis, neuron tracing, and 3D rendering of large, whole-brain datasets.

Proper citation: Texas University Southwestern Medical Center Whole Brain Microscopy Core Facility (RRID:SCR_017949) Copy   

•   Source: SciCrunch Registry