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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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University of Texas at San Antonio Laboratory of Professor Brenda Claiborne Resource Report Resource Website 1+ mentions |
University of Texas at San Antonio Laboratory of Professor Brenda Claiborne (RRID:SCR_008064) | UTSA Claiborne Lab | data or information resource, laboratory portal, data set, organization portal, portal | 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. | neuronal, structure, synaptic activity, rodent, human, neuron, neuronal morphology, synapse, neuronal development, learning, memory, estrogen, hippocampus, hippocampal formation, mammal, cell | has parent organization: University of Texas at San Antonio; Texas; USA | Aging | nif-0000-10481 | SCR_008064 | USTA Laboratory of Professor Brenda Claiborne | 2025-05-20 11:12:19 | 1 | |||||||
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Cambridge Neuroscience Department Resource Report Resource Website 1+ mentions |
Cambridge Neuroscience Department (RRID:SCR_008649) | data or information resource, organization portal, portal, department portal | This portal provides information about the neuroscience department at the University of Cambridge. Cambridge has a strong tradition in neuroscience having been host to the first analyses of neural signaling in the 1930s, determined the mechanisms of neuronal firing in the 1950s, and heralded some of the early theoretical approaches to the functions of neural circuitry in the 1960s. Neuroscience continues to grow at Cambridge, with an impressive record of achievement in multidisciplinary research. | education, analysis, circuitry, department, graduate, mechanism, neural, neuron, neuronal, neuroscience, research, signaling, theoretical, undergraduate | has parent organization: University of Cambridge; Cambridge; United Kingdom | nif-0000-33002 | SCR_008649 | Cambridge Neuroscience | 2025-05-20 11:12:53 | 1 | |||||||||
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Brain Facts Resource Report Resource Website |
Brain Facts (RRID:SCR_008788) | Brain Facts | data or information resource, training material, narrative resource, book | Brain Facts is a 74-page primer on the brain and nervous system, published by SfN. Designed for a lay audience as an introduction to neuroscience, Brain Facts is also a valuable educational resource used by high school teachers and students who participate in Brain Awareness Week. The 2008 edition updates all sections and includes new information on brain development, learning and memory, language, neurological and psychiatric illnesses, potential therapies, and more. Download the full book (PDF) or download individual sections. All downloads are PDFs. Educators, request a copy of the Brain Facts book (paperback or CD) - contact BAW@SfN.org. | k-12, brain, nervous system, brain development, learning, memory, language, neurological illness, psychiatric illness, therapy, movement, sleep, stress, neuron, sensation, perception, neuroethics | has parent organization: Society for Neuroscience | Aging | nlx_144227 | SCR_008788 | Brain Facts - A Primer on the Brain and Nervous System | 2025-05-20 11:12:57 | 0 | |||||||
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NEuronMOrphological analysis tool Resource Report Resource Website 1+ mentions |
NEuronMOrphological analysis tool (RRID:SCR_006304) | NEMO | image analysis software, software resource, image processing software, software application, data processing software | Software to handle and process large numbers of optical microscopy image files of neurons in culture or slices in order to automatically run batch routines, store data and apply multivariate classification and feature extraction using 3-way principal component analysis (PCA). This freeware for semi automated quantitative and dynamic analysis of neuron morphometry incorporates the most important microstructural quantification methods, such as fractal and sholl analysis with statistical and classification tools to provide an integrated image processing environment which enables fast and easy feature identification. It includes: * Friendly interactive graphical user interface * Image pre-processing * Morphological analysis * Topological analysis * Cell counting * 3-way PCA analysis (also available as an ImageJ plugin) * Plot of variables Sequential images of labeled or unlabelled neurons or tissue slices can be uploaded batch-wise in order to create a 3 axis (time, image coordinate) data base and a datamatrix of variables for 3-way Principal Component Analysis*. | morphometric analysis, neuron, morphology, principal component analysis, image pre-processing, neuron reconstruction, morphological analysis, neuron counting, neuron morphology, image processing, morphometrics, 3-way principal component analysis, topological analysis | has parent organization: University of Pisa; Pisa; Italy | Open-source | nlx_151981 | SCR_006304 | NEuronMOrphological analysis tool NEMO, NEMO (NEuron MOrphological analysis tool) | 2025-05-20 11:11:03 | 5 | |||||||
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General Neural Simulation System Resource Report Resource Website 100+ mentions |
General Neural Simulation System (RRID:SCR_006316) | GENESIS | data or information resource, simulation software, source code, software library, training material, software resource, narrative resource, data set, software toolkit, software application | General purpose simulation platform developed to support the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, simulations of large networks, and systems-level models. As such, GENESIS, and its version for parallel and networked computers (PGENESIS) was the first broad scale modeling system in computational biology to encourage modelers to develop and share model features and components. User contributed GENESIS models and simulations are available. You may to contribute a model or simulation. Educational tutorials for instruction in both neurobiology and computational methods have been developed. These tutorials and GENESIS are now being widely used in graduate and undergraduate instruction. These uses include full semester courses in computational neuroscience or neural modeling, short intensive courses or workshops, an option for a course project, and short units on computational neuroscience within courses on artificial neural nets. They also have a repository of user-contributed tutorials and materials for use in neuroscience education. If you have course descriptions, syllabi, exercises, tutorials, or short HOWTO documents, please upload them to Education. | electrophysiology, computer, in silico, model, modeling, simulation, neural system, network, neurobiology, computational neuroscience, neural modeling, subcellular, biochemical reaction, neuron, channel, cell, FASEB list |
is related to: GENESIS Neural Database and Modelers Workspace is related to: ChannelDB is related to: Topographica has parent organization: University of Texas at San Antonio; Texas; USA is parent organization of: The Book of GENESIS |
The community can contribute to this resource | nif-0000-00091 | http://www.nitrc.org/projects/genesis http://genesis-sim.org/GENESIS/ | SCR_006316 | GENESIS, GENESIS Simulator, GEneral NEural SImulation System | 2025-05-20 11:11:04 | 372 | ||||||
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SpiCoDyn Resource Report Resource Website 1+ mentions |
SpiCoDyn (RRID:SCR_015744) | source code, software resource, data analysis software, software application, data processing software | Software for the analysis of multi-site neuronal spike signals. SPICODYN processes electrophysiological signals, focusing on spiking and bursting dynamics and functional-effective connectivity analysis. | spike signal, neuron, multi-site neuronal spike signal, eeg, electrophysiology, brain imaging | Open source, Available for download | SCR_015744 | 2025-05-20 11:16:21 | 2 | |||||||||||
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SIGEN Resource Report Resource Website 1+ mentions |
SIGEN (RRID:SCR_016284) | segmentation software, image reconstruction software, image analysis software, software resource, software application, data processing software | Software to extract and trace neuronal structure from confocal laser scanning microscope images. It performs the automatic reconstruction of neurons for image stacks and can generate compartmental models of neurons as swc file format data. | segmentation, neuron, confocal, laser, scan, microscopy, reconstruction, swc, confocal, laser, microscopy | is related to: ParaView | Free, Available for download | SCR_016284 | SImulation of Geometrical and Electrical properties of Neuron, SIGEN: SImulation of Geometrical and Electrical properties of Neuron | 2025-05-20 11:16:43 | 2 | |||||||||
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NeuriteTracer Resource Report Resource Website 10+ mentions |
NeuriteTracer (RRID:SCR_014146) | software resource, data acquisition software, software application, data processing software | A set of ImageJ plugins for fully automated measurement of neurite outgrowth in fluorescence microscopy images of cultured neurons. The plugin analyzes fluorescence microscopy images of neurites and nuclei of dissociated cultured neurons. Given user-defined thresholds, the plugin counts neuronal nuclei, and traces and measures neurite length. NeuriteTracer accurately measures neurite outgrowth from cerebellar, DRG and hippocampal neurons. | plugin, data acquisition software, neurite outgrowth, fluorescence microscopy image, neuron |
is used by: ImageJ is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: McGill University; Montreal; Canada |
PMID:17936365 | Availalble to the research community | http://fournierlab.mcgill.ca/styled-6/NeuriteTracer.html | SCR_014146 | 2025-05-20 11:15:26 | 37 | ||||||||
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SenseLab Resource Report Resource Website 10+ mentions |
SenseLab (RRID:SCR_007276) | SenseLab | data or information resource, organization portal, portal, database | The SenseLab Project is a long-term effort to build integrated, multidisciplinary models of neurons and neural systems. It was founded in 1993 as part of the original Human Brain Project, which began the development of neuroinformatics tools in support of neuroscience research. It is now part of the Neuroscience Information Framework (NIF) and the International Neuroinformatics Coordinating Facility (INCF). The SenseLab project involves novel informatics approaches to constructing databases and database tools for collecting and analyzing neuroscience information, using the olfactory system as a model, with extension to other brain systems. SenseLab contains seven related databases that support experimental and theoretical research on the membrane properties: CellPropDB, NeuronDB, ModelDB, ORDB, OdorDB, OdorMapDB, BrainPharmA pilot Web portal that successfully integrates multidisciplinary neurocience data. | neuron, model, olfactory system, brain, disease, neuronal, olfactory |
is related to: Neuroscience Information Framework is related to: International Neuroinformatics Coordinating Facility has parent organization: Yale University; Connecticut; USA is parent organization of: SimToolDB |
Aging | Human Brain Project ; Multidisciplinary University Research Initiative ; NIMH ; NIA ; NICD ; NINDS ; NIDCD RO1 DC 009977 |
nif-0000-00017 | SCR_007276 | SenseLab Project, The SenseLab Project | 2025-05-20 11:11:46 | 41 | ||||||
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Neuroscience Gateway Resource Report Resource Website 10+ mentions |
Neuroscience Gateway (RRID:SCR_008915) | NSG | data or information resource, portal, project portal, software resource | Web portal that allows free access to supercomputing resources for large scale modeling and data processing. Portal facilitates access and use of National Science Foundation (NSF) High Performance Computing (HPC) resources by neuroscientists. | Large, scale, modeling, data, computing, neuroscience, neuron, BRAIN Initiative |
is recommended by: BRAIN Initiative lists: ModelRun is related to: XSEDE - Extreme Science and Engineering Discovery Environment is related to: NEURON is related to: GENESIS Neural Database and Modelers Workspace has parent organization: San Diego Supercomputer Center has parent organization: Neuroscience Information Framework has parent organization: Yale School of Medicine; Connecticut; USA |
NSF 1458840; NSF 1458495; BBSRC N005236; NIBIB R01 EB023297; NSF 1339856; NSF 1146949 |
Free, Freely available | nlx_151553, SCR_015767 | http://www.nitrc.org/projects/nsg/ | SCR_008915 | Neuroscience Gateway - A Portal for Computational Neuroscience, Neuroscience Gateway, Neuroscience Gateway (NSG) Portal | 2025-05-20 11:12:59 | 23 | |||||
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BarensLab Mini-Atlas Resource Report Resource Website 1+ mentions |
BarensLab Mini-Atlas (RRID:SCR_021115) | data or information resource, mni atlas, reference atlas, atlas | Phenotypic variation of transcriptomic cell types in mouse motor cortex.Repository contains analysis code and preprocessed data.Data includes exonic and intronic gene counts, extracted electrophysiological features, extracted morphological features and z-profiles. Datasets with recorded at room temperature and recorded at physiological temperature. | Phenotypic variation, transcriptomic cell types, mouse motor cortex, morpho-electric phenotypes, mouse primary motor cortex, analysis code, preprocessed data, exonic gene counts, intronic gene counts, extracted electrophysiological features, extracted morphological features, z-profiles, raw data, cellular taxonomy, neuron, morphological reconstruction | is related to: BICCN | DOI:10.1101/2020.10.19.343129v1 | Free, Freely available | SCR_021115 | 2025-05-20 11:18:13 | 3 | |||||||||
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Microns Explorer Resource Report Resource Website 10+ mentions |
Microns Explorer (RRID:SCR_021678) | data or information resource, portal, topical portal | Portal to release connectivity and functional imaging data collected by consortium of laboratories led by groups at Allen Institute for Brain Science, Princeton University, and Baylor College of Medicine, with support from broad array of teams, coordinated and funded by IARPA MICrONS program. Data include large scale electron microscopy based reconstructions of cortical circuitry from mouse visual cortex, with corresponding functional imaging data from those same neurons. | Connectome, mouse, cortex, electron microscopy, functional imaging data, cortical circuitry reconstruction, neuron |
is related to: Allen Institute for Brain Science is related to: Princeton University; New Jersey; USA is related to: Baylor College of Medicine; Houston; Texas |
IARPA MICrONS | Free, Freely available | SCR_021678 | MICrONS Explorer | 2025-05-20 11:18:30 | 10 | ||||||||
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Open Source Brain Resource Report Resource Website 10+ mentions |
Open Source Brain (RRID:SCR_001393) | OSB | data or information resource, service resource, database, storage service resource, data repository | A resource for sharing and collaboratively developing computational models of neural systems. While models can be submitted and developed in any format, the use of open standards such as NeuroML and PyNN is encouraged, to ensure transparency, modularity, accessibility and cross simulator portability. OSB will provide advanced facilities to analyze, visualize and transform models in these formats, and to connect researchers interested in models of specific neurons, brain regions and disease states. Research themes include: Basal ganglia modelling, Cerebellar Granule cell modelling, Cerebellar modelling, Hippocampal modelling, Neocortical modelling, Whole brain models. Additional themes are welcome. | model, neuroml, pynn, computational model, neural system, neuron, disease, data analysis service, visualization, 3d explorer, network, ion channel distribution, ion channel, microcircuit |
uses: PyNN uses: NeuroML is used by: NIF Data Federation is listed by: Integrated Models is related to: neuroConstruct is related to: NWB Explorer is related to: Allen Institute for Brain Science has parent organization: University College London; London; United Kingdom |
Wellcome Trust | Open unspecified license, The community can contribute to this resource | nlx_152590 | SCR_001393 | OpenSourceBrain | 2025-05-20 11:07:56 | 25 | ||||||
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Neurolucida Resource Report Resource Website 1000+ mentions |
Neurolucida (RRID:SCR_001775) | data visualization software, software resource, data analysis software, software application, data processing software | Neurolucida is advanced scientific software for brain mapping, neuron reconstruction, anatomical mapping, and morphometry. Since its debut more than 20 years ago, Neurolucida has continued to evolve and has become the worldwide gold-standard for neuron reconstruction and 3D mapping. Neurolucida has the flexibility to handle data in many formats: using live images from digital or video cameras; stored image sets from confocal microscopes, electron microscopes, and scanning tomographic sources, or through the microscope oculars using the patented LucividTM. Neurolucida controls a motorized XYZ stage for integrated navigation through tissue sections, allowing for sophisticated analysis from many fields-of-view. Neurolucidas Serial Section Manager integrates unlimited sections into a single data file, maintaining each section in aligned 3D space for full quantitative analysis. Neurolucidas neuron tracing capabilities include 3D measurement and reconstruction of branching processes. Neurolucida also features sophisticated tools for mapping delineate and map anatomical regions for detailed morphometric analyses. Neurolucida uses advanced computer-controlled microscopy techniques to obtain accurate results and speed your work. Plug-in modules are available for confocal and MRI analysis, 3D solid modeling, and virtual slide creation. The user-friendly interface gives you rapid results, allowing you to acquire data and capture the full 3D extent of neurons and brain regions. You can reconstruct neurons or create 3D serial reconstructions directly from slides or acquired images, and Neurolucida offers full microscope control for brightfield, fluorescent, and confocal microscopes. Its added compatibility with 64-bit Microsoft Vista enables reconstructions with even larger images, image stacks, and virtual slides. Adding the Solid Modeling Module allows you to rotate and view your reconstructions in real time. Neurolucida is available in two separate versions Standard and Workstation. The Standard version enables control of microscope hardware, whereas the Workstation version is used for offline analysis away from the microscope. Neurolucida provides quantitative analysis with results presented in graphical or spreadsheet format exportable to Microsoft Excel. Overall, features include: - Tracing Neurons - Anatomical Mapping - Image Processing and Analysis Features - Editing - Morphometric Analysis - Hardware Integration - Cell Analysis - Visualization Features Sponsors: Neurolucida is supported by MBF Bioscience. | electron microscope, fluorescent, 3d mapping, anatomical, brian, brightfield, camera, confocal, digital, hardware, mapping, microscope, morphometry, neuron, reconstruction, scanning tomographic, software, tissue, virtual, video, image | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:2224829 | nif-0000-10294 | http://www.nitrc.org/projects/neurolucida | http://www.mbfbioscience.com/neurolucida/neurolucida | SCR_001775 | MBF Neurolucida | 2025-05-20 11:08:09 | 3162 | ||||||
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GENSAT at NCBI - Gene Expression Nervous System Atlas Resource Report Resource Website 1+ mentions |
GENSAT at NCBI - Gene Expression Nervous System Atlas (RRID:SCR_003923) | NCBI GENSAT Database | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 19, 2012. Due to budgetary constraints, the National Center for Biotechnology Information (NCBI) has discontinued support for the NCBI GENSAT database, and it has been removed from the Entrez System. The Gene Expression Nervous System Atlas (GENSAT) project involves the large-scale creation of transgenic mouse lines expressing green fluorescent protein (GFP) reporter or Cre recombinase under control of the BAC promoter in specific neural and glial cell populations. BAC expression data for all the lines generated (over 1300 lines) are available in online, searchable databases (www.gensat.org and the Database of GENSAT BAC-Cre driver lines). If you have any specific questions, please feel free to contact us at info_at_ncbi.nlm.nih.gov The GENSAT project aims to map the expression of genes in the central nervous system of the mouse, using both in situ hybridization and transgenic mouse techniques. Search criteria include gene names, gene symbols, gene aliases and synonyms, mouse ages, and imaging protocols. Mouse ages are restricted to E10.5 (embryonic day 10.5), E15.5 (embryonic day 15.5), P7 (postnatal day 7), and Adult (adult). The project focuses on two techniques * Evaluation of unmodified mice lines for expression of a given gene using radiolabelled riboprobes and in-situ hybridization. * Creation of transgenic mice lines containing a BAC construct that expresses a marker gene in the same environment as the native gene | mouse, central nervous system, neuron, transgenic mouse, transgenic mouse line, cell line, in-situ hybridization, gene expression, embryonic, postnatal, adult, radiolabelled riboprobe, bac, gold standard |
has parent organization: NCBI is parent organization of: Retina Project |
NINDS | PMID:23457350 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02905 | http://www.ncbi.nlm.nih.gov/projects/gensat/ | SCR_003923 | 2025-05-20 11:09:35 | 3 | |||||
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Frozen Noise Resource Report Resource Website 1+ mentions |
Frozen Noise (RRID:SCR_016558) | software resource, data analysis software, software toolkit, software application, data processing software | Software analysis tools for electrophysiological somatosensory cortex databank. Allows to estimate the information content of spiking in single neuron resolution. It accompanies the open source intracellular recording database by Lantyer and colleagues. | electrophysiological, somatosensory, cortex, estimate, spiking, single, neuron, resolution | is related to: MATLAB | Free, Available for download, Freely available | SCR_016558 | 2025-05-20 11:16:48 | 1 | ||||||||||
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NeuroAnatomy Toolbox Resource Report Resource Website 1+ mentions |
NeuroAnatomy Toolbox (RRID:SCR_016716) | nat, NAT | image analysis software, data visualization software, software resource, data analysis software, software application, data processing software | Software R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons in the context of 3D brain structures. | biological, image, data, visualization, analysis, tracing, single, neuron, 3D, structure, brain |
is listed by: OMICtools is listed by: CRAN is related to: R Project for Statistical Computing is related to: elmr has parent organization: University of Cambridge; Cambridge; United Kingdom |
DOI:10.5281/zenodo.10171 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/nat/index.html |
SCR_016716 | NeuroAnatomy Toolbox, neuroanatomy toolbox, Neuro Anatomy Toolbox, neuro anatomy toolbox | 2025-05-20 11:16:52 | 5 | ||||||
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NeuroRD Resource Report Resource Website 10+ mentions |
NeuroRD (RRID:SCR_014769) | simulation software, software resource, software application | Stochastic reaction-diffusion simulator in Java which is used for simulating neuronal signaling pathways. | simulation software, simulator, java, neuronal signaling pathway, neuron | HFSP ; NIMH K21-MH01141; NSF IBN 0077509; CRCNS program R01 AA16022; CRCNS program AA18066 |
Available for download | https://github.com/neurord/stochdiff/releases | SCR_014769 | 2025-05-20 11:15:37 | 13 | |||||||||
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PCSIM Resource Report Resource Website 1+ mentions |
PCSIM (RRID:SCR_014770) | simulation software, software resource, software application | Software tool for simulating heterogeneous networks composed of different model neurons and synapses. It is intended to simulate networks containing up to millions of neurons and on the order of billions of synapses by distributing the network over different nodes of a computing cluster by using MPI. | simulation software, simulator, heterogenous network, model, neuron, synapse | is related to: CSIM | DOI:10.3389/neuro.11.011.2009 | Available for download | SCR_014770 | Parallel neural Circuit SIMulator, Parallel Neural Circuit Simulator (PCSIM), Parallel Neural Circuit Simulator | 2025-05-20 11:15:37 | 4 | ||||||||
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WormAtlas Resource Report Resource Website 100+ mentions |
WormAtlas (RRID:SCR_002861) | data or information resource, database, atlas | Anatomical atlas about structural anatomy of Caenorhabditis elegans. Provides simple interface allowing user to easily navigate through every anatomical structure of worm. Contains set of images which can be sorted by different characteristics: sex, genotype, age, body portion or tissue type. Includes links to other major worm websites and databases. Application for viewing and downloading thousands of unpublished electron micrographs and associated data. These images have been generated by several labs in the C. elegans community, including the MRC, the Hall lab (Center for C. elegans Anatomy), and the Culotti and Riddle labs. | electron, ganglion, anatomy, caenorhabditis elegan, c. elegan, cell, development, gfpworm, glossary, lineage, microscopy, morphology, video, nematode, nerve cord, nervous system, neuroanatomy, neuron, phenotype, wiring diagram, worm, image, FASEB list | has parent organization: Albert Einstein College of Medicine; New York; USA | NCRR ; NIH Office of the Director R24 OD010943 |
Free, Freely available | nif-0000-00098, nif-0000-25470, SCR_007295 | https://orip.nih.gov/comparative-medicine/programs/invertebrate-models | SCR_002861 | , WormImage, Worm Image Database | 2025-05-20 11:09:04 | 156 |
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