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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
http://rsb.info.nih.gov/nih-image/index.html
Public image processing and analysis program for Macintosh.
Proper citation: NIH Image (RRID:SCR_003073) Copy
National resource for investigators utilizing human post-mortem brain tissue and related biospecimens for their research to understand conditions of the nervous system. Federated network of brain and tissue repositories in the United States that collects, evaluates, stores, and makes available to researchers, brain and other tissues in a way that is consistent with the highest ethical and research standards. The NeuroBioBank ensures protection of the privacy and wishes of donors. Provides information to the public about the need for tissue donation and how to register as a donor.
Proper citation: NIH NeuroBioBank (RRID:SCR_003131) Copy
Software repository for comparing structural (MRI) and functional neuroimaging (fMRI, PET, EEG, MEG) software tools and resources. NITRC collects and points to standardized information about structural or functional neuroimaging tool or resource.
Proper citation: NeuroImaging Tools and Resources Collaboratory (NITRC) (RRID:SCR_003430) Copy
The U.S. National Institutes of Health Final NIH Statement on Sharing Research Data (NIH-OD-03-032) is now in effect. It specifies that all high-direct-cost NIH grant applications include plans for sharing of research data. To support and encourage collegial, enabling, and rewarding data sharing for neuroscience and beyond, the Laboratory of Neuroinformatics at Weill Medical College of Cornell University has established this site. A source of, and portal to, tools and proposals supporting the informed exchange of neuroscience data.
Proper citation: Datasharing.net (RRID:SCR_003312) Copy
BIAC strives for excellence in its dual mission of research and service. BIAC faculty members are leaders in imaging methodology development, in analysis techniques, as well as in their application in cognitive and clinical neurosciences. In addition, BIAC offers imaging service to other imaging faculty members on campus and at the University of North Carolina in Chapel Hill.
Proper citation: Duke University of North Carolina Brain Imaging and Analysis Center Core Facility (RRID:SCR_001712) Copy
Neurophysiology imaging core facility that provides anatomical and functional MRI scanning for researchers in the National Institute of Mental Health (NIMH), the National Eye Institute (NEI), and the National Institute for Neurological Disorders and Stroke (NINDS). The shared intramural resource centers on a cutting-edge 4.7T vertical bore scanner dedicated to imaging of nonhuman primates.
Proper citation: Neurophysiology Imaging Facility (RRID:SCR_004080) Copy
https://github.com/sccn/labstreaminglayer
System for unified collection of measurement time series in research experiments that handles networking, time synchronization, near real time access as well as optionally centralized collection, viewing and disk recording of data. System for synchronizing streaming data for live analysis or recording.
Proper citation: Lab Streaming Layer (RRID:SCR_017631) Copy
https://miracl.readthedocs.io/en/latest/
Automated software resource that combines histologically cleared volumes with connectivity atlases and MRI, enabling analysis of histological features across multiple fiber tracts and networks, and their correlation with in vivo biomarkers.Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI. Open source pipeline for automated registration of mice clarity data to Allen reference atlas, segmentation and feature extraction of mice clarity data in 3D, registration of mice multimodal imaging data to Allen reference atlas, tract or label specific connectivity analysis based on Allen connectivity atlas,comparison of diffusion tensort imaging/tractography, virus tracing using CLARITY and Allen connectivity atlas, statistical analysis of CLARITY and Imaging data, atlas generation and label manipulation.
Proper citation: MIRACL (RRID:SCR_020945) Copy
http://www.salk.edu/science/core-facilities/gene-transfer-targeting-and-therapeutics-core/
Core facility that provides consultation on the use of viral vector technologies as well as custom design and production services for multiple vector types. The GT3 facilitates the use of these research tools by Salk researchers and others across diverse fields of study such as systems neuroscience, stem cell biology, metabolism, ageing, cancer biology and gene therapy. The GT3 core is a designated Cancer Center Council (C3) core facility. Cancer Center members from participating C3 institutes have preferential rates.
Proper citation: Salk Institute Gene Transfer Targeting and Therapeutics Viral Vector Core Facility (RRID:SCR_014847) Copy
https://www.med.unc.edu/neuroscience/core-facilities/neuro-microscopy/
Microscopy Core for high resolution imaging and aims to make this technology accessible to neuroscientists and other scientific researchers.Provides advanced systems for cellular and molecular imaging of in vitro and in vivo samples, implements new imaging technologies, particularly related to real time and tissue clearing based imaging of neurodevelopment and neural functions, offers training, consultation, data analysis, image processing, and centralized technical expertise.
Proper citation: University of North Carolina at Chapel Hill School of Medicine Neuroscience Microscopy Core Facility (RRID:SCR_019060) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST
Software model based segmentation and registration tool. Used for segmentation of sub-cortical structures. Introduces basic segmentation and vertex analysis for detecting group differences.
Proper citation: FMRIB’s Integrated Registration and Segmentation Tool (RRID:SCR_024921) Copy
https://github.com/dattalab/keypoint-moseq
Software application as machine learning-based platform for identifying behavioral modules from keypoint data without human supervision. Package provides tools for fitting MoSeq model to keypoint tracking data. Used to infer pose dynamics with keypoint data in addition to behavioral syllables.
Proper citation: Keypoint MoSeq (RRID:SCR_025032) Copy
https://github.com/Aharoni-Lab/Ephys-Miniscope
Miniaturized calcium imaging microscope with integrated dense electrode technology for synchronous acquisition of neural activity across distant regions of the brain. Device based off open-sourced UCLA Miniscope to synchronously measure single cell activity at or near spike-time resolution across distant brain regions in freely behaving mice. Used to perform calcium imaging, with dense electrode electrophysiological recording, allowing simultaneous recordings from two remote brain regions in freely behaving mouse.
Proper citation: E-Scope (RRID:SCR_025396) Copy
https://sea-ad.shinyapps.io/ACEapp/
Web application for comparing cell type assignments and other cell-based annotations (e.g., donor demographics, anatomic locations, batch variables, and quality control metrics). Used for connecting brain cell types across studies of health and Alzheimer's Disease.
Proper citation: Annotation Comparison Explorer (RRID:SCR_026496) Copy
https://github.com/calico/borzoi
Software package to access the Borzoi models, which are convolutional neural networks trained to predict RNA-seq coverage at 32bp resolution given 524kb input sequences.
Proper citation: Borzoi (RRID:SCR_026619) Copy
https://github.com/TonnesenLab/Diffusion-Model/
Software code for simulating diffusion in brain extracellular space images.
Proper citation: Diffusion-Model (RRID:SCR_027942) Copy
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