Tools   Select Another Resource Report Type

http://www.ccnmd.pitt.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Conte Center for the Neuroscience of Mental Disorders (CCNMD) at the University of Pittsburgh offers a highly interactive scientific environment for the study of the neurobiology of schizophrenia. Integrates the laboratory and clinical research activities of investigators from the University of Pittsburgh Schools of Medicine and Arts and Sciences and the adjacent Carnegie Mellon University.

Proper citation: University of Pittsburgh Conte Center for the Neuroscience of Mental Disorders (RRID:SCR_000014) Copy   

•   Source: SciCrunch Registry

https://kimlab.io/brain-map/epDevAtlas/

Suite of open access resources including 3D atlases of early postnatally developing mouse brain and mapped cell type density growth charts, which can be used as standalone resources or to implement data integration. Web platform can be utilized to analyze and visualize the spatiotemporal growth of GABAergic, microglial, and cortical layer-specific cell type densities in 3D. Morphologically averaged symmetric template brains serve as the basis reference space and coordinate system with an isotropic resolution of 20 μm (XYZ in coronal plane). Average transformations were conducted at 20 μm voxel resolution by interpolating high resolution serial two photon tomography images from primarily Vip-IRES-Cre;Ai14 mice at postnatal (P) ages P4, P6, P8, P10, P12, and P14. For all ages, anatomical labels from the P56 Allen Mouse Brain Common Coordinate Framework (Allen CCFv3) were iteratively down registered to each early postnatal time point in a non-linear manner, aided by manual parcellations of landmarks in 3D, consistent with the Allen Mouse Reference Atlas Ontology.

Proper citation: Early Postnatal Developmental Mouse Brain Atlas (RRID:SCR_024725) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddyqc

Software tool allows to assess dMRI data both at single subject and group levels.Calculates average SNR across all voxels within brain mask to give summary measure of overall quality of dataset. Used to generate single subject and study wise reports and databases.

Proper citation: eddyqc (RRID:SCR_024936) Copy   

•   Source: SciCrunch Registry

https://github.com/xinhe-lab/GSFA

Software R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single cell CRISPR screening data.

Proper citation: Guided Sparse Factor Analysis (RRID:SCR_025023) Copy   

•   Source: SciCrunch Registry

https://beadl.org

Universal framework for describing behavioral tasks. Language to abstract and standardize behavioral task descriptions on two layers. Graphical layer specifies elements to describe behavioral tasks as state machine in formal flow diagram and how task controlling system interacts with subject. This graphical layer has been designed to be easy to understand while retaining all aspects of behavioral task. The second layer is corresponding, XML-based description of task. This layer forms rigid, yet extensible foundation of BEADL and hides hardware implementation related details form graphical representation.BEADL-specific extension for Neurodata Without Borders data standard defines how behavioral outcomes of task are stored in NWB including corresponding BEADL task description.

Proper citation: BEADL:BEhavioral tAsk Description Language (RRID:SCR_025464) Copy   

•   Source: SciCrunch Registry

http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/

Software tool for ultra fast eQTL analysis via large matrix operations.

Proper citation: MatrixEQTL (RRID:SCR_025513) Copy   

•   Source: SciCrunch Registry

https://portal.brain-map.org/genetic-tools/genetic-tools-atlas

Searchable catalog of enhancer-adeno-associated viruses (AAVs) that have been developed and tested at the Allen Institute for Brain Science. We present a suite of enhancer AAVs that can provide access to specific cell types when delivered to the whole brain. Multiple epigenomic and transcriptomic datasets were interrogated to reveal candidate enhancers that are selectively accessible in particular cell populations. Enhancer AAVs were constructed and screened for desirable expression and a sizeable subset of enhancer AAVs were subjected to further characterization by single cell transcriptomics and/or brain-wide expression imaging in mouse. In the GTA, we present a large toolkit for selective gene expression in cell types of interest. Genetic Tools Atlas is part of the growing Brain Knowledge Platform.

Proper citation: Genetic Tools Atlas (RRID:SCR_025643) Copy   

•   Source: SciCrunch Registry

https://kimlab.io/brain-map/DevATLAS/

Whole brain developmental map of neuronal circuit maturation. Generated by whole brain spatiotemporal mapping of circuit maturation during early postnatal development. Standard reference for normative developmental trajectory of neuronal circuit maturation, as well as high throughput platform to pinpoint when and where circuit maturation is disrupted in mouse models of neurodevelopmental disorders, such as fragile X syndrome.

Proper citation: DevATLAS (RRID:SCR_025718) Copy   

•   Source: SciCrunch Registry

https://github.com/Washington-University/HCPpipelines

Software package as set of tools, primarily shell scripts, for processing multi-modal, high-quality MRI images for the Human Connectome Project. Minimal preprocessing pipelines for structural, functional, and diffusion MRI that were developed by the HCP to accomplish many low level tasks, including spatial artifact/distortion removal, surface generation, cross-modal registration, and alignment to standard space.

Proper citation: HCP Pipelines (RRID:SCR_026575) Copy   

•   Source: SciCrunch Registry

https://github.com/kaizhang/SnapATAC2

Software Python/Rust package for single-cell epigenomics analysis.

Proper citation: SnapATAC2 (RRID:SCR_026622) Copy   

•   Source: SciCrunch Registry

https://github.com/ReproBrainChart

Open data resource for mapping brain development and its associations with mental health. Integrates data from 5 large studies of brain development in youth from three continents (N = 6,346). Bifactor models were used to create harmonized psychiatric phenotypes, capturing major dimensions of psychopathology. Neuroimaging data were carefully curated and processed using consistent pipelines in a reproducible manner.

Proper citation: Reproducible Brain Charts (RRID:SCR_027837) Copy   

•   Source: SciCrunch Registry

https://doi.org/10.17605/OSF.IO/WDR78

Open source resource of manually curated and expert reviewed infant brain segmentations hosted on OpenNeuro.org. and OSF.io. Anatomical MRI data was segmented from 71 infant imaging visits across 51 participants, using both T1w and T2w images per visit. Images showed dramatic differences in myelination and intensities across 1–9 months, emphasizing the need for densely sampled gold-standard segmentations across early life. This dataset provides a benchmark for evaluating and improving pipelines dependent upon segmentations in the youngest populations. As such, this dataset provides a vitally needed foundation for early-life large-scale studies such as HBCD.

Proper citation: Baby Open Brains (RRID:SCR_027836) Copy   

•   Source: SciCrunch Registry

https://github.com/noahbenson/neuropythy

Software neuroscience library for Python, intended to complement the existing nibabel library. Can automatic download data and interpret them into Python data structures.

Proper citation: neuropythy (RRID:SCR_027787) Copy   

•   Source: SciCrunch Registry

https://weghornlab.org/software.html

Software tool which derives gene-specific probabilistic estimates of the strength of negative and positive selection in cancer.

Proper citation: CBaSE (RRID:SCR_027765) Copy   

•   Source: SciCrunch Registry

http://www.fz-juelich.de/ime/spm_anatomy_toolbox

A MATLAB toolbox which uses three dimensional probabilistic cytoarchitechtonic maps to correlate microscopic, anatomic and functional data of the cerebral cortex. Correlating the activation foci identified in functional imaging studies of the human brain with structural (e.g., cytoarchitectonic) information on the activated areas is a major methodological challenge for neuroscience research. We here present a new approach to make use of three-dimensional probabilistic cytoarchitectonic maps, as obtained from the analysis of human post-mortem brains, for correlating microscopical, anatomical and functional imaging data of the cerebral cortex. We introduce a new, MATLAB based toolbox for the SPM2 software package which enables the integration of probabilistic cytoarchitectonic maps and results of functional imaging studies. The toolbox includes the functionality for the construction of summary maps combining probability of several cortical areas by finding the most probable assignment of each voxel to one of these areas. Its main feature is to provide several measures defining the degree of correspondence between architectonic areas and functional foci. The software, together with the presently available probability maps, is available as open source software to the neuroimaging community. This new toolbox provides an easy-to-use tool for the integrated analysis of functional and anatomical data in a common reference space.

Proper citation: SPM Anatomy Toolbox (RRID:SCR_013273) Copy   

•   Source: SciCrunch Registry

http://nunda.northwestern.edu/nunda/app

A resource for managing study data collected by the Northwestern University neuroimaging community. It includes a secure database, automated pipelines for processing managed data, and tools for exploring and accessing the data. Access to data in the NUNDA is restricted to users authorized by the specific study's investigators. The NUNDA is hosted by the Neuroimaging & Applied Computational Anatomy Lab, and it is modeled after the Washington University's Central Neuroimaging Data Archive (CNDA). The NUNDA is powered by XNAT, an open source software package for managing neuroimaging and related data.

Proper citation: NUNDA (RRID:SCR_013664) Copy   

•   Source: SciCrunch Registry

http://rsb.info.nih.gov/

Portal for NIH, NIMH, and NINDS scientific and computer resources including Mac sites, PC sites, Linux sites, intramural programs, intranet and the NIH JumpStart and Directory.

Proper citation: Research Services Branch National Institutes of Mental Health (RRID:SCR_001633) Copy   

•   Source: SciCrunch Registry

http://www.cpc.unc.edu/projects/addhealth

Longitudinal study of a nationally representative sample of adolescents in grades 7-12 in the United States during the 1994-95 school year. Public data on about 21,000 people first surveyed in 1994 are available on the first phases of the study, as well as study design specifications. It also includes some parent and biomarker data. The Add Health cohort has been followed into young adulthood with four in-home interviews, the most recent in 2008, when the sample was aged 24-32. Add Health combines longitudinal survey data on respondents social, economic, psychological and physical well-being with contextual data on the family, neighborhood, community, school, friendships, peer groups, and romantic relationships, providing unique opportunities to study how social environments and behaviors in adolescence are linked to health and achievement outcomes in young adulthood. The fourth wave of interviews expanded the collection of biological data in Add Health to understand the social, behavioral, and biological linkages in health trajectories as the Add Health cohort ages through adulthood. The restricted-use contract includes four hours of free consultation with appropriate staff; after that, there''s a fee for help. Researchers can also share information through a listserv devoted to the database.

Proper citation: Add Health (National Longitudinal Study of Adolescent Health) (RRID:SCR_007434) Copy   

•   Source: SciCrunch Registry

http://senselab.med.yale.edu/cellpropdb

A repository for data regarding membrane channels, receptor and neurotransmitters that are expressed in specific types of cells. The database is presently focused on neurons but will eventually include other cell types, such as glia, muscle, and gland cells. This resource is intended to: * Serve as a repository for data on gene products expressed in different brain regions * Support research on cellular properties in the nervous system * Provide a gateway for entering data into the cannonical neuron forms in NeuronDB * Identify receptors across neuron types to aid in drug development * Serve as a first step toward a functional genomics of nerve cells * Serve as a teaching aid

Proper citation: Cell Properties Database (RRID:SCR_007285) Copy   

•   Source: SciCrunch Registry

http://www.oreganno.org/oregano/

Open source, open access database and literature curation system for community based annotation of experimentally identified DNA regulatory regions, transcription factor binding sites and regulatory variants. Automatically cross referenced against PubMED, Entrez Gene, EnsEMBL, dbSNP, eVOC: Cell type ontology, and Taxonomy database. Community driven resource for curated regulatory annotation.

Proper citation: Open Regulatory Annotation Database (RRID:SCR_007835) Copy   

•   Source: SciCrunch Registry