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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://brainlife.io/docs/using_ezBIDS/

Web-based BIDS conversion tool to convert neuroimaging data and associated metadata to BIDS standard. Guided standardization of neuroimaging data interoperable with major data archives and platforms.

Proper citation: ezBIDS (RRID:SCR_025563) 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://bioconductor.org/packages/release/bioc/html/tximeta.html

Software R package for reference sequence checksums for provenance identification in RNA-seq. Performs numerous annotation and metadata gathering tasks on behalf of users during the import of transcript counts and abundance from quantification tools such as salmon. Data are imported as SummarizedExperiment objects with associated GenomicRanges metadata. Correct metadata is added automatically via reference sequence digests, facilitating genomic analyses and assisting in computational reproducibility.

Proper citation: tximeta (RRID:SCR_028005) 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

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/DeNardoLab/BehaviorDEPOT

Software tool for automated behavioral detection based on markerless pose tracking. Behavioral analysis tool to first compile and clean point-tracking output from DeepLabCut, and then classify behavioral epochs using custom behavior classifiers. Used to detect frame by frame behavior from video time series and can analyze results of common experimental assays, including fear conditioning, decision-making in T-maze, open field, elevated plus maze, and novel object exploration. Calculates kinematic and postural statistics from keypoint tracking data from pose estimation software outputs.

Proper citation: BehaviorDEPOT (RRID:SCR_023602) Copy   

•   Source: SciCrunch Registry

https://github.com/TADA-A/TADA-A/tree/master

Software statistical framework for mapping risk genes from de novo mutations in whole genome sequencing studies.

Proper citation: TADA-A (RRID:SCR_024538) 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/XTRACT

Software command line tool for automated tractography. Standardised protocols for automated tractography in human and macaque brain.

Proper citation: XTRACT (RRID:SCR_024933) 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

http://fcon_1000.projects.nitrc.org/indi/abide/

Resting state functional magnetic resonance imaging (R-fMRI) datasets from 539 individuals with autism spectrum disorder (ASD) and 573 typical controls. This initiative involved 16 international sites, sharing 20 samples yielding 1112 datasets composed of both MRI data and an extensive array of phenotypic information common across nearly all sites. This effort is expected to facilitate discovery science and comparisons across samples. All datasets are anonymous, with no protected health information included.

Proper citation: ABIDE (RRID:SCR_003612) Copy   

•   Source: SciCrunch Registry

http://www.nimh.nih.gov/funding/clinical-trials-for-researchers/datasets/nimh-procedures-for-requesting-data-sets.shtml

A listing of data sets from NIMH-supported clinical trials. Limited Access Datasets are available from numerous NIMH studies. NIMH requires all investigators seeking access to data from NIMH-supported trials held by NIMH to execute and submit as their request the appropriate Data Use Certification pertaining to the trial. The datasets distributed by NIMH are referred to as limited access datasets because access is limited to qualified researchers who complete Data Use Certifications.

Proper citation: Limited Access Datasets From NIMH Clinical Trials (RRID:SCR_005614) Copy   

•   Source: SciCrunch Registry

http://mialab.mrn.org/data/index.html

An MRI data set that demonstrates the utility of a mega-analytic approach by identifying the effects of age and gender on the resting-state networks (RSNs) of 603 healthy adolescents and adults (mean age: 23.4 years, range: 12-71 years). Data were collected on the same scanner, preprocessed using an automated analysis pipeline based in SPM, and studied using group independent component analysis. RSNs were identified and evaluated in terms of three primary outcome measures: time course spectral power, spatial map intensity, and functional network connectivity. Results revealed robust effects of age on all three outcome measures, largely indicating decreases in network coherence and connectivity with increasing age. Gender effects were of smaller magnitude but suggested stronger intra-network connectivity in females and more inter-network connectivity in males, particularly with regard to sensorimotor networks. These findings, along with the analysis approach and statistical framework described, provide a useful baseline for future investigations of brain networks in health and disease.

Proper citation: MIALAB - Resting State Data (RRID:SCR_008914) Copy   

•   Source: SciCrunch Registry

http://pubbrain.org/

A literature search and visualization tool that allows end users to enter any PubMed query and see that query rendered as a heatmap illustrating which regions of interest are most commonly mentioned within the search results. To use PubBrain, simply enter any valid PubMed search in the search box.

Proper citation: PubBrain (RRID:SCR_005387) Copy   

•   Source: SciCrunch Registry

http://neuromorphometrics.com

Neuromorphometrics provides brain labeling and measurement services. Given raw MRI brain scans, we make precise quantitative measurements of the volume, shape, and location of specific neuroanatomical structures. Web tool for brain measurement services. Used for modeling living human brain and make quantitative measurements of volume, shape, and location of specific neuroanatomical structures using given MRI brain scans. Automated analyses are manually guided, inspected and certified by a neuroanatomical expert. Resource of neuroanatomically labeled MRI brain scans database. Resource for neuroanatomical localization and identification: NeuAtlas.

Proper citation: Neuromorphometrics (RRID:SCR_005656) Copy   

•   Source: SciCrunch Registry

http://www.nimh.nih.gov/trials/index.shtml

NIMH supports research studies on mental health and disorders. Participate, refer a patient or learn about results of studies in ClinicalTrials.gov, the NIH/National Library of Medicine''''s registry of federally and privately funded clinical trials for all disease. Find NIH-funded studies currently recruiting participants in the following mental health topics: * Anxiety Disorders ** Generalized Anxiety Disorder ** Obsessive-Compulsive Disorder (OCD) ** Panic Disorder ** Post-traumatic Stress Disorder (PTSD) ** Social Phobia (Social Anxiety Disorder) * Attention Deficit Hyperactivity Disorder (ADHD, ADD) * Autism Spectrum Disorders (Pervasive Developmental Disorders) * Bipolar Disorder (Manic-Depressive Illness) * Borderline Personality Disorder * Depression * Eating Disorders * HIV/AIDS * Schizophrenia * Suicide Prevention Information Resources for NIMH Researchers Conducting Clinical Trials * Limited Access Datasets from NIMH-Supported Clinical Trials * NIMH Policy for Recruitment of Participants in Clinical Research * NIMH Policy on Data and Safety Monitoring in Extramural Investigator-Initiated Clinical Trials * Register a study with ClinicalTrials.gov

Proper citation: NIMH Clinical Trials (RRID:SCR_005613) Copy   

•   Source: SciCrunch Registry

http://www.nimh.nih.gov/educational-resources/neuroscience-and-psychiatry/neuroscience-and-psychiatry-module-1-translating-neural-circuits-into-novel-therapeutics.shtml

This is the first in a series of modules on neuroscience and psychiatry. This module explores research on cognitive deficits, a core feature of schizophrenia and the single best predictor of functional outcomes in this disorder for which we currently have no treatments. This module is an example of how translational neuroscience can provide clues for the development of promising novel therapeutics.

Proper citation: Neuroscience and Psychiatry Module 1: Translating Neural Circuits into Novel Therapeutics (RRID:SCR_005609) Copy   

•   Source: SciCrunch Registry