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

Open access multimodal 3D atlases of developing mouse brain that can be used to integrate mouse brain imaging data for visualization, education, cell census mapping, and more. Atlas ages include E11.5, E13.5, E15.5, E18.5, P4, P14, and P56. Web platform can be utilized to visualize and explore the atlas in 3D. Downloadable atlas can be used to align multimodal mouse brain data. Morphologically averaged symmetric template brains serve as the basis reference space and coordinate system. Anatomical labels are manually drawn in 3D based on the prosomeric model. For additional references, the P56 template includes templates and annotations from the aligned Allen Mouse Brain Common Coordinate Framework (Allen CCFv3) and aligned Molecular Atlas of the Adult Mouse Brain.

Proper citation: 3D Developmental Mouse Brain Common Coordinate Framework (RRID:SCR_025544) 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://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

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://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   

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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/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://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

http://clarityresourcecenter.org/

Protocols and other training materials related to the CLARITY protocol, a technique for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable.

Proper citation: Clarity resources (RRID:SCR_001387) Copy   

•   Source: SciCrunch Registry

http://qnl.bu.edu/obart

Tool that provides an interactive method to examine quantitative relationships between brain regions defined by different digital atlases or parcellation methods. Its current focus is for human brain imaging, though the techniques generalize to other domains. The method offers a quantitative answer to the nomenclature problem in neuroscience by comparing brain parts on the basis of their geometrical definitions rather than on the basis of name alone. Thus far these tools have been used to quantitatively compare eight distinct parcellations of the International Consortium for Brain Mapping (ICBM) single-subject template brain, each created using existing atlasing methods. This resources provides measures of global and regional similarity, and offers visualization techniques that allow users to quickly identify the correspondences (or lack of correspondences) between regions defined by different atlases.

Proper citation: OBART (RRID:SCR_001903) Copy   

•   Source: SciCrunch Registry

https://nda.nih.gov/

The National Institute of Mental Health Data Archive (NDA) makes available human subjects data collected from hundreds of research projects across many scientific domains. Research data repository for data sharing and collaboration among investigators. Used to accelerate scientific discovery through data sharing across all of mental health and other research communities, data harmonization and reporting of research results. Infrastructure created by National Database for Autism Research (NDAR), Research Domain Criteria Database (RDoCdb), National Database for Clinical Trials related to Mental Illness (NDCT), and NIH Pediatric MRI Repository (PedsMRI).

Proper citation: NIMH Data Archive (RRID:SCR_004434) Copy   

•   Source: SciCrunch Registry

http://trackvis.org/

TrackVis is software tool that can visualize and analyze fiber track data from diffusion MR imaging (DTI/DSI/HARDI/Q-Ball) tractography. It does NOT perform actual fiber tracking. Diffusion Toolkit is a set of tools that reconstruct diffusion imaging data and generate fiber track data for TrackVis to visualize. Because these two sets of tools were developed and maintained separately and each has distinguished funtionalities, they decided to distribute them as two separate programs for the ease of maintenance and upgrade. You do need both of them to perform complete diffusion data processing and analysis. Features of TrackVis include: * Cross-platform. Works on Windows, Mac OS X and Linux with native look and feel. * A variety of track filters (track selecting methods) allowing users to explore and locate specific bundles with ease. * Multiple rendering modes with customizable scalar-driven color codes. * Real-time parameter adjustment and 3D render. * Open format of the track data file allowing users to integrate customized scalar data into the track file and visualize and analyze it. Save and restore scenes in XML style scene file. * Statistical scalar analysis of tracks and ROIs. * Synchronized real-time multiple dataset analysis and display allowing time-point and/or subject comparison. Synchronized analysis and display on same dataset can also be performed in real-time remotely over the network. * Upfront in-line parameter adjustment in real-time. No tedious pop-up dialogs. TrackVis works with Track File created by Diffusion Toolkit. Diffusion Toolkit processes raw DICOM, Nifti format and ANALYZE images. TrackVis and Diffusion Toolkit are cross-platform software. They can run on Windows XP, Mac OS X as well as Linux.

Proper citation: TrackVis (RRID:SCR_004817) Copy   

•   Source: SciCrunch Registry