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https://imagej.net/

Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets.

Proper citation: ImageJ (RRID:SCR_003070) Copy   

•   Source: SciCrunch Registry

https://github.com/neitzlab/sbfsem-tools

Data analysis and 3D visualization for connectomics and serial electron microscopy. This toolbox provides missing 3D visualization and analysis tools for cylinder-based annotations. Integration with contour, skeleton based annotations and common morphology file formats is also supported.

Proper citation: SBFSEM-tools (RRID:SCR_017350) Copy   

•   Source: SciCrunch Registry

https://github.com/SilverLabUCL/SilverLab-Microscope-Software

Software for use with compact Acousto-Optic Lens Microscope (AOLM) developed in the Silver Lab at UCL. Written in LabVIEW. Performs multiple imaging modes and protocols including Z-stacks, multi-plane, single-plane, sub-volume, patches and points. It comes with tools for visualising data acquired with system.

Proper citation: Silver Lab Microscopy Software (RRID:SCR_017456) Copy   

•   Source: SciCrunch Registry

http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases

Probabilistic atlases covering 48 cortical and 21 subcortical structural areas, derived from structural data and segmentations kindly provided by the Harvard Center for Morphometric Analysis. T1-weighted images of 21 healthy male and 16 healthy female subjects (ages 18-50) were individually segmented by the CMA using semi-automated tools developed in-house. The T1-weighted images were affine-registered to MNI152 space using FLIRT (FSL), and the transforms then applied to the individual labels. Finally, these were combined across subjects to form population probability maps for each label. Segmentations used to create these atlases were provided by: David Kennedy and Christian Haselgrove, Centre for Morphometric Analysis, Harvard; Bruce Fischl, the Martinos Center for Biomedical Imaging, MGH; Janis Breeze and Jean Frazier from the Child and Adolescent Neuropsychiatric Research Program, Cambridge Health Alliance; Larry Seidman and Jill Goldstein from the Department of Psychiatry of Harvard Medical School.

Proper citation: Harvard - Oxford Cortical Structural Atlas (RRID:SCR_001476) Copy   

•   Source: SciCrunch Registry

http://www.tbi-impact.org/

Project focused on advancing knowledge of prognosis, trial design and treatment in Traumatic Brain Injury. IMPACT has developed and validated prognostic models for classification and characterization of TBI series, and participated in development of standardization of data collection in TBI studies.

Proper citation: IMPACT: International Mission for Prognosis and Analysis of Clinical Trials in TBI (RRID:SCR_000539) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/mni2orfromxyz/

Input either normalized MNI coordinates from a 3D image, or input real world XYZ matrix coordinates, and this code will convert coordinates of one type to the other.

Proper citation: Convert MNI coordinates to or from XYZ (RRID:SCR_000406) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/frats/

Software for the analysis of multiple diffusion properties along fiber bundle as functions in an infinite dimensional space and their association with a set of covariates of interest, such as age, diagnostic status and gender, in real applications. The resulting analysis pipeline can be used for understanding normal brain development, the neural bases of neuropsychiatric disorders, and the joint effects of environmental and genetic factors on white matter fiber bundles.

Proper citation: Functional Regression Analysis of DTI Tract Statistics (RRID:SCR_002293) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.biac.duke.edu/

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   

•   Source: SciCrunch Registry

http://nif.nimh.nih.gov/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://vox.pharmacology.ucla.edu/home.html

Two-dimensional images of gene expression for 20,000 genes in a coronal slice of the mouse brain at the level of the striatum by using microarrays in combination with voxelation at a resolution of 1 cubic mm gene expression patterns in the brain obtained through voxelation. Voxelation employs high-throughput analysis of spatially registered voxels (cubes) to produce multiple volumetric maps of gene expression analogous to the images reconstructed in biomedical imaging systems.

Proper citation: Voxelation Map of Gene Expression in a Coronal Section of the Mouse Brain (RRID:SCR_008065) Copy   

•   Source: SciCrunch Registry

https://stemcells.nindsgenetics.org/

Cell sources currently include fibroblasts and/or induced pluripotent stem cells for Alzheimer's Disease, Amyotrophic Lateral Sclerosis (ALS), Ataxia-telangiectasia, Frontotemporal Lobar Degeneration (FTD), Huntington's Disease, Parkinson's Disease, and healthy controls. Cell sources, including isogenic cell lines for current and new diseases covered by the NINDS will be added over the next several years.

Proper citation: The NINDS Human Cell and Data Repository (NHCDR) (RRID:SCR_016319) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/validate29/

Atlas was created from MRI scans of squirrel monkey brains. The atlas is currently comprised of multiple anatomical templates, diffusion MRI templates, and ex vivo templates. In addition, the templates are combined with histologically defined cortical labels, and diffusion tractography defined white matter labels.

Proper citation: VALiDATe29 Squirrel Monkey Brain Atlas (RRID:SCR_015542) Copy   

•   Source: SciCrunch Registry

https://www.rarediseasesnetwork.org/cms/create/researchers/biorepository

Biorepository of samples collected from patients with ALS, ALS-frontotemporal dementia (ALS-FTD), primary lateral sclerosis (PLS), progressive muscular atrophy (PMA), hereditary spastic paraplegia (HSP) and multisystem proteinopathy (MSP). Used by Consortium members and the scientific community to advance therapeutic development through study of the relationship between clinical phenotype and underlying genotype, and also through the discovery and development of biomarkers.

Proper citation: CReATE (RRID:SCR_016436) Copy   

•   Source: SciCrunch Registry

http://www.lincsproject.org/

Project to create network based understanding of biology by cataloging changes in gene expression and other cellular processes when cells are exposed to genetic and environmental stressors. Program to develop therapies that might restore pathways and networks to their normal states. Has LINCS Data Coordination and Integration Center and six Data and Signature Generation Centers: Drug Toxicity Signature Generation Center, HMS LINCS Center, LINCS Center for Transcriptomics, LINCS Proteomic Characterization Center for Signaling and Epigenetics, MEP LINCS Center, and NeuroLINCS Center.

Proper citation: LINCS Project (RRID:SCR_016486) Copy   

•   Source: SciCrunch Registry

http://marrvel.org/

Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research.

Proper citation: MARRVEL (RRID:SCR_016871) Copy   

•   Source: SciCrunch Registry

http://pklab.med.harvard.edu/scde/pagoda.links.html

Software tool for analyzing transcriptional heterogeneity to detect statistically significant ways in which measured cells can be classified. Used to resolve multiple, potentially overlapping aspects of transcriptional heterogeneity by testing gene sets for coordinated variability among measured cells.

Proper citation: PAGODA (RRID:SCR_017099) Copy   

•   Source: SciCrunch Registry

https://github.com/FeeLab/seqNMF

Software tool for unsupervised discovery of sequential structure. Used to detect sequences in neural data generated by internal behaviors, such as animal thinking or sleeping. Used for unsupervised discovery of temporal sequences in high dimensional datasets in neuroscience without reference to external markers.

Proper citation: seqNMF (RRID:SCR_017068) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/pennhippoatlas/

Atlas of segmented and normalized high-resolution postmortem MRI of the human hippocampus. Additional data (raw images) is available through the SCM link. It requires knowing how to use CVS.

Proper citation: Penn Hippocampus Atlas (RRID:SCR_000421) Copy   

•   Source: SciCrunch Registry