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http://med.emory.edu/ADRC/research/tissue_biospecimen_banking_facility.html

The Alzheimer's Disease Research Center at Emery University maintains an active brain bank to facilitate the acquisition, storage, handling and distribution of well-characterized autopsy brain tissue and other materials to investigators. It contains frozen tissue and brain specimens, formalin fixed tissue, paraformaldehyde fixed tissue, and cryopreserved tissue. The ADRC also has access to tissues and samples related to other neurodegenerative diseases. It contains plasma samples, serum samples, lymphoblast cell lines, and cerebrospinal fluid.

Proper citation: Emory ADRC Tissue and Biospecimen Banking Facility (RRID:SCR_000551) Copy   

•   Source: SciCrunch Registry

http://www.emouseatlas.org

Detailed multidimensional digital multimodal atlas of C57BL/6J mouse nervous system with data and informatics pipeline that can automatically register, annotate, and visualize large scale neuroanatomical and connectivity data produced in histology, neuronal tract tracing, MR imaging, and genetic labeling. MAP2.0 interoperates with commonly used publicly available databases to bring together brain architecture, gene expression, and imaging information into single, simple interface.Resource to visualise mouse development, identify anatomical structures, determine developmental stage, and investigate gene expression in mouse embryo. eMouseAtlas portal page allows access to EMA Anatomy Atlas of Mouse Development and EMAGE database of gene expression.EMAGE is freely available, curated database of gene expression patterns generated by in situ techniques in developing mouse embryo. EMA, e-Mouse Atlas, is 3-D anatomical atlas of mouse embryo development including histology and includes EMAP ontology of anatomical structure, provides information about shape, gross anatomy and detailed histological structure of mouse, and framework into which information about gene function can be mapped.

Proper citation: eMouseAtlas (RRID:SCR_002981) 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

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

https://github.com/mne-tools/mne-bids/

Software Python package to link Brain Imaging Data Structure and MNE-Python software for analyzing neurophysiology data with goal to make analyses faster to code, more robust to errors, and easily shareable with colleagues. Provides programmable interface for BIDS datasets in electrophysiology with MNE-Python. Used for organizing electrophysiological data into BIDS format and facilitating their analysis.

Proper citation: MNE-BIDS (RRID:SCR_018766) Copy   

•   Source: SciCrunch Registry

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

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/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

https://bwhbioinfo.shinyapps.io/powerEQTL/

Software R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis.

Proper citation: powereQTL (RRID:SCR_021653) Copy   

•   Source: SciCrunch Registry

http://llama.mshri.on.ca/funcassociate/

A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool

Proper citation: FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) 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

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

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/NeurodataWithoutBorders/aqnwb

Software C++ API for acquiring neurophysiological data directly into the NWB (Neurodata Without Borders) format. Our goal is to provide a lightweight API to integrate with existing acquisition systems.

Proper citation: AqNWB (RRID:SCR_028050) Copy   

•   Source: SciCrunch Registry

https://github.com/GabrielHoffman/dreamlet

Software R package enables differential expression analysis on multi-sample single cell datasets using linear (mixed) models with precision weights.

Proper citation: dreamlet (RRID:SCR_028168) Copy   

•   Source: SciCrunch Registry