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http://research.mssm.edu/cnic/

Center to advance research and training in mathematical, computational and modern imaging approaches to understanding the brain and its functions. Software tools and associated reconstruction data produced in the center are available. Researchers study the relationships between neural function and structure at levels ranging from the molecular and cellular, through network organization of the brain. This involves the development of new computational and analytic tools for imaging and visualization of 3-D neural morphology, from the gross topologic characteristics of the dendritic arbor to the fine structure of spines and their synapses. Numerical simulations of neural mechanisms based on these structural data are compared with in-vivo and in-vitro electrophysiological recordings. The group also develops new theoretical and analytic approaches to exploring the function of neural models of working memory. The goal of this analytic work is to combine biophysically realistic models and simulations with reduced mathematical models that capture essential dynamical behaviors while reproducing the functionally important features of experimental data. Research areas include: Imaging Studies, Volume Integration, Visualization Techniques, Medial Axis Extraction, Spine Detection and Classification, Applications of Rayburst, Analysis of Spatially Complex Structures, Computational Modeling, Mathematical and Analytic Studies

Proper citation: Computational Neurobiology and Imaging Center (RRID:SCR_013317) Copy   

•   Source: SciCrunch Registry

http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula

Software tool developed for automatically reconstructing a set of major white matter pathways in the brain from diffusion weighted images using probabilistic tractography. This method utilizes prior information on the anatomy of the pathways from a set of training subjects. By incorporating this prior knowledge in the reconstruction procedure, our method obviates the need for manual intervention with the tract solutions at a later stage and thus facilitates the application of tractography to large studies. The trac-all script is used to preprocess raw diffusion data (correcting for eddy current distortion and B0 field inhomogenities), register them to common spaces, model and reconstruct major white matter pathways (included in the atlas) without any manual intervention. trac-all may be used to execute all the above steps or parts of it depending on the dataset and user''''s preference for analyzing diffusion data. Alternatively, scripts exist to execute chunks of each processing pipeline, and individual commands may be run to execute a single processing step. To explore all the options in running trac-all please refer to the trac-all wiki. In order to use this script to reconstruct tracts in Diffusion images, all the subjects in the dataset must have Freesurfer Recons.

Proper citation: TRACULA (RRID:SCR_013152) Copy   

•   Source: SciCrunch Registry

http://www.omicsdi.org/

Portal for dataset discovery across a heterogeneous, distributed group of transcriptomics, genomics, proteomics and metabolomics data resources. These resources span eight repositories in three continents and six organisations, including both open and controlled access data resources.

Proper citation: Omics Discovery Index (RRID:SCR_010494) Copy   

•   Source: SciCrunch Registry

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

A software application developed to support computational anatomy and shape analysis. The capabilities of CAWorks include: interactive landmark placement to create segmentation (mask) of desired region of interest; specialized landmark placement plugins for subcortical structures such as hippocampus and amygdala; support for multiple Medical Imaging data formats, such as Nifti, Analyze, Freesurfer, DICOM and landmark data; Quadra Planar view visualization; and shape analysis plugin modules, such as Large Deformation Diffeomorphic Metric Mapping (LDDMM). Specific plugins are available for landmark placement of the hippocampus, amygdala and entorhinal cortex regions, as well as a browser plugin module for the Extensible Neuroimaging Archive Toolkit.

Proper citation: CAWorks (RRID:SCR_014185) Copy   

•   Source: SciCrunch Registry

https://github.com/kstreet13/slingshot

Software R package for identifying and characterizing continuous developmental trajectories in single cell data. Cell lineage and pseudotime inference for single-cell transcriptomics.

Proper citation: Slingshot (RRID:SCR_017012) Copy   

•   Source: SciCrunch Registry

https://cloudreg.neurodata.io/

Software automated, terascale, cloud based image analysis pipeline for preprocessing and cross modal, nonlinear registration between volumetric datasets with artifacts. Automatic terabyte scale cross modal brain volume registration.

Proper citation: CloudReg (RRID:SCR_022795) Copy   

•   Source: SciCrunch Registry

http://senselab.med.yale.edu

The SenseLab Project is a long-term effort to build integrated, multidisciplinary models of neurons and neural systems. It was founded in 1993 as part of the original Human Brain Project, which began the development of neuroinformatics tools in support of neuroscience research. It is now part of the Neuroscience Information Framework (NIF) and the International Neuroinformatics Coordinating Facility (INCF). The SenseLab project involves novel informatics approaches to constructing databases and database tools for collecting and analyzing neuroscience information, using the olfactory system as a model, with extension to other brain systems. SenseLab contains seven related databases that support experimental and theoretical research on the membrane properties: CellPropDB, NeuronDB, ModelDB, ORDB, OdorDB, OdorMapDB, BrainPharmA pilot Web portal that successfully integrates multidisciplinary neurocience data.

Proper citation: SenseLab (RRID:SCR_007276) Copy   

•   Source: SciCrunch Registry

https://github.com/kukionfr/VAMPIRE_open

Software tool for analysis of cell and nuclear morphology from fluorescence or bright field images. Enables profiling and classification of cells into shape modes based on equidistant points along cell and nuclear contours. Robust method to quantify cell morphological heterogeneity.

Proper citation: VAMPIRE (RRID:SCR_021721) Copy   

•   Source: SciCrunch Registry

https://adrc.mc.duke.edu/index.php/research/brain-bank

A research repository of human brains with neurological disorders and normal controls, recruited through the Autopsy and Brain Donation Program coordinator. The Kathleen Price Bryan Brain Bank contains brains from patients with Alzheimer's disease, Parkinson's disease, Amyotrophic Lateral Sclerosis, Huntington's disease, Muscular Dystrophy, and other neurological and dementing disorders. The brain tissue is subjected to a detailed neuropathological evaluation and then stored as fixed and frozen hemispheres, paraffin blocks and histological slides. After receipt of an IRB approved request, tissue is supplied to investigators at Duke University, major medical centers and pharmaceutical companies across the United States and worldwide.

Proper citation: Duke University Kathleen Price Bryan Brain Bank (RRID:SCR_005022) Copy   

•   Source: SciCrunch Registry

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

OdorMapDB is designed to be a database to support the experimental analysis of the molecular and functional organization of the olfactory bulb and its basis for the perception of smell. It is primarily concerned with archiving, searching and analyzing maps of the olfactory bulb generated by different methods. The first aim is to facilitate comparison of activity patterns elicited by odor stimulation in the glomerular layer obtained by different methods in different species. It is further aimed at facilitating comparison of these maps with molecular maps of the projections of olfactory receptor neuron subsets to different glomeruli, especially for gene targeted animals and for antibody staining. The main maps archived here are based on original studies using 2-deoxyglucose and on current studies using high resolution fMRI in mouse and rat. Links are also provided to sites containing maps by other laboratories. OdorMapDB thus serves as a nodal point in a multilaboratory effort to construct consensus maps integrating data from different methodological approaches. OdorMapDB is integrated with two other databases in SenseLab: ORDB, a database of olfactory receptor genes and proteins, and OdorDB, a database of odor molecules that serve as ligands for the olfactory receptor proteins. The combined use of the three integrated databases allows the user to identify odor ligands that activate olfactory receptors that project to specific glomeruli that are involved in generating the odor activity maps.

Proper citation: Olfactory Bulb Odor Map DataBase (OdorMapDB) (RRID:SCR_007287) Copy   

•   Source: SciCrunch Registry

http://cerad.mc.duke.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023.Consortium that developed brief, standardized and reliable procedures for the evaluation and diagnosis of patients with Alzheimer's disease (AD) and other dementias of the elderly. These procedures included data forms, flipbooks, guidebooks, brochures, instruction manuals and demonstration tapes, which are now available for purchase. The CERAD assessment material can be used for research purposes as well as for patient care. CERAD has developed several basic standardized instruments, each consisting of brief forms designed to gather data on normal persons as well as on cognitively impaired or behaviorally disturbed individuals. Such data permit the identification of dementia based on clinical, neuropsychological, behavioral or neuropathological criteria. Staff at participating CERAD sites were trained and certified to administer the assessment instruments and to evaluate the subjects enrolled in the study. Cases and controls were evaluated at entry and annually thereafter including (when possible) autopsy examination of the brain to track the natural progression of AD and to obtain neuropathological confirmation of the clinical diagnosis. The CERAD database has become a major resource for research in Alzheimer's disease. It contains longitudinal data for periods as long as seven years on the natural progression of the disorder as well as information on clinical and neuropsychological changes and neuropathological manifestations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CERAD - Consortium to Establish a Registry for Alzheimer's Disease (RRID:SCR_003016) Copy   

•   Source: SciCrunch Registry

https://www.accordtrial.org/public

Study testing whether strict glucose control lowers the risk of heart disease and stroke in adults with type 2 diabetes. In addition the study is exploring: 1) Whether in the context of good glycemic control the use of different lowering lipid drugs will further improve these outcomes and 2) If strict control of blood pressure will also have additional beneficial effects on reducing cardiovascular disease. The design was a randomized, multicenter, double 2 X 2 factorial trial in 10,251 patients with type 2 diabetes mellitus. It was designed to test the effects on major CVD events of intensive glycemia control, of fibrate treatment to increase HDL-cholesterol and lower triglycerides (in the context of good LDL-C and glycemia control), and of intensive blood pressure control (in the context of good glycemia control), each compared to an appropriate control. All 10,251 participants were in an overarching glycemia trial. In addition, one 2 X 2 trial addressed the lipid question in 5,518 of the participants and the other 2 X 2 trial addressed the blood pressure question in 4,733 of the participants. The glycemia trial was terminated early due to higher mortality in the intensive compared with the standard glycemia treatment strategies. The results were published in June 2008 (N Eng J Med 2008;358:2545-59). Study-delivered treatment for all ACCORD participants was stopped on June 30, 2009, and the participants were assisted as needed in transferring their care to a personal physician. The lipid and blood pressure results (as well as the microvascular outcomes and eye substudy results) were published in 2010. All participants are continuing to be followed in a non-treatment observational study.

Proper citation: ACCORD (RRID:SCR_009015) Copy   

•   Source: SciCrunch Registry

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

A Matlab implementation for efficient permutation testing by using matrix completion.

Proper citation: Efficient Permutation Testing (RRID:SCR_014104) Copy   

•   Source: SciCrunch Registry

https://knightadrc.wustl.edu/professionals-clinicians/request-center-resources/

Provides on request resources including Data: clinical and cognitive measures as well as MRI and amyloid imaging scans; Tissue: frozen brain tissue, paraffin brain sections, antemortem CSF, DNA, fibroblast, dermal fibroblasts, plasma (fasting and non-fasting) and iPSC; Participants: eligible participants may be invited to enroll in research of other investigators after appropriate review. Researchers can use the request portal to review Center guidelines and policies; view available data and tissue; access data tables and codebooks; and submit request for resources.

Proper citation: Washington University School of Medicine Knight ADRC Request Center Resources Core Facility (RRID:SCR_025254) Copy   

•   Source: SciCrunch Registry

https://github.com/bsml320/Scupa/

Software R package for immune cell polarization assessment of scRNA-seq data. Single-cell unified polarization assessment of immune cells using single-cell foundation model. Used for comprehensive immune cell polarization analysis.

Proper citation: Scupa (RRID:SCR_025755) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/SpaGCN/

Software graph convolutional network to integrate gene expression and histology to identify spatial domains and spatially variable genes. SpaGCN integrates information from gene.

Proper citation: SpaGCN (RRID:SCR_025978) Copy   

•   Source: SciCrunch Registry

https://github.com/cafferychen777/ggpicrust2

Software R package for analyzing and interpreting results of PICRUSt2 functional prediction. Offers range of features, including pathway name/description annotations, advanced differential abundance methods, and visualization of differential abundance results. Used for PICRUSt2 predicted functional profile analysis and visualization.

Proper citation: ggpicrust2 (RRID:SCR_025965) Copy   

•   Source: SciCrunch Registry

https://github.com/j-rub/scVital

Software tool to embed scRNA-seq data into species-agnostic latent space to overcome batch effect and identify cell states shared between species. Deep learning algorithm for cross-species integration of scRNA-seq data.

Proper citation: scVital (RRID:SCR_026215) Copy   

•   Source: SciCrunch Registry

https://www.c4r-nih.org

Portal provides information about nationwide study of more than 50,000 individuals to determine factors that predict disease severity and long-term health impacts of COVID-19.

Proper citation: Collaborative Cohort of Cohorts for COVID-19 Research (RRID:SCR_026322) 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