Curator Dashboard

This MATLAB toolbox implements a data fitting routine for Neurite Orientation Dispersion and Density Imaging (NODDI). NODDI is a new diffusion MRI technique for imaging brain tissue microstructure. Compared to DTI, it has the advantage of providing measures of tissue microstructure that are much more direct and hence more specific. It achieves this by adopting the model-based strategy which relates the signals from diffusion MRI to geometric models of tissue microstructure. In contrast to typical model-based techniques, NODDI is much more clinically feasible and can be acquired on standard MR scanners with an imaging time comparable to DTI.

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• SciCrunch
• 14 years ago - by Anonymous

Core with capacity for approximately 2 million to 3 million samples, serves CHOP’s biobanking needs, avoiding specimen duplication, preserving precious materials, and providing organized data and materials. The BioRC operates under the following principles: An Operational Committee, which coordinates central and investigator-specific biobanking resources and programs at CHOP, governs and approves requests to utilize the BioRC; BioRC facilitates integration and enhancement of access to information about biorepository specimens and resources; BioRC assists investigators in developing new projects that require the collection and processing of shareable samples not currently available, or helps investigators with existing projects who would like to migrate storage and management of their shareable banked specimens and data to the BioRC. BioRC institutes and follows best-practice standard procedures for collection, processing, and storage of samples to ensure high quality specimens and data for all CHOP investigators.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. Software that provides quality control and quality assessment tools for flow cytometry data.

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• SciCrunch
• 12 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. A suite of tools to generate the cortical surface of the brain. The surface is generated in the middle of grey matter and can be used to measure surface features including cortical depth and curvature.

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• SciCrunch
• 14 years ago - by Anonymous

Provides access to equipment to work on research projects, including cancer treatment research, vaccine development, and prosthetic creation. Instruments including micro-computed tomography (CT) scanner; scanning electron microscope (SEM); histology equipment; inverted fluorescence compound microscope; and stereoscope is available to FAU students (high school, undergraduate, graduate), post doctoral researchers, and faculty.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of physiologic data and associated metadata related to feeding behavior for a number of mammalian species, including human. The data contain information on muscle activity, bone and muscle strain, jaw and oropharyngeal apparatus motion, and intra-oral pressure and were generated using several techniques (e.g., electromyography, cineradiography, sonomicrometry). The data are searchable and can be downloaded into csv format.

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• SciCrunch
• 14 years ago - by Anonymous

A tool for automated registration of 3D (and 2D) images within and across subjects and within and sometimes across imaging modalities. The AIR library can easily incorporate automated image registration into site specific programs adapted to your particular needs.

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• SciCrunch
• 17 years ago - by Anonymous

Core Facility offers equipment for wide range of light microscopy applications as well as access to advanced bioimaging software. Specialized staff offers personal training and assistance.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A web application framework that helps build applications or run protocols for the web. It allows the user to manage various tasks being run on the web both manually and through existing Perl modules.

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• SciCrunch
• 17 years ago - by Anonymous

A JAVA application designed to create taxonomies or hierarchies in order to classify and organize information.

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• SciCrunch
• 14 years ago - by Anonymous

Central micro/nano fabrication facility of Northwestern University. Provides range of nanofabrication equipment and technical expertise. Supports research in all areas of science, engineering, medicine, and interdisciplinary fields.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Bio Resource for array genes is a free online resource for easy access to collective and integrated information from various public biological resources for human, mouse, rat, fly and c. elegans genes. The resource includes information about the genes that are represented in Unigene clusters. This resource provides interactive tools to selectively view, analyze and interpret gene expression patterns against the background of gene and protein functional information. Different query options are provided to mine the biological relationships represented in the underlying database. Search button will take you to the list of query tools available. This Bio resource is a platform designed as an online resource to assist researchers in analyzing results of microarray experiments and developing a biological interpretation of the results. This site is mainly to interpret the unique gene expression patterns found as biological changes that can lead to new diagnostic procedures and drug targets. This interactive site allows users to selectively view a variety of information about gene functions that is stored in an underlying database. Although there are other online resources that provide a comprehensive annotation and summary of genes, this resource differs from these by further enabling researchers to mine biological relationships amongst the genes captured in the database using new query tools. Thus providing a unique way of interpreting the microarray data results based on the knowledge provided for the cellular roles of genes and proteins. A total of six different query tools are provided and each offer different search features, analysis options and different forms of display and visualization of data. The data is collected in relational database from public resources: Unigene, Locus link, OMIM, NCBI dbEST, protein domains from NCBI CDD, Gene Ontology, Pathways (Kegg, Genmapp and Biocarta) and BIND (Protein interactions). Data is dynamically collected and compiled twice a week from public databases. Search options offer capability to organize and cluster genes based on their Interactions in biological pathways, their association with Gene Ontology terms, Tissue/organ specific expression or any other user-chosen functional grouping of genes. A color coding scheme is used to highlight differential gene expression patterns against a background of gene functional information. Concept hierarchies (Anatomy and Diseases) of MESH (Medical Subject Heading) terms are used to organize and display the data related to Tissue specific expression and Diseases. Sponsors: BioRag database is maintained by the Bioinformatics group at Arizona Cancer Center. The material presented here is compiled from different public databases. BioRag is hosted by the Biotechnology Computing Facility of the University of Arizona. 2002,2003 University of Arizona.

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• SciCrunch
• 17 years ago - by Anonymous

A suite of applications to fulfill all of your computerized experiment needs. Used by more than 15,000 professionals in the research community, E-Prime provides a truly easy-to-use environment for computerized experiment design, data collection, and analysis. E-Prime provides millisecond precision timing to ensure the accuracy of your data. E-Prime's flexibility to create simple to complex experiments is ideal for both novice and advanced users. The E-Prime suite of applications includes: * E-Studio ? Drag and drop graphical interface for experiment design * E-Basic ? Underlying scripting language of E-Prime * E-Run ? Once the experiment is generated with a single click, E-Run affords you the millisecond precision of stimulus presentation, synchronizations, and data collection. * E-Merge ? Merges your single session data files for group analysis * E-DataAid ? Data management utility * E-Recovery ? Recovers data files

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• SciCrunch
• 14 years ago - by Anonymous

THIS TEST is a

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• NIF
• 3 years ago - by Anonymous

A web-based neuroimaging and neuropsychology software suite that offers versatile, automatable data upload/import/entry options, rapid and secure sharing of data among PIs, querying and export all data, real-time reporting, and HIPAA and IRB compliant study-management tools suitable to large institutions as well as smaller scale neuroscience and neuropsychology researchers. COINS manages over over 400 studies, more than 265,000 clinical neuropsychological assessments, and 26,000 MRI, EEG, and MEG scan sessions collected from 18,000 participants at over ten institutions on topics related to the brain and behavior. As neuroimaging research continues to grow, dynamic neuroinformatics systems are necessary to store, retrieve, mine and share the massive amounts of data. The Collaborative Informatics and Neuroimaging Suite (COINS) has been created to facilitate communication and cultivate a data community. This tool suite offers versatile data upload/import/entry options, rapid and secure sharing of data among PIs, querying of data types and assessments, real-time reporting, and study-management tools suitable to large institutions as well as smaller scale researchers. It manages studies and their data at the Mind Research Network, the Nathan Kline Institute, University of Colorado Boulder, the Olin Neuropsychiatry Research Center (at) Hartford Hospital, and others. COINS is dynamic and evolves as the neuroimaging field grows. COINS consists of the following collaboration-centric tools: * Subject and Study Management: MICIS (Medical Imaging Computer Information System) is a centralized PostgreSQL-based web application that implements best practices for participant enrollment and management. Research site administrators can easily create and manage studies, as well as generate reports useful for reporting to funding agencies. * Scan Data Collection: An automated DICOM receiver collects, archives, and imports imaging data into the file system and COINS, requiring no user intervention. The database also offers scan annotation and behavioral data management, radiology review event reports, and scan time billing. * Assessment Data Collection: Clinical data gathered from interviews, questionnaires, and neuropsychological tests are entered into COINS through the web application called Assessment Manager (ASMT). ASMT's intuitive design allows users to start data collection with little or no training. ASMT offers several options for data collection/entry: dual data entry, for paper assessments, the Participant Portal, an online tool that allows subjects to fill out questionnaires, and Tablet entry, an offline data entry tool. * Data Sharing: De-identified neuroimaging datasets with associated clinical-data, cognitive-data, and associated meta-data are available through the COINS Data Exchange tool. The Data Exchange is an interface that allows investigators to request and share data. It also tracks data requests and keeps an inventory of data that has already been shared between users. Once requests for data have been approved, investigators can download the data directly from COINS.

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• SciCrunch
• 16 years ago - by Anonymous

Software application which aims to assign metric distances on the space of anatomical images in Computational Anatomy thereby allowing for the direct comparison and quantization of morphometric changes in shapes. As part of these efforts the Center for Imaging Science at Johns Hopkins University developed techniques to not only compare images, but also to visualize the changes and differences. For additional information please refer to: Faisal Beg, Michael Miller, Alain Trouve, and Laurent Younes. Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision, Volume 61, Issue 2; February 2005. M.I. Miller and A. Trouve and L. Younes, On the Metrics and Euler-Lagrange Equations of Computational Anatomy, Annual Review of biomedical Engineering, 4:375-405, 2002. Software developed with support from National Institutes of Health NCRR grant P41 RR15241.

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• SciCrunch
• 14 years ago - by Anonymous

Software tools for common BAM file manipulations.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A reference MINC set of files that currently includes human head images only of standard modalities. The goal is to build a well curated collection of files that demonstrate the capabilities of MINC

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• SciCrunch
• 14 years ago - by Anonymous

Blog presenting some scripts that can be used to facilitate and automate processing and analysis of brain data. In addition, it could be helpful explaining non clear stages and steps of brain data processing using some software such as; Freesurfer, FSL, Brainvoyager QX... At the moment, there are more than 10 applescripts in the main website http://www.easyneuroimaging.com that control different tools and commands (aparcstats2table, asegstats2table, BET, dcm2nii, FIRST, fslsplit, fslswapdim, fslview, mri_convert, Qdec, Recon-all, SIENAX, tkmedit, tksurfer)

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• SciCrunch
• 14 years ago - by Anonymous

Open Source software modular Java libraries for cheminformatics.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth