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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
VTT Technical Research Centre of Finland
 
Resource Report
Resource Website
1+ mentions
VTT Technical Research Centre of Finland (RRID:SCR_003914) VTT data or information resource, portal, service resource, organization portal A multitechnological applied non-profit research organisation in Northern Europe that provides high-end technology solutions and innovation services. They enhance their customers'' competitiveness, thereby creating prerequisites for society''s sustainable development, employment, and well-being. VTT has ISO9001:2008 certificate and ISO14001:2004 certificate. technology, innovation is related to: PREDECT
is related to: EMIF
has parent organization: Finnish Ministry of Employment and the Economy
nlx_158261 SCR_003914 Teknologian Tutkimuskeskus VTT, Valtion Teknillinen Tutkimuskeskus 2026-08-12 10:48:54 1
CLEAVE
 
Resource Report
Resource Website
10+ mentions
CLEAVE (RRID:SCR_007113) CLEAVE data processing software, software resource, software application A UNIX-style command-line program which quickly computes multifactorial ANOVAs for very large data sets with minimal memory use (without loading all of the data into memory). It has been used for fMRI analysis, e.g. CLEAVE adds the following to the standard ANOVA analyses: # Unlimited numbers of factors can be analyzed. # Factor Correlation and Unequal Variance Corrections # Treatment Magnitudes: omega^2, partial eta^2, and R^2 # A convenient Ranking of Factors based upon treatment magnitudes and significance levels. # Post-Hoc Significance Tests # Post-Hoc Power Table to gauge how many subjects will be needed to achieve significance. # Allows the use of Random Factors. # A Configuration File to make the program more tunable # A Histogram and Cell Line Diagrams: which help the user to detect outliers. # Associated MATLAB functions: port CLEAVE-style data sets in or out of MATLAB. c, console (text based), macos, microsoft, magnetic resonance, posix/unix-like, statistical operation is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: University of California at Davis; California; USA
Creative Commons Attribution License nlx_155530 http://www.nitrc.org/projects/cleave SCR_007113 2026-08-12 10:49:34 17
COILS: Prediction of Coiled Coil Regions in Proteins
 
Resource Report
Resource Website
100+ mentions
COILS: Prediction of Coiled Coil Regions in Proteins (RRID:SCR_008440) data processing software, software resource, software application COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation. software, prediction, database, sequence, coil, globular, protein, probability, bio.tools, FASEB list is listed by: 3DVC
is listed by: Debian
is listed by: bio.tools
is listed by: OMICtools
DOI:10.1126/science.252.5009.1162 biotools:ncoils, OMICS_07850, nif-0000-30263 https://bio.tools/ncoils, https://sources.debian.org/src/ncoils/ https://sources.debian.org/src/ncoils/ SCR_008440 COILS Server 2026-08-12 10:49:42 169
Graphtools
 
Resource Report
Resource Website
1+ mentions
Graphtools (RRID:SCR_009490) Graphtools data processing software, software resource, software application A set of MATLAB scripts for analysis of networks derived from neuroimaging data. Some of these scripts are entirely original, while some are adapted (or just copied) from the Brain Connectivity Toolbox (https://sites.google.com/a/brain-connectivity-toolbox.net/bct) The source code is available via git: git clone ssh://user magnetic resonance, matlab is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: Brain Connectivity Toolbox
BSD License nlx_155638 SCR_009490 2026-08-12 10:49:57 4
OwlSim
 
Resource Report
Resource Website
1+ mentions
OwlSim (RRID:SCR_006819) OwlSim data processing software, software resource, software application Software package that provides the ability to do a number of standard semantic similarity methods and includes novel methods for combining these with dynamic selection of anonymous grouping classes. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible functional similarity, semantic similarity, ontology, phenotype, annotation, windows, mac os x, linux, unix is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: Berkeley Bioinformatics Open-Source Projects
has parent organization: OWLTools
Biomedical Information Science and Technology Initiative ;
National Center for Biomedical Ontology ;
NHGRI U54 HG004028;
NHGRI HG002659
PMID:19956802 Open unspecified license - Free for academic use nlx_149312 SCR_006819 2026-08-12 10:49:34 5
TrakEM2
 
Resource Report
Resource Website
100+ mentions
TrakEM2 (RRID:SCR_008954) TrakEM2 data processing software, image analysis software, software resource, software application An ImageJ plugin for morphological data mining, three-dimensional modeling and image stitching, registration, editing and annotation. Two independent modalities exist: either XML-based projects, working directly with the file system, or database-based projects, working on top of a local or remote PostgreSQL database. What can you do with it? * Semantic segmentation editor: order segmentations in tree hierarchies, whose template is exportable for reuse in other, comparable projects. * Model, visualize and export 3D. * Work from your laptop on your huge, remote image storage. * Work with an endless number of images, limited only by the hard drive capacity. Dozens of formats supported thanks to LOCI Bioformats and ImageJ. * Import stacks and even entire grids (montages) of images, automatically stitch them together and homogenize their histograms for best montaging quality. * Add layers conveniently. A layer represents, for example, one 50 nm section (for TEM) or a confocal section. Each layer has its own Z coordinate and thickness, and contains images, labels, areas, nodes of 3d skeletons, profiles... * Insert layer sets into layers: so your electron microscopy serial sections can live inside your optical microscopy sections. * Run any ImageJ plugin on any image. * Measure everything: areas, volumes, pixel intensities, etc. using both built-in data structures and segmentation types, and standard ImageJ ROIs. And with double dissectors! * Visualize RGB color channels changing the opacity of each on the fly, non-destructively. * Annotate images non-destructively with floating text labels, which you can rotate/scale on the fly and display in any color. * Montage/register/stitch/blend images manually with transparencies, semiautomatically, or fully automatically within and across sections, with translation, rigid, similarity and affine models with automatically extracted SIFT features. * Correct the lens distortion present in the images, like those generated in transmission electron microscopy. * Add alpha masks to images using ROIs, for example to split images in two or more parts, or to remove the borders of an image or collection of images. * Model neuronal arbors with 3D skeletons (with areas or radiuses), and synapses with connectors. * Undo all steps. And much more... java, imagej plugin, neuronal circuit, reconstruction, electron microscopy, optical image volume, arbor, synapse, image, align, register, FASEB list is listed by: 3DVC
is related to: Segmented ssTEM stack of neural tissue
is related to: ImageJ
has parent organization: University of Zurich; Zurich; Switzerland
Swiss National Science Foundation 31003A_132969;
NINDS 1-R01 NS054814-05
PMID:22723842
PMID:20957184
If your work uses TrakEM2 or its associated image registration libraries, Please cite. nlx_151924 SCR_008954 2026-08-12 10:49:48 344
WebApollo: A Web-Based Sequence Annotation Editor for Community Annotation
 
Resource Report
Resource Website
10+ mentions
WebApollo: A Web-Based Sequence Annotation Editor for Community Annotation (RRID:SCR_005321) WebApollo production service resource, source code, software resource, service resource WebApollo is an extensible web-based sequence annotation editor for community annotation. No software download is required and the annotations are saved to a centralized database with real-time annotation updating. (The edit server mediates annotation changes made by multiple users.) The Web based client uses JBrowse, is fast and highly interactive. WebApollo accesses many types of genomic data including access to public data from UCSC, Ensembl, and GMOD Chado databases. Source code (BSD License) * Client source code: https://github.com/berkeleybop/jbrowse * Annotation editing engine: http://code.google.com/p/apollo-web * Data model and I/O layer: http://code.google.com/p/gbol * Trellis server code: http://code.google.com/p/genomancer sequence, annotation, genome has parent organization: Lawrence Berkeley National Laboratory
has parent organization: University of California at Berkeley; Berkeley; USA
has parent organization: Georgetown University; Washington D.C.; USA
nlx_144381 SCR_005321 WebApollo - A Web-Based Sequence Annotation Editor for Community Annotation 2026-08-12 10:49:08 13
Division of Nutrition, Physical Activity and Obesity
 
Resource Report
Resource Website
1+ mentions
Division of Nutrition, Physical Activity and Obesity (RRID:SCR_008557) data or information resource, database, portal, organization portal Our vision a world where regular physical activity, good nutrition, and healthy weight are part of everyone''s life. Our mission to lead strategic public health efforts to prevent and control obesity, chronic disease, and other health conditions though regular physical activity and good nutrition. Our goals: * Increase health-related physical activity through population-based approaches. * Improve those aspects of dietary quality most related to the population burden of chronic disease and unhealthy child development. * Decrease prevalence of obesity through preventing excess weight gain and maintenance of healthy weight loss. Our Work With fiscal year (FY) 2008 funding of 38 million, CDC''s DNPAO is working to reduce obesity and obesity-related diseases. This is done through state programs, research, surveillance, training, intervention development and evaluation, leadership, policy and environmental change, communication and social marketing, and partnership development. See At A Glance 2009 for more. Supporting State Programs The Nutrition, Physical Activity and Obesity Program (NPAO) is a cooperative agreement between the Centers for Disease Control and Prevention''s Division of Nutrition, Physical Activity and Obesity (DNPAO) and 23 state health departments. The program goal is to prevent and control obesity and other chronic diseases through healthful eating and physical activity. The state program will develop strategies to leverage resources and coordinate statewide efforts with multiple partners to address all of the following DNPAO principal target areas: 1. Increase physical activity. 2. Increase the consumption of fruits and vegetables. 3. Decrease the consumption of sugar sweetened beverages. 4. Increase breastfeeding initiation, duration and exclusivity. 5. Reduce the consumption of high energy dense foods. 6. Decrease television viewing. Our Research DNPAO supports research to enhance the effectiveness of physical activity and nutrition programs. Topics of these research activities include: * the effectiveness of parent-focused strategies to reduce the time children spend watching television * the influences of the home environment on sugar-sweetened beverage consumption * the use of policy interventions to promote physical activity * the effectiveness of breastfeeding interventions in various settings. Publications: http://www.cdc.gov/nccdphp/DNPAO/aboutus/manuscripts/index.html has parent organization: Centers for Disease Control and Prevention nif-0000-31429 SCR_008557 Division of Nutrition, Physical Activity and Obesity 2026-08-12 10:49:51 1
Brain Computer Interface 2000 Software Package
 
Resource Report
Resource Website
100+ mentions
Brain Computer Interface 2000 Software Package (RRID:SCR_007346) data processing software, software resource, software application BCI2000 is a general-purpose system for brain-computer interface (BCI) and adaptive neurotechnology research. It can also be used for data acquisition, stimulus presentation, and brain monitoring applications. The mission of the BCI2000 project is to facilitate research and applications in the areas described. Their vision is that BCI2000 will become a widely used software tool for diverse areas of real-time biosignal processing. In order to achieve this vision, BCI2000 system is available for free for non-profit research and educational purposes. BCI2000 supports a variety of data acquisition systems, brain signals, and study/feedback paradigms. During operation, BCI2000 stores data in a common format (BCI2000 native or GDF), along with all relevant event markers and information about system configuration. BCI2000 also includes several tools for data import/conversion (e.g., a routine to load BCI2000 data files directly into Matlab) and export facilities into ASCII. BCI2000 also facilitates interactions with other software. For example, Matlab scripts can be executed in real-time from within BCI2000, or BCI2000 filters can be compiled to execute as stand-alone programs. Furthermore, a simple network-based interface allows for interactions with external programs written in any programming language. For example, a robotic arm application that is external to BCI2000 may be controlled in real time based on brain signals processed by BCI2000, or BCI2000 may use and store along with brain signals behavioral-based inputs such as eye-tracker coordinates. Because it is based on a framework whose services can support any BCI implementation, the use of BCI2000 provides maximum benefit to comprehensive research programs that operate multiple BCI2000 installations to collect data for a variety of studies. The most important benefits of the system in such situations are: - A Proven Solution - Facilitates Operation of Research Programs - Facilitates Deployment in Multiple Sites - Cross-Platform and Cross-Compiler Compatibility - Open Resource Sponsors: BCI2000 development is sponsored by NIH/NIBIB R01 and NIH/NINDS U24 grants. Keywords: General, Purpose, Systems, Brain, Computer, Interface, Research, Application, Brain, Diverse, Educational, Laboratory, Software, Network, Signals, Behavioral, Eye, Tracker, is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: National Institutes of Health
NIBIB R01 EB026439;
NINDS U24 NS109103;
NIBIB P41 EB018783
nif-0000-00251 http://www.nitrc.org/projects/bci2000, http://www.bci2000.org, https://www.neurotechcenter.org/software SCR_007346 BCI2000 2026-08-12 10:49:44 180
GRETNA
 
Resource Report
Resource Website
100+ mentions
GRETNA (RRID:SCR_009487) GRETNA data processing software, software resource, software application A graph theoretical network analysis toolbox which allows researchers to perform comprehensive analysis on the topology of brain connectome by integrating the most of network measures studied in current neuroscience field. computational neuroscience, eeg, meg, electrocorticography, magnetic resonance, pet, spect is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is affiliated with: Functional Connectivity Analysis Tool for near-infrared spectroscopy data
GNU General Public License nlx_155634 SCR_009487 2026-08-12 10:49:57 493
Human Brain Atlas
 
Resource Report
Resource Website
1+ mentions
Human Brain Atlas (RRID:SCR_006131) Human Brain Atlas data or information resource, atlas, video resource A labeled three-dimensional atlas of the human brain created from MRI images. In conjunction are presented anatomically labeled stained sections that correspond to the three-dimensional MRI images. The stained sections are from a different brain than the one which was scanned for the MRI images. Also available the major anatomical features of the human hypothalamus, axial sections stained for cell bodies or for nerve fibers, at six rostro-caudal levels of the human brain stem; images and Quicktime movies. The MRI subject was a 22-year-old adult male. Differing techniques used to study the anatomy of the human brain all have their advantages and disadvantages. Magnetic resonance imaging (MRI) allows for the three-dimensional viewing of the brain and structures, precise spatial relationships and some differentiation between types of tissue, however, the image resolution is somewhat limited. Stained sections, on the other hand, offer excellent resolution and the ability to see individual nuclei (cell stain) or fiber tracts (myelin stain), however, there are often spatial distortions inherent in the staining process. The nomenclature used is from Paxinos G, and Watson C. 1998. The Rat Brain in Stereotaxic Coordinates, 4th ed. Academic Press. San Diego, CA. 256 pp human, adult, mri, fiber stain, anatomy, normal, neuroanatomy, nissl stain, image, brainstem, cell body, nerve fiber, brain, coronal, sagittal, horizontal, 3d model, montage, weil, hypothalamus is used by: NIF Data Federation
has parent organization: Michigan State University; Michigan; USA
NSF IBN 0131267;
NSF 0131826;
NSF 0131028
Copyrighted, Public, Request that you secure their permission, Acknowledgement required nif-0000-00088 SCR_006131 MSU Brain Biodiversity Bank - Human Brain Atlas, Michigan State University Brain Biodiversity Bank - Human Brain Atlas 2026-08-12 10:49:20 3
Generalized Covariance Analysis
 
Resource Report
Resource Website
1+ mentions
Generalized Covariance Analysis (RRID:SCR_009488) gCVA data processing software, image analysis software, software resource, software application A platform for any Principal Component Analysis (PCA)-based analysis on functional neuroimaging data (PET and fMRI). Includes: * Ordinal Trend Canonical Variance Analysis for parametric designs (C. Habeck et al. A New Approach to Spatial Covariance Modeling of Functional Brain Imaging Data: Ordinal Trend Analysis. Neural Computation 2005; 17: 1602-1645) * Partial Least Squares for any design matrix * Subprofile Scaling Model for cross-sectional designs (JR. Moeller, Strother SC. A regional covariance approach to the analysis of functional patterns in positron emission tomographic data.J Cereb Blood Flow Metab. 1991 Mar;11(2):A121-35.) magnetic resonance, pet, spect, fmri is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) GNU General Public License nlx_155635 SCR_009488 Generalized Covariance Analysis (gCVA) 2026-08-12 10:50:00 9
GAMMA
 
Resource Report
Resource Website
500+ mentions
GAMMA (RRID:SCR_009484) GAMMA data processing software, image analysis software, software resource, software application GAMMA suite is an open-source cross-platform data mining software package designed to analyze neuroimaging data. A neuroimaging study often focuses on biomarker detection and classification. We designed and implemented a Bayesian, multivariate, nonparametric suite of algorithms for analyzing neuroimaging data. The GAMMA suite can be used for brain morphometric analysis, lesion-deficit analysis, and functional MR data analysis. reusable library, analyze, c, c++, console (text based), computed tomography, cygwin, hp-ux, linux, macos, microsoft, modeling, magnetic resonance, nifti, pet, spect, posix/unix-like, quantification, statistical operation, volumetric analysis, win32 (ms windows), windows, neuroimaging is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) GNU General Public License nlx_155632 SCR_009484 GAMMA Suite 2026-08-12 10:49:57 692
Virtual Fly Brain
 
Resource Report
Resource Website
10+ mentions
Virtual Fly Brain (RRID:SCR_004229) VFB data or information resource, expression, atlas, neurons An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the adult Drosophila melanogaster brain. Drosophila, brain, neurons, innervation patterns, gene expression, transgene expression, phenotypes, neuroanatomy, neurobiology uses: Drosophila Gross Anatomy Ontology
uses: Drosophila Development Ontology
is related to: FlyBase
is related to: Flycircuit
is related to: Janelia Research
has parent organization: University of Edinburgh; Scotland; United Kingdom
has parent organization: University of Cambridge; Cambridge; United Kingdom
has parent organization: European Bioinformatics Institute
Wellcome Trust PMID:22180411 nlx_143644 http://www.virtualflybrain.org/site/vfb_site/home.htm SCR_004229 VirtualFlyBrain.org, VFB, Virtual Fly Brain 2026-08-12 10:48:57 47
SPInDel
 
Resource Report
Resource Website
1+ mentions
SPInDel (RRID:SCR_004509) SPInDel data or information resource, data set, software resource A multifunctional workbench for species identification using insertion/deletion variants. The SPInDel workbench provides a step-by-step environment for the alignment of target sequences, selection of informative hypervariable regions, design of PCR primers and the statistical validation of the species-identification process. It includes a large dataset comprising nearly 1,800 numeric profiles for the identification of eukaryotic, prokaryotic and viral species. virus, indel, dna barcoding, alignment, nucleotide sequence, visualization, conserved region, pcr primer, phylogenetic, variant is listed by: OMICtools
has parent organization: University of Porto; Porto; Portugal
has parent organization: SourceForge
PMID:22978681
PMID:20923781
Acknowledgement requested, Free, Public OMICS_01496 SCR_004509 SPecies Identification by Insertions/Deletions, SPInDel - Species identification by insertions/deletions 2026-08-12 10:48:59 2
Pedianet
 
Resource Report
Resource Website
10+ mentions
Pedianet (RRID:SCR_004107) data or information resource, database, portal Independent network and system used to collect epidemiological information for clinical research from family paediatricians in Italy. It is based on the transmission of specific data from computerised clinical files. Such data is collected anonymously by a central server in Padua, where it is validated and elaborated. pediatric, clinical, epidemiology, child, young human, pharmacovigilance, primary care, pediatrician is related to: EMIF Wellcome Glaxo nlx_158583 SCR_004107 Pedianet project 2026-08-12 10:48:55 18
epigenomix
 
Resource Report
Resource Website
1+ mentions
epigenomix (RRID:SCR_006407) epigenomix data processing software, software resource, software application Software package for the integrative analysis of microarray based gene expression and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types. epigenetic, gene expression, microarray, histone modification, chip-seq, classification, differential expression, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Bioconductor
PMID:24403540 GNU Lesser General Public License, v3 biotools:epigenomix, OMICS_02205 https://bio.tools/epigenomix SCR_006407 epigenomix - Epigenetic and gene expression data normalization and integration with mixture models 2026-08-12 10:49:25 2
ASL data processing tool box
 
Resource Report
Resource Website
1+ mentions
ASL data processing tool box (RRID:SCR_005997) data processing software, software application, software toolkit, software resource Tool box for arterial spin labeled perfusion MRI data processing. It is based on SPM and Matlab. More detailed documentation can be found in asl_perf_subtract.m, the main function for calculating CBF value. It supports 3D or 4D Analyze or Nifiti format and PASL, CASL, and PCASL data. It contains the code for calculating CBF and a set of SPM batch scripts for preprocessing and statistical analysis. quantification, statistical operation, spm, arterial spin label, perfusion, mri, matlab, magnetic resonance is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: SPM
is related to: ASL spm8
has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA
GNU General Public License nlx_151371 SCR_005997 2026-08-12 10:49:18 3
AutoSeg
 
Resource Report
Resource Website
10+ mentions
AutoSeg (RRID:SCR_009438) AutoSeg data processing software, image analysis software, software resource, software application A novel C++ based application developped at UNC-Chapel Hill that performs automatic brain tissue classification and structural segmentation. AutoSeg is designed for use with human and non-human primate pediatric, adolescent and adult data. AutoSeg uses a BatchMake pipeline script that includes the main steps of the framework entailing N4 bias field correction, rigid registration to a common coordinate image, tissue segmentation, skull-stripping, intensity rescaling, atlas-based registration, subcortical segmentation and lobar parcellation, regional cortical thickness and intensity statistics. AutoSeg allows efficient batch processing and grid computing to process large datasets and provides quality control visualizations via Slicer3 MRML scenes. analyze, c++, expectation minimization, image-to-image, image-to-template, labeling, linux, macos, microsoft, magnetic resonance, nonlinear warp, nrrd, posix/unix-like, region of interest, registration, resampling, segmentation, spatial transformation, spline interpolation, volumetric analysis, warping, win32 (ms windows), windows, workflow, pediatric, adolescent, adult, young is used by: UNC-Wisconsin Neurodevelopment Rhesus MRI Database
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA
BSD License nlx_155582 SCR_009438 2026-08-12 10:49:56 24
BXH/XCEDE Tools
 
Resource Report
Resource Website
1+ mentions
BXH/XCEDE Tools (RRID:SCR_009439) BXH/XCEDE Tools data processing software, image analysis software, software resource, software application A collection of data processing and image analysis tools for data in BXH or XCEDE format. This includes data format encapsulation/conversion, event-related analysis, QA tools, and more. These tools form the basis of the fBIRN QA procedures and are also distributed as part of the fBIRN Data Upload Scripts. analyze, c, c++, console (text based), dicom, format conversion, linux, macos, mgh/mgz, microsoft, minc, magnetic resonance, nifti, perl, posix/unix-like, quantification, sh/bash, statistical operation, unix shell, windows is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Function BIRN
BIRN License nlx_155583 SCR_009439 2026-08-12 10:49:56 4

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