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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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TrumpetPlots Resource Report Resource Website 1+ mentions |
TrumpetPlots (RRID:SCR_023742) | software application, data processing software, data visualization software, software toolkit, software resource, 3d visualization software | Software R package to visualize relationship between allele frequency and effect size in genetic association studies. | genetic association studies, visualization of genetic association studies, allele frequency, effect size, genetics, | NIMH R01 MH122866; Brain and Behavior Research Foundation ; Icahn School of Medicine at Mount Sinai |
DOI:10.1101/2023.04.21.23288923 | Free, Available for downlaod, Freely available | https://juditgg.shinyapps.io/shinytrumpets/ | SCR_023742 | 2026-02-16 09:50:52 | 1 | ||||||||
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PyMVPA Resource Report Resource Website 100+ mentions |
PyMVPA (RRID:SCR_006099) | PyMVPA | software application, software resource, software toolkit | A Python package intended to ease statistical learning analyses of large datasets. It offers an extensible framework with a high-level interface to a broad range of algorithms for classification, regression, feature selection, data import and export. While it is not limited to the neuroimaging domain, it is eminently suited for such datasets. PyMVPA is truly free software (in every respect) and additionally requires nothing but free-software to run. Decoding patterns of neural activity onto cognitive states is one of the central goals of functional brain imaging. Standard univariate fMRI analysis methods, which correlate cognitive and perceptual function with the blood oxygenation-level dependent (BOLD) signal, have proven successful in identifying anatomical regions based on signal increases during cognitive and perceptual tasks. Recently, researchers have begun to explore new multivariate techniques that have proven to be more flexible, more reliable, and more sensitive than standard univariate analysis. Drawing on the field of statistical learning theory, these new classifier-based analysis techniques possess explanatory power that could provide new insights into the functional properties of the brain. However, unlike the wealth of software packages for univariate analyses, there are few packages that facilitate multivariate pattern classification analyses of fMRI data. This Python-based, cross-platform, open-source software toolbox software toolbox for the application of classifier-based analysis techniques to fMRI datasets makes use of Python's ability to access libraries written in a large variety of programming languages and computing environments to interface with the wealth of existing machine learning packages. | python, machine learning, fmri, eeg, neuroimaging, image analysis, scripting, multivariate pattern analysis, brain, meg, extracellular recording, algorithm, reusable library, analyze, c, console (text based), eeg, meg, electrocorticography, frequency domain, independent component analysis, linear, modeling, magnetic resonance, multivariate analysis, nifti, nonlinear, os independent, pet, spect, principal component analysis, python, regression, spatial transformation, statistical operation, temporal transformation, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: neurodebian is related to: CoSMoMVPA has parent organization: Dartmouth College; New Hampshire; USA has parent organization: Otto-von-Guericke University Magdeburg; Saxony-Anhalt; Germany |
German Academic Exchange Service PPP-USA D/05/504/7; NIMH MH080526; NSF SBE 0751008; James McDonnell Foundation 220020127 |
PMID:19184561 PMID:19212459 PMID:20582270 |
MIT License | nlx_151596 | http://www.nitrc.org/projects/pymvpa | SCR_006099 | Python MVPA, Multivariate Pattern Analysis in Python, PyMVPA - Multivariate Pattern Analysis in Python | 2026-02-16 09:46:37 | 140 | ||||
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Eagle Resource Report Resource Website 50+ mentions |
Eagle (RRID:SCR_015991) | software resource, software toolkit | Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods. | hmm, hidden markov model, statistic, estimation, haplotype, phase, reference, panel, sequencing, algorithm, analysis, probability |
is listed by: Debian is listed by: OMICtools has parent organization: Broad Institute |
NHGRI R01 HG006399; NIMH R01 MH101244; NHGRI F32HG007805; Wellcome Trust WT098051; Austrian Science Fund J-3401; NHGRI HG007022; NHLBI HL117626; Fannie and John Hertz Foundation ; NCRR S10 RR028832; NWO 480-05-003; Dutch Brain Foundation |
PMID:27694958 PMID:27270109 |
Free, Available for download, Freely available | OMICS_14099, SCR_017262 | https://sources.debian.org/src/bio-eagle/ https://github.com/poruloh/Eagle https://data.broadinstitute.org/alkesgroup/Eagle/downloads/ |
SCR_015991 | Bio-eagle, Eagle1, Eagle2 | 2026-02-16 09:48:58 | 51 | |||||
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ALICE Resource Report Resource Website 1+ mentions |
ALICE (RRID:SCR_017463) | software resource, software toolkit | Software tool for automatic localization of intra-cranial electrodes for clinical and high density grids. Software for coregistering high density ECoG grids to MRI anatomy. | Localization, intra-cranial, electrode, clinical, high density, grid, coregistering, ECoG, MRI, BRAIN Initiative | is recommended by: BRAIN Initiative | NIMH MH111417; BrainGain Smart Mix Programme ; Dutch Technology Foundation ; Netherlands Organization for Scientific Research |
PMID:29100838 | Restricted | SCR_017463 | Automatic Localization of Intra-Cranial Electrodes | 2026-02-16 09:49:14 | 1 | |||||||
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lapdftext Resource Report Resource Website |
lapdftext (RRID:SCR_006167) | lapdftext, LA-PDFText, | software application, software resource, text extraction software | Software that facilitates accurate extraction of text from PDF files of research articles for use in text mining applications. It is intended for both scientists and natural language processing (NLP) engineers interested in getting access to text within specific sections of research articles. The system extracts text blocks from PDF-formatted full-text research articles and classifies them into logical units based on rules that characterize specific sections. The LA-PDFText system focuses only on the textual content of the research articles. The current version of LA-PDFText is a baseline system that extracts text using a three-stage process: * identification of blocks of contiguous text * classification of these blocks into rhetorical categories * extraction of the text from blocks grouped section-wise. | text mining, pdf, text extraction, natural language processing |
is listed by: FORCE11 has parent organization: University of Southern California; Los Angeles; USA |
NSF 0849977; NIGMS RO1-GM083871; NIMH 1R01MH079068-01A2; NCRR U24 RR025736-01 |
PMID:22640904 | Acknowledgement requested, GNU General Public License, v3 | nlx_151668 | SCR_006167 | Layout-Aware PDF Text Extraction, Layout-Aware Text Extraction from Full-text PDF of Scientific Articles, lapdftext: Layout-Aware Text Extraction from Full-text PDF of Scientific Articles | 2026-02-16 09:46:38 | 0 | |||||
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NIMH Psychoactive Drug Screening Program Resource Report Resource Website 50+ mentions |
NIMH Psychoactive Drug Screening Program (RRID:SCR_005630) | PDSD, NIMH PDSP | production service resource, service resource, analysis service resource, material analysis service | This service provides screening of novel psychoactive compounds for pharmacological and functional activity at cloned human or rodent CNS receptors, channels, and transporters. Bryan Roth MD, PhD (University of North Carolina Chapel Hill) will perform pharmacological and functional screening of novel compounds as a contractor to NIMH. Screening of compounds is provided to qualified academic investigators at no cost. * Assays using for a large number of cloned human or rodent cDNAs for CNS receptors, channels and transporters. For a list of current receptors/transporters go to:clones.html * Ki determinations * Functional assays to determine effects on second messenger systems, channel activity and transporter function * Cloned receptors are also available at no cost to qualified investigators. * Assays are now available for bioavailability predictions (CaCo2, MDR-1) and cardiovascular toxicity predictions (HERG, 5-HT2B) Who is eligible * Academic investigators involved in basic or clinical research relevant to mental health. * Projects from research and development areas in small businesses relevant to mental and behavioral science. * Areas of interest to NIMH include the design and development of new chemical entities and small molecules as research tools, probes, targeted drug delivery systems, and PET ligands for brain imaging. * Research areas of interest are described in the Division of Basic and Clinical Neuroscience Research webpage, http://www.nimh.nih.gov/about/organization/dnbbs/index.shtml. | has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA | NIMH contract HHSN-271-2008-00025-C | nlx_146244 | SCR_005630 | National Institute of Mental Health Psychoactive Drug Screening Program | 2026-02-16 09:46:30 | 75 | ||||||||
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NIMH Toxicological Screens of Novel Ligands Resource Report Resource Website |
NIMH Toxicological Screens of Novel Ligands (RRID:SCR_005631) | Toxicological Evaluation of Novel Ligands | production service resource, service resource, analysis service resource, material analysis service | The purpose of the NIMH Toxicological Evaluation of Novel Ligands Program is to accelerate the discovery, development, and application of novel ligands for PET, SPECT, and MRI imaging in humans by providing toxicology and safety assessment of promising, target-selective compounds. The program will also provide limited assessment of novel psychoactive agents for clinical research and as potential therapeutics. Toxicology and safety data generated by the program will be used to support an Investigational New Drug (IND) application to the Food and Drug Administration (FDA), or for Radioactive Drug Research Committee (RDRC) evaluation of a compound for human studies. The contract will evaluate toxicity and safety of compounds submitted for testing which may include, but are not limited to, novel chemical entities, structural analogs of compounds with an IND, or analogs of FDA-approved drugs. The services available under this program fall under four general phases: (1) analytical, (2) pharmacokinetics, (3) preliminary safety, and (4) IND-directed toxicity including safety pharmacology. What is available A broad range of tasks are available for assessing the safety and/or pharmacokinetics of each ligand. Specific capabilities available to investigators include: * Validation of the analytical methods for quantitating drug concentrations in dosing solutions, biological fluids, and tissues, as required. Determination of plasma drug levels in animals administered the agent under study, and calculation of pharmacokinetic parameters derived from these data. * Determination of bioavailability of the drug after different routes of administration, including oral, intravenous (i.v.), subcutaneous (s.c.), intramuscular (i.m.), or intraperitoneal (i.p.), as needed. Calculation of the pharmacokinetic parameters from the derived data. * In vitro evaluation of hepatotoxicity in human and animal liver cells. * Preclinical acute toxicity evaluations on lead compounds, evaluating clinical observations, body weights, clinical pathology, histopathology, and plasma drug levels in rodents and non-rodent species. Other toxicology endpoints may be selected if needed. * Subacute and subchronic toxicity evaluations in rodents and large animal species, evaluating clinical observations, body weights, clinical pathology, and histopathology. * Genotoxicity assessments using a battery of appropriate assays. Since these preclinical studies are needed to demonstrate to the FDA that a candidate medication or imaging agent is understood well enough for designing appropriate clinical treatment regimens, most of the work to be conducted to achieve these objectives must be performed and the resulting data analyzed and reported in strict compliance with the FDA''s GLP regulations for nonclinical laboratory studies (21 CFR 58). These data must be obtained by carefully planned and skillfully executed methods that are specific, accurate, and precise. The applicable portions of the accumulated safety data will be included in documents submitted to the FDA in support of regulatory applications. Who is eligible Academic investigators involved in basic or clinical research relevant to mental health. Research areas are described on the NIMH website. | ligand, toxicology, pet, spect, mri, imaging, safety | has parent organization: Stanford Research Institute International | NIMH | nlx_146245 | SCR_005631 | Toxicological Evaluation of Novel Ligands Program, NIMH Toxicological Screens of Novel Ligands Program | 2026-02-16 09:46:30 | 0 | |||||||
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Mouse Brain Atlases Resource Report Resource Website 1+ mentions |
Mouse Brain Atlases (RRID:SCR_007127) | Mouse Brain Atlases | data or information resource, atlas | High-resolution electronic atlases for mouse strains c57bl/6j, a/j, and dba/2j in either coronal or horizontal section. About this Atlas: The anterior-posterior coordinates are taken from an excellent print atlas of a C57BL/6J brain by K. Franklin and G. Paxinos (The Mouse Brain in Stereotaxic Coordinates, Academic Press, San Diego, 1997, ISBN Number 0-12-26607-6; Library of Congress: QL937.F72). The abbreviations we have used to label the sections conform to those in the Franklin-Paxinos atlas. A C57BL/6J mouse brain may contain as many as 75 million neurons, 23 million glial cells, 7 million endothelial cells associated with blood vessels, and 3 to 4 million miscellaneous pial, ependymal, and choroid plexus cells (see data analysis in Williams, 2000). We have not yet counted total cell number in DBA/2J mice, but the counts are probably appreciably lower.The brain and sections were all processed as described in our methods section. The enlarged images have a pixel count of 1865 x 1400 and the resolution is 4.5 microns/pixel for the processed sections.Plans: In the next several years we hope to add several additional atlases of the same sort for other strains of mice. A horizontal C57BL/6J atlas and a DBA/2J coronal atlas were completed by Tony Capra, summer 2000, and additional atlases may be made over the next several years. As describe in the MBL Procedures Section is not hard to make your own strain-specific atlas from the high resolution images in the MBL. | genetics, anatomy, coronal, cerebellum, c57bl/6j, dba/2j, a/j, horizontal, morphology, subcortical, volume | has parent organization: Mouse Brain Library | Human Brain Project ; NIDA ; NSF ; NIMH P20-MH 62009 |
nif-0000-00044 | SCR_007127 | 2026-02-16 09:46:53 | 7 | ||||||||
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NIMH Director's Blog Resource Report Resource Website |
NIMH Director's Blog (RRID:SCR_008841) | data or information resource, blog, narrative resource | Blog by the NIMH Director, Thomas R. Insel, M.D. Users may sort posts by topic and/or subsribe to the RSS Feed, http://www.nimh.nih.gov/site-info/feed-directors-blog.atom | attention deficit-hyperactivity disorder, autism, bipolar disorder, borderline personality disorder, depression, depressive disorder, eating disorder, obsessive-compulsive disorder, post-traumatic stress disorder, schizophrenia, woman, mental health, child, adolescent, research, military, trauma, diversity, ethnicity, genetics, aids, hiv, imaging, medication, suicide, treatment, human, anxiety disorder, prevention | has parent organization: National Institute of Mental Health | NIMH | nlx_146220 | SCR_008841 | National Institute of Mental Health Directors Blog, National Institute of Mental Health Director's Blog, NIMH Directors Blog | 2026-02-16 09:47:17 | 0 | ||||||||
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Allen Brain Cell Atlas Resource Report Resource Website 10+ mentions |
Allen Brain Cell Atlas (RRID:SCR_024440) | expression atlas, data or information resource, atlas | Provides platform for visualizing multimodal single cell data across mammalian brain and aims to empower researchers to explore and analyze multiple whole brain datasets simultaneously. Allen Institute and its collaborators continue to add new modalities, species, and insights to the ABC Atlas. Atlas as part of Brain Knowledge Platform will enable neuroscience community to identify more cell types in brain; Investigate spatial location of cell types; Investigate gene expression and co-expression patterns in cell types; Refine boundaries and knowledge of brain regions defined by gene expression. | visualizing multimodal single cell data across mammalian brain, explore and analyze multiple whole brain datasets, identify cell types in brain, brain regions defined by gene expression, |
has parent organization: Allen Institute is organization facet of: BICCN |
NIMH MH130919 | Free, Freely available | SCR_024440 | Allen Brain Cell (ABC) Atlas, The Allen Brain Cell Atlas, ABC Atlas | 2026-02-16 09:50:49 | 42 | ||||||||
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Harvard - Oxford Cortical Structural Atlas Resource Report Resource Website 100+ mentions |
Harvard - Oxford Cortical Structural Atlas (RRID:SCR_001476) | Atlases | reference atlas, data or information resource, atlas | 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. | male, female, t1-weighted image, cortical, subcortical, neuroanatomy, cortex |
has parent organization: Harvard University; Cambridge; United States is a plug in for: FSL |
Healthy | NCRR R01 RR16594-01A1; NIMH K01 MH01798; NINDS R01 NS052585-01; NIMH K08 MH01573 |
Free, Freely available | nlx_152707 | SCR_001476 | , Harvard Oxford Cortical Structural Atlas, Harvard-Oxford cortical and subcortical structural atlases, Harvard Oxford Atlas | 2026-02-16 09:45:29 | 144 | |||||
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HUDSEN Electronic Atlas of the Developing Human Brain Resource Report Resource Website 1+ mentions |
HUDSEN Electronic Atlas of the Developing Human Brain (RRID:SCR_002056) | EADHB, HUDSEN EADHB | data or information resource, video resource, atlas | Interactive digital atlas and movies comprising 3-D reconstructions at all stages of human development from Carnegie Stage 12 (CS12; ~26 days post conception (dpc)) to CS23 (~ 56 dpc) and anatomical annotations of the 3-D models linked to an anatomical database. The 3D models are generated using Optical Projection Tomography (OPT; Sharpe et al 2002). The digital atlas is also linked to a gene expression database that has been developed from the Edinburgh Mouse Atlas Project gene expression database (EMAGE). In the future, the HUDSEN EADHB aims to provide the wider scientific and medical communities with a dynamic tool for documenting and analyzing gene expression patterns and morphological changes in the developing human brain. | human development, carnegie stage, annotation, optical projection tomography, embryonic human, embryo, 3d, 3d model, brain, gene expression, anatomy, molecular neuroanatomy resource, developing |
is related to: EMAGE Gene Expression Database has parent organization: HUDSEN has parent organization: Newcastle University; Newcastle upon Tyne; United Kingdom |
NIMH R01 MH070370; NICHD HD39928-02 |
PMID:20979583 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-12494 | http://www.ncl.ac.uk/ihg/EADHB/ | SCR_002056 | Electronic Atlas of the Developing Human Brain | 2026-02-16 09:45:43 | 1 | ||||
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Functional Regression Analysis of DTI Tract Statistics Resource Report Resource Website |
Functional Regression Analysis of DTI Tract Statistics (RRID:SCR_002293) | FRATS | data processing software, software application, software resource, image analysis software | 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. | computational neuroscience, imaging genomics, magnetic resonance, regression analysis, dti, statistics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
NSF BCS-08-26844; NCRR UL1-RR025747-01; NIMH MH086633; NIA AG033387; NIMH MH064065; NICHD HD053000; NIMH MH070890; NINDS R01NS055754; NIBIB U54 EB005149-01 |
PMID:20335089 | Academic Free License | nlx_155629 | SCR_002293 | Functional Regression Analysis of DTI | 2026-02-16 09:45:43 | 0 | |||||
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DTI-TEMPLATE-RHESUS-MACAQUES Resource Report Resource Website 1+ mentions |
DTI-TEMPLATE-RHESUS-MACAQUES (RRID:SCR_002482) | DTI-TEMPLATE-RHESUS-MACAQUES | reference atlas, data or information resource, atlas | A population-specific DTI template for young adolescent Rhesus Macaque (Macaca mulatta) monkeys using 271 high-quality scans. Using such a large number of animals in generating a template allows it to account for variability in the species. Their DTI template is based on the largest number of animals ever used in generating a computational brain template. It is anticipated that their DTI template will help facilitate voxel-based and tract specific WM analyses in non-human primate species, which in turn may increase our understanding of brain function, development, and evolution. | magnetic resonance, dti, young, adolescent, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
NIMH MH62015; NIMH MH084051; NIMH MH080826; NIMH MH46729; NIMH MH81884; NIMH MH018931; NIBIB R03-EB009321 |
PMID:21803162 | Free, Available for download, Freely available | nlx_155872 | SCR_002482 | 2026-02-16 09:45:48 | 3 | ||||||
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FMRLAB Resource Report Resource Website 1+ mentions |
FMRLAB (RRID:SCR_005164) | FMRLAB | data processing software, software application, software resource | A Matlab toolbox for fMRI data analysis using Independent Component Analysis (ICA). It provides an integrated environment to manage, process and analyze fMRI data in a single framework so that users can complete the analysis without switching between software. In addition, it provides an interactive Matlab graphic user interface (GUI). All the necessary processes to apply ICA to fMRI data and review its results can be run from the graphic interface. The FMRLAB processing flow is straightforward. Custom analyses can be performed with Matlab scripts using the FMRLAB functions and data structure. Since fMRI data analysis is a complex enterprise, including digital image processing, statistical analysis and data visualization, an integrated framework combining processing elements is desired eagerly by users in the neuroimaging community. Recently, large number of software tools for data analysis and visualization have been developed for this purpose. However, most of these tools use model-based statistical methods which assume that the users know the hemodynamic response (HR) for their paradigm in advance and can specify a reasonable HR model. Often, however, accurate or reasonable response HR models are unavailable. An alternative data-driven method, infomax ICA (McKeown et al., 1998), does not require that an a priori HR model, instead deriving HRs of spatially independent components of the entire data set from the higher-order statistics of the data themselves. FMRLAB is a toolbox running under Matlab containing necessary components for data-driven fMRI data analysis using the highly reliable infomax ICA algorithm (Bell & Sejnowski, 1995), normalized (Amari, 1999), extended (Lee, Girolami and Sejnowski, 1999) and automated by Makeig et al. FMRLAB has been developed under Matlab 6.1 running on Red Hat Linux. FMRLAB Features * Graphic user interface * Flexible data importing * Interactive data plotting * Computationally efficient * Defined FMRI data structure * Independent component browser * Smooth, transparent component exporting and spatial normalization process * Interface with other software for further analysis or visualization. * SPM-style component plots (MIP, 2-D slice overlay and 3-D) | fmri, fmr lab, anatomy, brain mapping, data analysis, independent component analysis, neuroimaging, image processing, statistical analysis, data visualization, matlab |
is related to: FreeSurfer has parent organization: Swartz Center for Computational Neuroscience |
NIMH 5RO1MHO61619-03 | nif-0000-00077 | SCR_005164 | 2026-02-16 09:46:26 | 3 | ||||||||
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NeuroSynth Resource Report Resource Website 1000+ mentions |
NeuroSynth (RRID:SCR_006798) | Neurosynth | data or information resource, database, source code, software resource | Platform for large-scale, automated synthesis of functional magnetic resonance imaging (fMRI) data extracted from published articles. It''s a website wrapped around a set of open-source Python and JavaScript packages. Neurosynth lets you run crude but useful analyses of fMRI data on a very large scale. You can: * Interactively visualize the results of over 3,000 term-based meta-analyses * Select specific locations in the human brain and view associated terms * Browse through the nearly 10,000 studies in the database Their ultimate goal is to enable dynamic real-time analysis, so that you''ll be able to select foci, tables, or entire studies for analysis and run a full-blown meta-analysis without leaving your browser. You''ll also be able to do things like upload entirely new images and obtain probabilistic estimates of the cognitive states most likely to be associated with the image. | activation foci, magnetic resonance imaging assay, brain, human, fmri, neuroimaging, python, image, functional neuroimaging, FASEB list |
is used by: NeuroVault is used by: NIF Data Federation is listed by: GitHub is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Brainspell has parent organization: University of Texas at Austin; Texas; USA |
NIMH R01MH096906 | PMID:21706013 | Neurosynth Automated Coordinate Extraction (ACE) tools under, Open unspecified license, Open Software License, v3, Http://www.nitrc.org/include/glossary.php#552, Software is, Free, Copyright and permission notice required | nlx_55906 | http://www.nitrc.org/projects/neurosynth https://github.com/tyarkoni/neurosynth |
SCR_006798 | Neurosynth.org | 2026-02-16 09:46:48 | 1174 | ||||
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CellTax vignette Resource Report Resource Website 1+ mentions |
CellTax vignette (RRID:SCR_017000) | data set, data or information resource | Cellular Taxonomy of Mouse Visual Cortex by analyzing gene expression patterns at single cell level. Construction of cellular taxonomy of one cortical region, primary visual cortex, in adult mice done on basis of single cell RNA sequencing. | data, classification, cell, type, mammalian, brain, cellular, taxonomy, mouse, visual, cortex, gene, expression, pattern, cortical, region |
is related to: Allen Brain Atlas API is related to: Allen Mouse Brain Reference Atlas is related to: Allen Cell Types Database has parent organization: Allen Institute for Brain Science has parent organization: Allen Brain Atlas |
Allen Institute for Brain Science ; NEI R01 EY023173; NIMH U01 MH105982 |
PMID:26727548 | Free, Public | SCR_017000 | Cellular Taxonomy of the Mouse Visual Cortex, Cellular Taxonomy of the Mouse Visual Cortex Allen Institue for Brain Science | 2026-02-16 09:49:08 | 3 | |||||||
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Multimodal Surface Matching Resource Report Resource Website |
Multimodal Surface Matching (RRID:SCR_024929) | MSM | software application, data processing software, registration software, image analysis software, software resource | Software tool for registering cortical surfaces. Capable of driving alignment using wide variety of descriptors of brain architecture, function and connectivity. | registering cortical surfaces, brain architecture, function and connectivity, | is a plug in for: FSL | NIMH 1U54MH091657; NIMH F30 MH097312 |
PMID:24939340 | Free, Freely available | SCR_024929 | MSM:Multimodal Surface Matching | 2026-02-16 09:50:55 | 0 | ||||||
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FMRIB’s Integrated Registration and Segmentation Tool Resource Report Resource Website 1+ mentions |
FMRIB’s Integrated Registration and Segmentation Tool (RRID:SCR_024921) | FIRST | software application, data processing software, data analysis software, registration software, image analysis software, software resource, segmentation software | Software model based segmentation and registration tool. Used for segmentation of sub-cortical structures. Introduces basic segmentation and vertex analysis for detecting group differences. | Functional Magnetic Resonance Imaging of the Brain, segmentation, registration, volumetric segmentation, performing vertex analysis, |
is related to: Multimodal Image Segmentation Tool is a plug in for: FSL |
NCRR P41 RR14075; NINDS R01 NS052585; NCRR R01 RR16594; NIMH K08 MH01573; NIMH K01 MH01798; NIDA R01 DA017905 |
PMID:21352927 | Free, Freely available | SCR_024921 | , Functional Magnetic Resonance Imaging of the Brain's Integrated Registration and Segmentation Tool | 2026-02-16 09:50:50 | 2 | ||||||
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Borzoi Resource Report Resource Website 1+ mentions |
Borzoi (RRID:SCR_026619) | software toolkit, source code, software resource | 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. | Borzoi models access, convolutional neural networks, predict RNA-seq coverage, | Common Fund of the Office of the Director ; NCI ; NHGRI ; NHLBI ; NIDA ; NIMH ; NINDS |
PMID:39779956 | Free, Available for download, Freely available | SCR_026619 | 2026-02-16 09:51:12 | 1 |
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