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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Collaborative Cohort of Cohorts for COVID-19 Research
 
Resource Report
Resource Website
1+ mentions
Collaborative Cohort of Cohorts for COVID-19 Research (RRID:SCR_026322) C4R data or information resource, topical portal, disease-related portal, portal 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. nationwide study, determine factors, predict disease severity, long-term health impacts, COVID-19 COVID-19 NHLBI ;
NINDS ;
NIA
SCR_026322 2026-02-15 09:23:14 1
ArUco
 
Resource Report
Resource Website
10+ mentions
ArUco (RRID:SCR_026572) instrument resource, source code, software resource Automated rodent behavioral scoring system, complete with 3D design files and code/software. System monitors behavioral engagement using open-source software. 3D design files and necessary software has been made available, as well as code that can be used for data analysis. OpenBehavior, Aruco marker based tracking, pose estimation, rodent behavioral session, is listed by: OpenBehavior NINDS R01NS110823;
United States (US) Department of Veterans Affairs Rehabilitation Research and Development Service ;
University of Texas at Dallas
DOI:10.1523/ENEURO.0500-23.2024 Free, Available for download, Freely available https://edspace.american.edu/openbehavior/project/aruco-markers/ SCR_026572 Augmented Reality University of Cordoba, Aruco 2026-02-15 09:24:01 14
HCP Pipelines
 
Resource Report
Resource Website
10+ mentions
HCP Pipelines (RRID:SCR_026575) software application, image processing software, data processing software, software resource, software toolkit 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. Minimal preprocessing pipelines, Human Connectome Project, MRI images processing, MRI images, NIMH MH091657;
NIH Blueprint for Neuroscience Research ;
NIMH F30 MH097312;
NIMH ROI MH60974;
NCRR U24 RR021382;
NIBIB R01EB006758;
NIA R01AG008122;
NINDS R01 NS052585;
NINDS R21NS072652;
NINDS R01NS070963
PMID:23668970 Free, Available for download, Freely available https://www.humanconnectome.org/software/hcp-mr-pipelines SCR_026575 Human Connectome Project Pipelines 2026-02-15 09:24:13 20
TEProf3
 
Resource Report
Resource Website
TEProf3 (RRID:SCR_027288) source code, software toolkit, software resource Software pipeline to detect Transposable Elements transcripts. Used to identify TE-derived promoters and transcripts using transcriptomic data from multiple sources, including short-read RNA-seq data, long-read RNA-seq data and single cell RNA-seq data. Transposable Elements, Transposable Elements transcripts, detect TE transcripts, transcriptomic data, short-read RNA-seq data, long-read RNA-seq data, single cell RNA-seq data, NHGRI R01HG007175;
NIA R01AG078958;
NINDS U24NS132103;
NHGRI U01HG013227
PMID:40360186 Free, Available for download, Freely available, SCR_027288 , TE-derived Promoter Finder 3 2026-02-15 09:24:06 0
hdWGCNA
 
Resource Report
Resource Website
1+ mentions
hdWGCNA (RRID:SCR_027496) source code, software toolkit, software resource Software R package for performing weighted gene co-expression network analysis in high dimensional transcriptomics data such as single-cell RNA-seq or spatial transcriptomics. weighted gene co-expression network, high dimensional transcriptomics data, single-cell RNA-seq, transcriptomics NIA 1RF1AG071683;
NINDS P01NS084974;
NIDA 1U01DA053826;
NIA U54 AG054349;
NIA 3U19AG068054
PMID:37426759 Free, Available for download, Freely available SCR_027496 hd Weighted Gene Co-expression Network Analysis 2026-02-15 09:24:13 6
NeuroJSON.io
 
Resource Report
Resource Website
NeuroJSON.io (RRID:SCR_027793) data or information resource, project portal, portal Web application for human-readable, searchable neuroimaging datasets using universally accessible JSON format and URL-based RESTful APIs. NeuroJSON.io is built upon highly scalable document-store NoSQL database technologies, specifically, open-source Apache CouchDB engine, that can handle millions of datasets without major performance penalties. Provides fine-grained data search capabilities to allow users to find, preview and re-combine complex data records from public datasets before download. neuroimaging datasets, JSON format, URL-based RESTful APIs, data search, public datasets, NINDS U24 NS124027 Free, Freely available SCR_027793 NeuroJSON 2026-02-15 09:24:20 0
PowerMap
 
Resource Report
Resource Website
1+ mentions
PowerMap (RRID:SCR_006721) PowerMap software resource Software tool specifically designed for neuroimaging data that implements theoretical power calculation algorithms based on non-central random field theory. It can also calculate power for statistical analyses with FDR (false discovery rate) corrections. This GUI (graphical user interface)-based tool enables neuroimaging researchers without advanced knowledge in imaging statistics to calculate power and sample size in the form of 3D images. This tool is currently under limited release for beta testing. At this time, only users that have been directed to this site by the PowerMap developers will receive support. neuroimaging, statistical analyses, false discovery rate, 3d spatial image, power calculation, sample size has parent organization: Wake Forest School of Medicine; North Carolina; USA
has parent organization: SourceForge
NINDS NS059793 PMID:22644868 Free, Public nlx_152808 SCR_006721 2026-02-14 02:01:14 3
SPM Anatomy Toolbox
 
Resource Report
Resource Website
100+ mentions
SPM Anatomy Toolbox (RRID:SCR_013273) SPM Anatomy Toolbox software resource A MATLAB toolbox which uses three dimensional probabilistic cytoarchitechtonic maps to correlate microscopic, anatomic and functional data of the cerebral cortex. Correlating the activation foci identified in functional imaging studies of the human brain with structural (e.g., cytoarchitectonic) information on the activated areas is a major methodological challenge for neuroscience research. We here present a new approach to make use of three-dimensional probabilistic cytoarchitectonic maps, as obtained from the analysis of human post-mortem brains, for correlating microscopical, anatomical and functional imaging data of the cerebral cortex. We introduce a new, MATLAB based toolbox for the SPM2 software package which enables the integration of probabilistic cytoarchitectonic maps and results of functional imaging studies. The toolbox includes the functionality for the construction of summary maps combining probability of several cortical areas by finding the most probable assignment of each voxel to one of these areas. Its main feature is to provide several measures defining the degree of correspondence between architectonic areas and functional foci. The software, together with the presently available probability maps, is available as open source software to the neuroimaging community. This new toolbox provides an easy-to-use tool for the integrated analysis of functional and anatomical data in a common reference space. human, brain, imaging, functional magnetic resonance imaging, structure, mapping, atlas, pet, neuroimaging is related to: SPM NIMH ;
NINDS ;
NIBIB ;
DFG KFO-112;
DFG Schn 362/13-2
PMID:15850749 nif-0000-10477 SCR_013273 2026-02-14 02:02:28 107
HED Tags
 
Resource Report
Resource Website
1+ mentions
HED Tags (RRID:SCR_014074) HED data or information resource, narrative resource, standard specification Strategy guide for HED Annotation. Framework for systematically describing laboratory and real world events.HED tags are comma separated path strings. Organized in forest of groups with roots Event, Item, Sensory presentation, Attribute, Action, Participant, Experiment context, and Paradigm. Used for preparing brain imaging data for automated analysis and meta analysis. Applied to brain imaging EEG, MEG, fNIRS, multimodal mobile brain or body imaging, ECG, EMG, GSR, or behavioral data. Part of Brain Imaging Data Structure standard for brain imaging. Data, structure, standard, EEG, brain, imaging, comma, separated, path, string, analysis, MEG, fNIRS, multimodal, ECG, EMG, GSR, behavioral, BRAIN Initiative is used by: NIMH Data Archive
is used by: HeadIT
is used by: OpenNeuro
is recommended by: BRAIN Initiative
has parent organization: University of California at San Diego; California; USA
Swartz Foundation ;
Army Research Laboratory Cooperative Agreement ;
NIMH R01MH084819;
NINDS R01 NS047293
PMID:27799907 Free, Freely available SCR_017630 SCR_014074 Hierarchical Event Descriptor Tags, Hierarchical Event Descriptor, HED, HED tags 2026-02-14 02:02:56 7
NIH MRI Study of Normal Brain Development
 
Resource Report
Resource Website
1+ mentions
NIH MRI Study of Normal Brain Development (RRID:SCR_003394) Pediatric MRI Study data or information resource, experimental protocol, narrative resource, data set Data sets of clinical / behavioral and image data are available for download by qualified researchers from a seven year, multi-site, longitudinal study using magnetic resonance technologies to study brain maturation in healthy, typically-developing infants, children, and adolescents and to correlate brain development with cognitive and behavioral development. The information obtained in this study is expected to provide essential data for understanding the course of normal brain development as a basis for understanding atypical brain development associated with a variety of developmental, neurological, and neuropsychiatric disorders affecting children and adults. This study enrolled over 500 children, ranging from infancy to young adulthood. The goal was to study each participant at least three times over the course of the project at one of six Pediatric Centers across the United States. Brain MR and clinical/behavioral data have been compiled and analyzed at a Data Coordinating Center and Clinical Coordinating Center. Additionally, MR spectroscopy and DTI data are being analyzed. The study was organized around two objectives corresponding to two age ranges at the time of enrollment, each with its own protocols. * Objective 1 enrolled children ages 4 years, 6 months through 18 years (total N = 433). This sample was recruited across the six Pediatric Study Centers using community based sampling to reflect the demographics of the United States in terms of income, race, and ethnicity. The subjects were studied with both imaging and clinical/behavioral measures at two year intervals for three time points. * Objective 2 enrolled newborns, infants, toddlers, and preschoolers from birth through 4 years, 5 months, who were studied three or more times at two Pediatric Study Centers at intervals ranging from three months for the youngest subjects to one year as the children approach the Objective 1 age range. Both imaging and clinical/behavioral measures were collected at each time point. Participant recruitment used community based sampling that included hospital venues (e.g., maternity wards and nurseries, satellite physician offices, and well-child clinics), community organizations (e.g., day-care centers, schools, and churches), and siblings of children participating in other research at the Pediatric Study Centers. At timepoint 1, of those enrolled, 114 children had T1 scans that passed quality control checks. Staged data release plan: The first data release included structural MR images and clinical/behavioral data from the first assessments, Visit 1, for Objective 1. A second data release included structural MRI and clinical/behavioral data from the second visit for Objective 1. A third data release included structural MRI data for both Objective 1 and 2 and all time points, as well as preliminary spectroscopy data. A fourth data release added cortical thickness, gyrification and cortical surface data. Yet to be released are longitudinally registered anatomic MRI data and diffusion tensor data. A collaborative effort among the participating centers and NIH resulted in age-appropriate MR protocols and clinical/behavioral batteries of instruments. A summary of this protocol is available as a Protocol release document. Details of the project, such as study design, rationale, recruitment, instrument battery, MRI acquisition details, and quality controls can be found in the study protocol. Also available are the MRI procedure manual and Clinical/Behavioral procedure manuals for Objective 1 and Objective 2. young human, child, pediatric, experimental protocol, brain, brain development, development, mri, minc, clinical, behavior, anatomical mri, diffusion tensor imaging, mr spectroscopy, adolescent, clinical data, behavioral data, data visualization software, clinical measure, behavioral measure, physical neurological examination, behavioral rating, neuropsychological testing, structured psychiatric interview, hormonal measure, image collection, neonate, clinical neuroinformatics, dicom, minc2, magnetic resonance, nifti is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Biositemaps
is listed by: NIH Data Sharing Repositories
is related to: NIH Data Sharing Repositories
has parent organization: National Institutes of Health
Healthy, Normal NICHD ;
NIDA ;
NIMH ;
NINDS ;
NIH Blueprint for Neuroscience Research
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-00201 http://www.bic.mni.mcgill.ca/nihpd/info/, https://nihpd.crbs.ucsd.edu/nihpd/info/index.html SCR_003394 NIH Pediatric MRI Data Repository, Pediatric MRI Data Repository 2026-02-14 02:00:26 6
Neural Circuit Tracer
 
Resource Report
Resource Website
1+ mentions
Neural Circuit Tracer (RRID:SCR_000116) NCTracer software resource Open source software for automated and manual tracing of neurites from light microscopy stacks of images. NCTracer 2.0 is developed for the Windows 7, 64-bit operating system and requires a minimum of 4 GB of RAM. This version does not run on 32-bit computers, Mac or Linux OS. neuronal circuit, neuron tracing, branch structure, automated tracing is related to: Dataset of dendritic spine neck lengths and head sizes
is related to: experimental studies reporting connection probabilities and/or unitary PSP amplitudes
has parent organization: Northeastern University; Massachusetts; USA
NINDS NS063494 PMID:21562803 nlx_152603 https://bpb-us-w2.wpmucdn.com/sites.northeastern.edu/dist/9/312/files/2020/09/User-Guide-V-4-0.pdf SCR_000116 2026-02-14 01:59:37 2
Research Services Branch National Institutes of Mental Health
 
Resource Report
Resource Website
500+ mentions
Research Services Branch National Institutes of Mental Health (RRID:SCR_001633) RSB data or information resource, portal Portal for NIH, NIMH, and NINDS scientific and computer resources including Mac sites, PC sites, Linux sites, intramural programs, intranet and the NIH JumpStart and Directory. mac, pc, linux has parent organization: National Institutes of Health
is parent organization of: ImageJ
NIMH ;
NINDS
THIS RESOURCE IS NO LONGER IN SERVICE nlx_156832 SCR_001633 Research Services Branch National Institutes of Mental Health National Institutes of Neurological Disorders and Stroke 2026-02-14 02:05:15 547
Public Expression Profiling Resource
 
Resource Report
Resource Website
10+ mentions
Public Expression Profiling Resource (RRID:SCR_007274) PEPR data or information resource, database An experiment in web-database access to large multi-dimensional data sets using a standardized experimental platform to determine if the larger scientific community can be given simple, intuitive, and user-friendly web-based access to large microarray data sets. All data in PEPR is also available via NCBI GEO. The structure and goals of PEPR differ from other mRNA expression profiling databases in a number of important ways. * The experimental platform in PEPR is standardized, and is an Affymetrix - only database. All microarrays available in the PEPR web database should ascribe to quality control and standard operating procedures. A recent publication has described the QC/SOP criteria utilized in PEPR profiles ( The Tumor Analysis Best Practices Working Group 2004 ). * PEPR permits gene-based queries of large Affymetrix array data sets without any specialized software. For example, a number of large time series projects are available within PEPR, containing 40-60 microarrays, yet these can be simply queried via a dynamic web interface with no prior knowledge of microarray data analysis. * Projects in PEPR originate from scientists world-wide, but all data has been generated by the Research Center for Genetic Medicine, Children''''s National Medical Center, Washington DC. Future developments of PEPR will allow remote entry of Affymetrix data ascribing to the same QC/SOP protocols. They have previously described an initial implementation of PEPR, and a dynamic web-queried time series graphical interface ( Chen et al. 2004 ). A publication showing the utility of PEPR for pharmacodynamic data has recently been published ( Almon et al. 2003 ). microarray, expression profiling, affymetrix, metadata standard, gene, time series, data sharing, visualization, data mining, platform, blood, cell, cancer, bone, brain, eye, gut, heart, kidney, liver, lung, muscle, spinal cord, spleen, analysis is listed by: OMICtools
is related to: Gene Expression Omnibus
NINDS ;
United States Department of Defense ;
NHGRI ;
NHLBI
PMID:14681485
PMID:14596642
Public, Account required, (to download, For the analysis and visualization tools), The community can contribute to this resource nif-0000-00014, OMICS_00776 SCR_007274 2026-02-14 02:06:28 16
Cell Properties Database
 
Resource Report
Resource Website
Cell Properties Database (RRID:SCR_007285) CellPropDB data or information resource, database A repository for data regarding membrane channels, receptor and neurotransmitters that are expressed in specific types of cells. The database is presently focused on neurons but will eventually include other cell types, such as glia, muscle, and gland cells. This resource is intended to: * Serve as a repository for data on gene products expressed in different brain regions * Support research on cellular properties in the nervous system * Provide a gateway for entering data into the cannonical neuron forms in NeuronDB * Identify receptors across neuron types to aid in drug development * Serve as a first step toward a functional genomics of nerve cells * Serve as a teaching aid genetics, cellular, molecular, cerebellum, cortex, human, ion channel, mouse, olfactory, invertebrate, mammalian, physiology, rat, receptor, cat, molecular neuroanatomy resource has parent organization: Yale University; Connecticut; USA Aging Multidisciplinary University Research Initiative ;
NIMH ;
NIA ;
NICD ;
NINDS ;
NIDCD RO1 DC 009977
nif-0000-00055 http://senselab.med.yale.edu/senselab/cellpropdb SCR_007285 Cellular Properties Database 2026-02-14 02:06:28 0
BAMS Nested Regions
 
Resource Report
Resource Website
1+ mentions
BAMS Nested Regions (RRID:SCR_000238) BAMS Nested Regions data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 7th, 2019. BAMS is an online resource for information about neural circuitry. The BAMS Nested Regions view focuses on the major brain regions and their relationships. neural circuitry, brain region, brain is used by: NIF Data Federation
has parent organization: Brain Architecture Management System
NIMH MH61223;
NINDS NS16686;
NINDS/NIMH/NIBIB NS50792-01
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-10175 SCR_000238 Brain Architecture Management System Nested Regions 2026-02-14 02:05:59 3
BraVa
 
Resource Report
Resource Website
1+ mentions
BraVa (RRID:SCR_001407) BraVa data or information resource, database A database of digital reconstructions of the human brain arterial arborizations from 61 healthy adult subjects along with extracted morphological measurements. The arterial arborizations include the six major trees stemming from the circle of Willis, namely: the left and right Anterior Cerebral Arteries (ACAs), Middle Cerebral Arteries (MCAs), and Posterior Cerebral Arteries (PCAs). digital reconstruction, morphometric analysis, cerebrum, arterial vasculature, magnetic resonance angiography, adult human, morphology, artery, arborization, circle of willis, cerebral artery, male, female, magnetic resonance is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: Bravissima
has parent organization: George Mason University: Krasnow Institute for Advanced Study
Healthy NINDS NS39600;
NIBIB EB001955;
NINDS NS061770;
NIMH P20 MH52176
PMID:23727319 Free, Freely Available nlx_152630 http://www.nitrc.org/projects/breva SCR_001407 2026-02-14 02:06:04 8
rMATS
 
Resource Report
Resource Website
10+ mentions
rMATS (RRID:SCR_023485) software resource Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P-value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user-defined threshold. From RNA-Seq data can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design. detection of differential alternative splicing, replicate RNA-Seq data, analysis of paired and unpaired replicates, clinical RNA-Seq datasets, genome studies, NIGMS R01GM088342;
NINDS R01NS076631;
NIEHS R01ES024995;
NIGMS R01GM105431;
NSF DMS1055286;
NSF DMS1310391;
Alfred Sloan Research Fellowship
PMID:25480548 Free, Available to download, Freely available SCR_023485 2026-02-14 02:05:11 18
Wellcome-CTC Mouse Strain SNP Genotype Set
 
Resource Report
Resource Website
1+ mentions
Wellcome-CTC Mouse Strain SNP Genotype Set (RRID:SCR_003216) Wellcome-CTC Mouse Strain SNP Genotype Set data or information resource, data set THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Data set of genotypes available for 480 strains and 13370 successful SNP assays that are mapped to build34 of the mouse genome, including 107 SNPs that are mapped to random unanchored sequence 13374 SNPs are mapped onto Build 33 of the mouse genome. You can access the data relative to Build 33 or Build 34. genome, genotype, snp, chromosome, haplotype, haplotype structure, recombinant inbred mouse strain has parent organization: Wellcome Trust Centre for Human Genetics Wellcome Trust ;
NCRR R24RR015116;
NIGMS R01GM072863;
NIAAA U01AA014425;
NINDS R01NS049445;
NIMH P20-MH 62009;
NIAAA U24AA13513
THIS RESOURCE IS NO LONGER IN SERVICE nlx_156947 SCR_003216 2026-02-14 02:07:20 3
Hippocampome.org
 
Resource Report
Resource Website
10+ mentions
Hippocampome.org (RRID:SCR_009023) Hippocampome data or information resource, database A curated knowledge base of the circuitry of the hippocampus of normal adult, or adolescent, rodents at the mesoscopic level of neuronal types. Knowledge concerning dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex is distilled from published evidence and is continuously updated as new information becomes available. Each reported neuronal property is documented with a pointer to, and excerpt from, relevant published evidence, such as citation quotes or illustrations. Please note: This is an alpha-testing site. The content is still being vetted for accuracy and has not yet undergone peer-review. As such, it may contain inaccuracies and should not (yet) be trusted as a scholarly resource. The content does not yet appear uniformly across all combinations of browsers and screen resolutions. interneuron, classification, neuroinformatics, network, hippocampus, neuron, property, morphology, molecular marker, electrophysiology, adult, adolescent, dentate gyrus, ca3, ca2, ca1, subiculum, entorhinal cortex, bio.tools is used by: BICCN
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Debian
is listed by: bio.tools
has parent organization: George Mason University; Virginia; USA
Normal Air Force Office of Scientific Research ;
Office of Naval Research MURI N00014-10-1-0198;
NINDS R01NS39600;
NINDS R21NS58816
Except otherwise noted, Creative Commons Attribution-ShareAlike License nlx_152892, biotools:Hippocampome.org http://www.nitrc.org/projects/hippocampome
https://bio.tools/Hippocampome.org
SCR_009023 Hippocampome Portal 2026-02-14 02:06:16 32
Neuroimaging Informatics Technology Initiative
 
Resource Report
Resource Website
100+ mentions
Neuroimaging Informatics Technology Initiative (RRID:SCR_003141) NIfTI knowledge environment, training resource Coordinated and targeted service, training, and research to speed the development and enhance the utility of informatics tools related to neuroimaging. The initial focus will be on tools that are used in fMRI. If NIfTI proves useful in addressing informatics issues in the fMRI research community, it may be expanded to address similar issues in other areas of neuroimaging. Objectives of NIfTI * Enhancement of existing informatics tools used widely in neuroimaging research * Dissemination of neuroimaging informatics tools and information about them * Community-based approaches to solving common problems, such as lack of interoperability of tools and data * Unique training activities and research career development opportunities to those in the tool-user and tool-developer communities * Research and development of the next generation of neuroimaging informatics tools neuroimaging, neuroinformatics, technology, service, training, research, mri, fmri, software, algorithm or reusable library, c, computed tomography, developers, information resource, java, matlab, magnetic resonance, nifti, other information resource, pet, spect, software is used by: Stark Cross-Sectional Aging
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: GIFTI
has parent organization: National Institute of Mental Health
is parent organization of: NIfTI Data Format Working Group
NIH Blueprint for Neuroscience Research ;
NIMH ;
NINDS
Free, Freely available nif-0000-00561 http://www.nitrc.org/projects/nifti http://www.bic.mni.mcgill.ca/nifti/ SCR_003141 NIfTI: Neuroimaging Informatics Technology Initiative, Neuroimaging Informatics Technology Initiative (NIfTI) 2026-02-14 02:06:43 309

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