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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
JIST: Java Image Science Toolkit
 
Resource Report
Resource Website
10+ mentions
JIST: Java Image Science Toolkit (RRID:SCR_008887) JIST data processing software, software application, software resource A native Java-based imaging processing environment similar to the ITK/VTK paradigm. Initially developed as an extension to MIPAV (CIT, NIH, Bethesda, MD), the JIST processing infrastructure provides automated GUI generation for application plug-ins, graphical layout tools, and command line interfaces. This repository maintains the current multi-institutional JIST development tree and is recommended for public use and extension. JIST was originally developed at IACL and MedIC (Johns Hopkins University) and is now also supported by MASI (Vanderbilt University). experimental control, modeling, quantification, segmentation, shape analysis, spatial transformation, workflow, macos, windows, os independent, bsd, linux, sunos/solaris, java, afni brik, analyze, cor, dicom, gifti, mgh/mgz, minc, minc2, nifti-1, nrrd, philips par/rec, magnetic resonance is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Debian
is related to: Maps4Mipav (Exploratory JIST)
is related to: MR Connectome Automated Pipeline
is related to: Multi-Modal MRI Reproducibility Resource
is related to: TOADS-CRUISE Brain Segmentation Tools
is related to: CBS High-Res Brain Processing Tools
is related to: JHU Proj. in Applied Medical Imaging
is related to: DOTS WM tract segmentation
has parent organization: Johns Hopkins University; Maryland; USA
has parent organization: Vanderbilt University; Tennessee; USA
NINDS 5R01NS037747;
NINDS 1R01NS056307;
NIA N01-AG-4-0012
PMID:20077162 GNU Lesser General Public License nlx_151344 https://sources.debian.org/src/jist/ SCR_008887 Java Image Science Toolkit 2026-09-12 01:00:59 20
EEGLAB
 
Resource Report
Resource Website
5000+ mentions
EEGLAB (RRID:SCR_007292) EEGLAB data processing software, software application, software resource, software toolkit Interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data incorporating independent component analysis (ICA), time/frequency analysis, artifact rejection, event-related statistics, and several useful modes of visualization of the averaged and single-trial data. First developed on Matlab 5.3 under Linux, EEGLAB runs on Matlab v5 and higher under Linux, Unix, Windows, and Mac OS X (Matlab 7+ recommended). EEGLAB provides an interactive graphic user interface (GUI) allowing users to flexibly and interactively process their high-density EEG and other dynamic brain data using independent component analysis (ICA) and/or time/frequency analysis (TFA), as well as standard averaging methods. EEGLAB also incorporates extensive tutorial and help windows, plus a command history function that eases users'' transition from GUI-based data exploration to building and running batch or custom data analysis scripts. EEGLAB offers a wealth of methods for visualizing and modeling event-related brain dynamics, both at the level of individual EEGLAB ''datasets'' and/or across a collection of datasets brought together in an EEGLAB ''studyset.'' For experienced Matlab users, EEGLAB offers a structured programming environment for storing, accessing, measuring, manipulating and visualizing event-related EEG data. For creative research programmers and methods developers, EEGLAB offers an extensible, open-source platform through which they can share new methods with the world research community by publishing EEGLAB ''plug-in'' functions that appear automatically in the EEGLAB menu of users who download them. For example, novel EEGLAB plug-ins might be built and released to ''pick peaks'' in ERP or time/frequency results, or to perform specialized import/export, data visualization, or inverse source modeling of EEG, MEG, and/or ECOG data. EEGLAB Features * Graphic user interface * Multiformat data importing * High-density data scrolling * Defined EEG data structure * Open source plug-in facility * Interactive plotting functions * Semi-automated artifact removal * ICA & time/frequency transforms * Many advanced plug-in toolboxes * Event & channel location handling * Forward/inverse head/source modeling visualization, eeg modeling, independent component analysis, meg modeling, eeg, erp, spectral decomposition, single-trial, matlab, meg, electrophysiology, format conversion, source separation analysis, fourier time-domain analysis, spectral analysis, temporal wavelet analysis, anova, event related potential, three dimensional display, two dimensional display uses: ERPwavelab
is used by: PeriodAmplitudeAnalysis
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Biositemaps
is listed by: SoftCite
is related to: Neural Maestro
is related to: Measure Projection Toolbox
is related to: NFT
is related to: Source Information Flow Toolbox
is related to: HeadIT
is related to: BCILAB
is related to: EEGVIS
is related to: EYE-EEG (combined eye-tracking & EEG)
is related to: Libeep EEGLAB plugin
is related to: The Bergen fMRI Toolbox Plugin for EEGLab
is related to: BVA import/export EEGLAB plugin
has parent organization: Swartz Center for Computational Neuroscience
has plug in: Dusk2Dawn
works with: FieldTrip
NINDS PMID:15102499 Free, Available for download, Freely available nif-0000-00076 https://eeglab.org/others/EEGLAB_References.html http://www.nitrc.org/projects/incf_eeglab/, http://sccn.ucsd.edu/eeglab/index.html SCR_007292 2026-09-12 01:00:57 7215
3D DTI Atlas of the Rat Brain In Postnatal Day 5 14 and Adulthood
 
Resource Report
Resource Website
1+ mentions
3D DTI Atlas of the Rat Brain In Postnatal Day 5 14 and Adulthood (RRID:SCR_009437) 3D DTI Atlas of the Rat Brain atlas, data or information resource, reference atlas 3D DTI anatomical rat brain atlases have been created by the UNC- Chapel Hill Department of Psychiatry and the CAMID research collaboration. There are three age groups, postnatal day 5, postnatal day 14, and postnatal day 72. The subjects were Sprague-Dawley rats that were controls in a study on cocaine abuse and development. The P5 and P14 templates were made from scans of twenty rats each (ten female, ten male); the P72, from six females. The individual cases have been resampled to isotropic resolution, manually skull-stripped, and deformably registered via an unbiased atlas building method to create a template for each age group. Each template was then manually segmented using itk-SNAP software. Each atlas is made up of 3 files, a template image, a segmentation, and a label file. magnetic resonance, adult rat, newborn rat, infant rat, young rat, sprague dawley, male, female is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA
Control, Normal UNC Neurodevelopment Disorders Research Center ;
NICHD HD 03110;
NINDS R41 NS059095;
NIDA IP01DA022446-02
nlx_155577 SCR_009437 3-Dimensional Diffusion Tensor Imaging (DTI) Atlas of the Rat Brain In Postnatal Day 5 14 and Adulthood 2026-09-12 01:00:59 2
FuncAssociate: The Gene Set Functionator
 
Resource Report
Resource Website
10+ mentions
FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) FuncAssociate analysis service resource, data analysis service, production service resource, service resource A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool gene, gene ontology, statistical analysis, web service, bio.tools is listed by: Gene Ontology Tools
is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: Gene Ontology
has parent organization: Roth Laboratory
NIH ;
Canadian Institute for Advanced Research ;
NINDS NS054052;
NINDS NS035611;
NHLBI HL081341;
NHGRI HG0017115;
NHGRI HG004233;
NHGRI HG003224
PMID:19717575
PMID:14668247
Free for academic use, Acknowledgement requested biotools:funcassociate, OMICS_02264, nlx_149233 http://llama.mshri.on.ca/cgi/func/funcassociate, https://bio.tools/funcassociate SCR_005768 2026-09-12 01:01:39 36
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 2026-09-12 01:01:46 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 2026-09-12 01:01:46 0
Duke University of North Carolina Brain Imaging and Analysis Center Core Facility
 
Resource Report
Resource Website
1+ mentions
Duke University of North Carolina Brain Imaging and Analysis Center Core Facility (RRID:SCR_001712) Duke-UNC BIAC, BIAC access service resource, core facility, service resource BIAC strives for excellence in its dual mission of research and service. BIAC faculty members are leaders in imaging methodology development, in analysis techniques, as well as in their application in cognitive and clinical neurosciences. In addition, BIAC offers imaging service to other imaging faculty members on campus and at the University of North Carolina in Chapel Hill. Imaging methodology development, analysis techniques, cognitive neurosciences application, clinical neurosciences application, imaging service has parent organization: Duke University; North Carolina; USA National Institutes of Health ;
Autism Speaks ;
NINDS
Restricted nif-0000-10210 SCR_001712 Duke University of North Carolina Brain Imaging and Analysis Center, Brain Imaging and Analysis Center, Brain Imaging and Analysis Center (BIAC) 2026-09-12 01:03:12 2
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 2026-09-12 01:03:13 3
Neurophysiology Imaging Facility
 
Resource Report
Resource Website
Neurophysiology Imaging Facility (RRID:SCR_004080) NIF access service resource, core facility, service resource Neurophysiology imaging core facility that provides anatomical and functional MRI scanning for researchers in the National Institute of Mental Health (NIMH), the National Eye Institute (NEI), and the National Institute for Neurological Disorders and Stroke (NINDS). The shared intramural resource centers on a cutting-edge 4.7T vertical bore scanner dedicated to imaging of nonhuman primates. mri, fmri, neuroimaging, neurophysiology, brain has parent organization: National Institute of Mental Health NIMH ;
NINDS ;
NEI
nlx_158530 SCR_004080 Neurophysiology Imaging Facility (NIF) 2026-09-12 01:03:14 0
Salk Institute Gene Transfer Targeting and Therapeutics Viral Vector Core Facility
 
Resource Report
Resource Website
10+ mentions
Salk Institute Gene Transfer Targeting and Therapeutics Viral Vector Core Facility (RRID:SCR_014847) GT3 access service resource, core facility, service resource Core facility that provides consultation on the use of viral vector technologies as well as custom design and production services for multiple vector types. The GT3 facilitates the use of these research tools by Salk researchers and others across diverse fields of study such as systems neuroscience, stem cell biology, metabolism, ageing, cancer biology and gene therapy. The GT3 core is a designated Cancer Center Council (C3) core facility. Cancer Center members from participating C3 institutes have preferential rates. core facility, gene, vector, viral vector, manipulation, gene therapy, cancer, stem cell is listed by: ABRF CoreMarketplace
has parent organization: Salk Institute for Biological Studies
NINDS R24 Core Grant ;
NEI ;
Salk Institute GT3 Core Facility ;
NCI CCSG P30 014195;
NINDS R24NS092943
Restricted ABRF_1642 https://coremarketplace.org/?FacilityID=1642&citation=1 SCR_014847 , Salk Institute Gene Transfer Targeting and Therapeutics Viral Vector Core (GT3), Salk Institute Gene Transfer Targeting and Therapeutics Core 2026-09-12 01:03:48 10
FMRIB’s Integrated Registration and Segmentation Tool
 
Resource Report
Resource Website
1+ mentions
FMRIB’s Integrated Registration and Segmentation Tool (RRID:SCR_024921) FIRST data analysis software, data processing software, image analysis software, registration software, segmentation software, software application, software resource 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;
NCRR R01 RR16594;
NIDA R01 DA017905;
NIMH K01 MH01798;
NIMH K08 MH01573;
NINDS R01 NS052585
PMID:21352927 Free, Freely available SCR_024921 , Functional Magnetic Resonance Imaging of the Brain's Integrated Registration and Segmentation Tool 2026-09-12 01:04:34 7
Keypoint MoSeq
 
Resource Report
Resource Website
10+ mentions
Keypoint MoSeq (RRID:SCR_025032) software resource, source code Software application as machine learning-based platform for identifying behavioral modules from keypoint data without human supervision. Package provides tools for fitting MoSeq model to keypoint tracking data. Used to infer pose dynamics with keypoint data in addition to behavioral syllables. OpenBehavior, infer pose dynamics, keypoint data, identifying behavioral modules, keypoint tracking data, parsing behavior, linking point tracking to pose dynamics, has parent organization: Harvard University; Cambridge; United States Alfred P. Sloan Foundation ;
NIA RF1AG073625;
NINDS F31NS113385;
NINDS F31NS122155;
NINDS R01NS114020;
NINDS U19NS113201;
NINDS U24NS109520;
Salk Collaboration Grant ;
Simons Collaboration on Plasticity and the Aging Brain ;
Simons Collaboration on the Global Brain ;
Simons Foundation Autism Research Initiative
DOI:10.1101/2023.03.16.532307 Free, Available for download, Freely available SCR_025032 2026-09-12 01:04:36 12
E-Scope
 
Resource Report
Resource Website
1+ mentions
E-Scope (RRID:SCR_025396) instrument resource, software resource, source code Miniaturized calcium imaging microscope with integrated dense electrode technology for synchronous acquisition of neural activity across distant regions of the brain. Device based off open-sourced UCLA Miniscope to synchronously measure single cell activity at or near spike-time resolution across distant brain regions in freely behaving mice. Used to perform calcium imaging, with dense electrode electrophysiological recording, allowing simultaneous recordings from two remote brain regions in freely behaving mouse. OpenBehavior, miniatured microscope, calcium imaging microscope, microscope, synchronous acquisition, freely behaving mice, neural activity, brain distant regions, synchronously measure single cell activity, is listed by: OpenBehavior
is related to: UCLA Miniscope project
NICHD P50HD103577;
NINDS 1R61NS119708;
NINDS R01NS090930;
NINDS U01NS122124;
NSF NeuroNex Award
PMID:37066345 Free, Available for download, Freely available http://miniscope.org/index.php/Main_Page, https://edspace.american.edu/openbehavior/?s=E-Scope SCR_025396 2026-09-12 01:04:43 3
Annotation Comparison Explorer
 
Resource Report
Resource Website
1+ mentions
Annotation Comparison Explorer (RRID:SCR_026496) ACE software resource, web application Web application for comparing cell type assignments and other cell-based annotations (e.g., donor demographics, anatomic locations, batch variables, and quality control metrics). Used for connecting brain cell types across studies of health and Alzheimer's Disease. comparing cell type assignments, cell-based annotations, connecting brain cell types, has parent organization: Allen Institute
is organization facet of: BRAIN Initiative Cell Atlas Network
NIA U19AG060909;
NINDS U24NS133077
PMID:39990500 Free, Freely available github.com/AllenInstitute/ACE SCR_026496 Annotation Comparison Explorer (ACE) 2026-09-12 01:05:06 1
Borzoi
 
Resource Report
Resource Website
1+ mentions
Borzoi (RRID:SCR_026619) software resource, software toolkit, source code 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 2026-09-12 01:05:08 2
University of North Carolina at Chapel Hill School of Medicine Neuroscience Microscopy Core Facility
 
Resource Report
Resource Website
50+ mentions
University of North Carolina at Chapel Hill School of Medicine Neuroscience Microscopy Core Facility (RRID:SCR_019060) NMC access service resource, core facility, service resource Microscopy Core for high resolution imaging and aims to make this technology accessible to neuroscientists and other scientific researchers.Provides advanced systems for cellular and molecular imaging of in vitro and in vivo samples, implements new imaging technologies, particularly related to real time and tissue clearing based imaging of neurodevelopment and neural functions, offers training, consultation, data analysis, image processing, and centralized technical expertise. USEDit, microscopy, high resolution imaging, neuroscience microscopy, cellular imaging, molecular imaging, in vitro imaging, in vivo imaging, neurodevelopment, neural function, data analysis, image processing, ABRF, ABRF is listed by: ABRF CoreMarketplace
has parent organization: University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA
NICHD U54 HD079124;
NINDS P30 NS045892
Open ABRF_1052 https://coremarketplace.org/?FacilityID=1052 SCR_019060 UNC Neuroscience Microscopy Core, University of North Carolina at Chapel Hill UNC Neuroscience Microscopy Core, UNC School of Medicine Neuroscience Microscopy Core Facility 2026-09-12 01:04:08 70
CytoVerse
 
Resource Report
Resource Website
CytoVerse (RRID:SCR_028854) data access protocol, data analysis software, data processing software, data visualization software, software application, software resource, web service Web application to map single-cell RNA data into AI foundation model spaces. Lets search millions of reference cells and view cell types locally without uploading private data or needing powerful cloud servers. Using ONNX model deployment and compressed IVFPQ indexing, it annotates local datasets against a 23-million-cell reference without server computation, installation, or data upload, and shares embeddings as lightweight files, enabling private, interactive, and collaborative single-cell analysis. single-cell RNA-seq, foundation models, browser based analysis, WebAssembly, ONNX, scFM, approximate nearest neighbors, latent space collaboration, data privacy, Brain and Behavior Research Foundation ;
California Institute for Regenerative Medicine ;
NHGRI RM1HG011543;
NIMH U24MH132628;
NINDS U24NS146314;
NSF ;
University of California Office of the President
PMID:41659670 Free, Available for download, Freely available https://github.com/braingeneers/cytoverse SCR_028854 2026-09-12 01:06:01 0
Diffusion-Model
 
Resource Report
Resource Website
1+ mentions
Diffusion-Model (RRID:SCR_027942) software resource, source code Software code for simulating diffusion in brain extracellular space images. simulating diffusion, brain, extracellular space, images NINDS R01NS130759;
NSF ;
Spanish Government
PMID:41279667 Free, Available for download, Freely available SCR_027942 , Diffusion Flux, DifFlux, Diffusion Flux Model 2026-09-12 01:05:39 1
AqNWB
 
Resource Report
Resource Website
AqNWB (RRID:SCR_028050) application programming interface, data access protocol, data or information resource, license, narrative resource, open-source license, software resource, source code Software C++ API for acquiring neurophysiological data directly into the NWB (Neurodata Without Borders) format. Our goal is to provide a lightweight API to integrate with existing acquisition systems. NWB, data acquisition, C++, is listed by: Neurodata Without Borders
works with: Neurodata Without Borders
NINDS R03NS145401 Free, Available for download, Freely available https://nwb.org/aqnwb/ SCR_028050 2026-09-12 01:05:42 0
dreamlet
 
Resource Report
Resource Website
1+ mentions
dreamlet (RRID:SCR_028168) software resource, software toolkit, source code Software R package enables differential expression analysis on multi-sample single cell datasets using linear (mixed) models with precision weights. Perform differential expression analysis, multi-sample single cell datasets, linear mixed models, precision weights, NIA P30AG066514;
NIA R01AG050986;
NIA R01AG065582;
NIA R01AG067025;
NIMH R01MH109677;
NIMH R01MH125246;
NIMH RF1MH128970;
NIMH U01MH116442;
NINDS U01NS125580
PMID:36993704 Free, Available for download, Freely available SCR_028168 2026-09-12 01:05:44 1

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