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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Spectroscopic Imaging, VIsualization, and Computing (SIVIC) Resource Report Resource Website |
Spectroscopic Imaging, VIsualization, and Computing (SIVIC) (RRID:SCR_027875) | SIVIC | software application, software resource | Software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies. | DICOM MR Spectroscopy Workflows, data processing, data visualization, DICOM MR spectroscopy data, | NCI RO1 CA127612; NCI P01 CA11816; NIBIB P41EB013598 |
PMID:23970895 | Free, Available for download, Freely available | SCR_027875 | 2026-02-15 09:24:13 | 0 | ||||||||
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Open Anatomy Project Resource Report Resource Website |
Open Anatomy Project (RRID:SCR_022141) | data or information resource, project portal, portal | Project aims to change anatomy atlas by building atlases through open data, community based collaborative development, and free distribution of medical knowledge. Provides access to several 2D and 3D browser based tools. | Atlas, Brigham and Women's Hospital in Boston, digital anatomy atlas, open data, community based collaborative development, medical knowledge | NIBIB ; NCRR |
Free, Freely available | SCR_022141 | The Open Anatomy Project | 2026-02-16 09:50:16 | 0 | |||||||||
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UNC Infant 0-1-2 Atlases Resource Report Resource Website 1+ mentions |
UNC Infant 0-1-2 Atlases (RRID:SCR_002569) | UNC Infant 0-1-2 Atlases | data or information resource, atlas | 3 atlases dedicated for neonates, 1-year-olds, and 2-year-olds. Each atlas comprises a set of 3D images made up of the intensity model, tissue probability maps, and anatomical parcellation map. These atlases are constructed with the help of state-of-the-art infant MR segmentation and groupwise registration methods, on a set of longitudinal images acquired from 95 normal infants (56 males and 39 females) at neonate, 1-year-old, and 2-year-old. | analyze, atlas application, linux, macos, microsoft, magnetic resonance, posix/unix-like, infant, pediatric, template, longitudinal, neonate, male, female, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA |
Normal | NIH ; NIBIB EB006733; NIBIB EB008760; NIBIB EB008374; NIBIB EB009634; NIMH MH088520; NIMH MH070890; NIMH MH064065; NINDS NS055754; NICHD HD053000 |
PMID:21533194 | Free, Available for download, Freely available | nlx_155971 | http://www.nitrc.org/projects/pediatricatlas | SCR_002569 | UNC 0-1-2 Infant Atlases | 2026-02-16 09:45:46 | 2 | |||
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Annotare Resource Report Resource Website |
Annotare (RRID:SCR_000319) | software application, software resource, standalone software | A software tool for annotating biomedical investigations and the resulting data, then producing a MAGE-TAB file. This software is a standalone desktop which features: an editor function, an annotation modifier, incorporation of terms from biomedical ontologies, standard templates for common experiment types, a design aid to help create a new document, and a validator that checks for syntactic and semantic violations. | biomedical research, magetab, editor, annotation, biomedical ontology | is listed by: OMICtools | NIBIB ; NCI ; NHGRI P41 HG003619 |
PMID:20733062 | Free, Available for download, Freely available | OMICS_00741 | SCR_000319 | annotare: a tool for annotating high-throughput biomedical investigations and resulting data | 2026-02-16 09:45:14 | 0 | ||||||
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Advanced Neuroscience Imaging Research Laboratory Software Packages Resource Report Resource Website 10+ mentions |
Advanced Neuroscience Imaging Research Laboratory Software Packages (RRID:SCR_002926) | ANSIR Software | software resource, software toolkit | Research group based in the Department of Radiology of Wake Forest University School of Medicine devoted to the application of novel image analysis methods to research studies. The ANSIR lab also maintains a fully-automated functional and structural image processing pipeline supporting the image storage and analysis needs of a variety of scientists and imaging studies at Wake Forest. Software packages and toolkits are currently available for download from the ANSIR Laboratory, including: WFU Biological Parametric Mapping Toolbox, WFU_PickAtlas, and Adaptive Staircase Procedure for E-Prime. | multimodal, image, analysis, biological, parametric, mapping, voxel, linear, model, regressor, software, matlab, visualization, statistical, inference, in vivo, brain imaging, brain | has parent organization: Wake Forest School of Medicine; North Carolina; USA | NIBIB R01EB004673; NIBIB 1R03EB008670 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30033 | SCR_002926 | Advanced Neuroscience Imaging Research Software, ANSIR Laboratory Software Packages | 2026-02-16 09:45:57 | 37 | ||||||
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SPHARM-MAT Resource Report Resource Website 1+ mentions |
SPHARM-MAT (RRID:SCR_002545) | SPHARM-MAT | software application, software resource, software toolkit | A matlab-based 3D shape modeling and analysis toolkit, and is designed to aid statistical shape analysis for identifying morphometric changes in 3D structures of interest related to different conditions. SPHARM-MAT is implemented based on a powerful 3D Fourier surface representation method called SPHARM, which creates parametric surface models using spherical harmonics. | analyze, c, matlab, microsoft, morphology, magnetic resonance, nifti, posix/unix-like, quantification, quantitative shape analysis, shape analysis, shape decomposition, spherical harmonics, surface analysis, win32 (ms windows), windows, parametric surface model, spherical harmonics, 3d, shape modeling, analysis, morphometry |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Indiana University School of Medicine; Indiana; USA |
NIBIB R03EB008674-01 | Free, Available for download, Freely available | nlx_155952 | http://www.nitrc.org/projects/spharm-mat | SCR_002545 | 2026-02-16 09:45:46 | 2 | ||||||
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DeepNeuro Resource Report Resource Website 1+ mentions |
DeepNeuro (RRID:SCR_016911) | software resource, software toolkit | Software Python package for neuroimaging data. Framework to design and train neural network architectures. Used in medical imaging community to ensure consistent performance of networks across variable users, institutions, and scanners. | Design and train neural network architectures, medical imaging, neuroimaging data, neuroimaging |
uses: Python Programming Language is related to: Massachusetts General Hospital has parent organization: Harvard University; Cambridge; United States |
NIDA T90 DA022759; NIDA R90 DA023427; NIH Blueprint for Neuroscience Research ; NIBI ; NIBIB T32 EB1680; NCI U01 CA154601; NCI U24 CA180927; NCI U24 CA180918; NIBIB P41 EB015896 |
PMID:32578020 | Free, Available for download, Freely available | SCR_016911 | 2026-02-16 09:49:07 | 2 | ||||||||
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Automated Fiber Quantification in Python Resource Report Resource Website 10+ mentions |
Automated Fiber Quantification in Python (RRID:SCR_023366) | pyAFQ | software resource, software toolkit | Software package focused on automated delineation of major fiber tracts in individual human brains, and quantification of tissue properties within the tracts.Software for automated processing and analysis of diffusion MRI data. Automates tractometry. | Automates tractometry, automated delineation of major fiber tracts, individual human brains, quantification of tissue properties, tissue properties within fiber tracts, diffusion MRI data, | NIMH 1RF1MH121868; The BRAIN Initiative ; Gordon and Betty Moore Foundation ; Alfred P. Sloan Foundation ; NIBIB R01EB027585; NSF 1551330 |
PMID:35079748 | Free, Available for download, Freely available | SCR_023366 | 2026-02-16 09:50:29 | 12 | ||||||||
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Laser Biomedical Research Center Resource Report Resource Website 1+ mentions |
Laser Biomedical Research Center (RRID:SCR_000106) | LBRC | service resource, access service resource, biomedical technology research center | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Biomedical technology research center that develops basic scientific understanding and new techniques required for advancing clinical applications of lasers and spectroscopy. LBRC merges optical spectroscopy, imaging, scattering, and interferometry techniques to study biophysics and biochemistry of healthy and diseased biological structures from subcellular to entire-organ scale. | spectroscopy, laser, biomedicine, optical spectroscopy, imaging, scattering, interferometry, optical probe, microscopy | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | Pre-cancer, Cancer, Atherosclerosis, Healthy, Diseased | NIBIB 4P41EB015871-30 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152645 | SCR_000106 | MIT Laser Biomedical Research Center, Laser Biomedical Research Center (LBRC) | 2026-02-16 09:45:11 | 4 | |||||
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Radiological Research Accelerator Facility Resource Report Resource Website 1+ mentions |
Radiological Research Accelerator Facility (RRID:SCR_001425) | RARAF | service resource, access service resource, biomedical technology research center, training resource | Biomedical technology research center dedicated for radiobiological research with available ionizing radiations such as protons, alpha particles, and neutrons. RARAF is well-established and highly user-friendly. The focus of RARAF is the development of high-throughput single-cell/single-particle microbeams, which can deliver defined amounts of ionizing radiation into individual cells with a spatial resolution of a few microns or better. The ability of a microbeam to put double strand break damage at any specific known location in a given cell has allowed new approaches to the study of damage signaling. | radiobiological, ionizing radiation, proton, alpha particle, neutron, radiation, microbeam, irradiator, accelerator, ion, x-ray, cell | has parent organization: Columbia University; New York; USA | NIBIB P41 EB002033 | Free, Freely Available | nlx_152647 | SCR_001425 | Columbia University Radiological Research Accelerator Facility | 2026-02-16 09:45:28 | 1 | ||||||
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3D Developmental Mouse Brain Common Coordinate Framework Resource Report Resource Website 1+ mentions |
3D Developmental Mouse Brain Common Coordinate Framework (RRID:SCR_025544) | data or information resource, atlas | Open access multimodal 3D atlases of developing mouse brain that can be used to integrate mouse brain imaging data for visualization, education, cell census mapping, and more. Atlas ages include E11.5, E13.5, E15.5, E18.5, P4, P14, and P56. Web platform can be utilized to visualize and explore the atlas in 3D. Downloadable atlas can be used to align multimodal mouse brain data. Morphologically averaged symmetric template brains serve as the basis reference space and coordinate system. Anatomical labels are manually drawn in 3D based on the prosomeric model. For additional references, the P56 template includes templates and annotations from the aligned Allen Mouse Brain Common Coordinate Framework (Allen CCFv3) and aligned Molecular Atlas of the Adult Mouse Brain. | multimodal 3D atlases, developing mouse brain, mouse brain data, |
is related to: Allen Mouse Brain Common Coordinate Framework is organization facet of: BRAIN Initiative |
NIMH RF1MH12460501; NINDS R01NS108407; NIMH R01MH116176; NIBIB R01EB031722 |
PMID:37745386 | Free, Freely available | SCR_025544 | DevCCF | 2026-02-16 09:50:58 | 2 | |||||||
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Adult Wistar Rat Atlas Resource Report Resource Website 1+ mentions |
Adult Wistar Rat Atlas (RRID:SCR_006288) | Adult Wistar Rat Atlas | data or information resource, atlas | Multidimensional atlas of the adult Wistar rat brain based on magnetic resonance histology (MRH). The atlas has been carefully aligned with the widely used Paxinos-Watson atlas based on optical sections to allow comparisons between histochemical and immuno-marker data, and the use of the Paxinos-Watson abbreviation set. Our MR atlas attempts to make a seamless connection with the advantageous features of the Paxinos-Watson atlas, and to extend the utility of the data through the unique capabilities of MR histology: a) ability to view the brain in the skull with limited distortion from shrinkage or sectioning; b) isotropic spatial resolution, which permits sectioning along any arbitrary axis without loss of detail; c) three-dimensional (3D) images preserving spatial relationships; and d) widely varied contrast dependent on the unique properties of water protons. 3D diffusion tensor images (DTI) at what we believe to be the highest resolution ever attained in the rat provide unique insight into white matter structures and connectivity. The 3D isotropic data allow registration of multiple data sets into a common reference space to provide average atlases not possible with conventional histology. The resulting multidimensional atlas that combines Paxinos-Watson with multidimensional MRH images from multiple specimens provides a new, comprehensive view of the neuroanatomy of the rat and offers a collaborative platform for future rat brain studies. To access the atlas, click view supplementary materials in CIVMSpace at the bottom of the following webpage. | magnetic resonance histology, wistar rat, brain, mri, diffusion tensor imaging, histology, magnetic resonance imaging, neuroanatomy, histology | has parent organization: Duke University; North Carolina; USA | NIBIB ; NCRR P41 RR005959 |
PMID:22634863 | Free for academic use, We ask that you provide contact information, Acknowledgement required | nlx_151935 | SCR_006288 | Multidimensional Magnetic Resonance Histology Atlas of the Wistar Rat Brain | 2026-02-16 09:46:44 | 6 | |||||
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HCP Pipelines Resource Report Resource Website 10+ mentions |
HCP Pipelines (RRID:SCR_026575) | software application, data processing software, software toolkit, image processing software, software resource | 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 | 2026-02-16 09:51:14 | 20 | |||||||
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Center for Magnetic Resonance Research Resource Report Resource Website 1+ mentions |
Center for Magnetic Resonance Research (RRID:SCR_003148) | CMRR | service resource, access service resource, biomedical technology research center, training resource | Biomedical technology research center that focuses on development of unique magnetic resonance (MR) imaging and spectroscopy methodologies and instrumentation for the acquisition of structural, functional, and biochemical information non-invasively in humans, and utilizing this capability to investigate organ function in health and disease. The distinctive feature of this resource is the emphasis on ultrahigh magnetic fields (7 Tesla and above), which was pioneered by this BTRC. This emphasis is based on the premise that there exists significant advantages to extracting biomedical information using ultrahigh magnetic fields, provided difficulties encountered by working at high frequencies corresponding to such high field strengths can be overcome by methodological and engineering solutions. This BTRC is home to some of the most advanced MR instrumentation in the world, complemented by human resources that provide unique expertise in imaging physics, engineering, and signal processing. No single group of scientists can successfully carry out all aspects of this type of interdisciplinary biomedical research; by bringing together these multi-disciplinary capabilities in a synergistic fashion, facilitating these interdisciplinary interactions, and providing adequate and centralized support for them under a central umbrella, this BTRC amplifies the contributions of each of these groups of scientists to basic and clinical biomedical research. Collectively, the approaches and instrumentation developed in this BTRC constitute some of the most important tools used today to study system level organ function and physiology in humans for basic and translational research, and are increasingly applied world-wide. CMRR Faculty conducts research in a variety of areas including: * High field functional brain mapping in humans; methodological developments, mechanistic studies, and neuroscience applications * Metabolism, bioenergetics, and perfusion studies of human pathological states (tumors, obesity, diabetes, hepatic encephalopathy, cystic fibrosis, and psychiatric disorders) * Cardiac bioenergetics under normal and pathological conditions * Automated magnetic field shimming methods that are critical for spectroscopy and ultrafast imaging at high magnetic fields * Development of high field magnetic resonance imaging and spectroscopy techniques for anatomic, physiologic, metabolic, and functional studies in humans and animal models * Radiofrequency (RF) pulse design based on adiabatic principles * Development of magnetic resonance hardware for high fields (e.g. RF coils, pre-amplifiers, digital receivers, phased arrays, etc.) * Development of software for data analysis and display for functional brain mapping. | mri, imaging, magnetic resonance spectroscopy, clinical, core facility, in vivo, brain mapping | has parent organization: University of Minnesota Twin Cities; Minnesota; USA | NCRR ; NIH Blueprint for Neuroscience Research ; NIBIB ; W. M. Keck Foundation |
Free, Freely available | nif-0000-00563 | SCR_003148 | NMR Imaging and Localized Spectroscopy | 2026-02-16 09:45:59 | 5 | ||||||
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MIALAB - Resting State Data Resource Report Resource Website 10+ mentions |
MIALAB - Resting State Data (RRID:SCR_008914) | data set, data or information resource | An MRI data set that demonstrates the utility of a mega-analytic approach by identifying the effects of age and gender on the resting-state networks (RSNs) of 603 healthy adolescents and adults (mean age: 23.4 years, range: 12-71 years). Data were collected on the same scanner, preprocessed using an automated analysis pipeline based in SPM, and studied using group independent component analysis. RSNs were identified and evaluated in terms of three primary outcome measures: time course spectral power, spatial map intensity, and functional network connectivity. Results revealed robust effects of age on all three outcome measures, largely indicating decreases in network coherence and connectivity with increasing age. Gender effects were of smaller magnitude but suggested stronger intra-network connectivity in females and more inter-network connectivity in males, particularly with regard to sensorimotor networks. These findings, along with the analysis approach and statistical framework described, provide a useful baseline for future investigations of brain networks in health and disease. | fmri, functional connectivity, resting-state, independent component analysis, connectome, adolescent, adult, mri, resting state network, connectivity, dataset | has parent organization: MIALAB - Medical Image Analysis Lab | Aging | NRC Bilatgrunn ; NIBIB 1R01-EB006841; NIBIB 1R01- EB005846; NIBIB 2R01-EB000840; NIBIB 1 P20 RR021938-01; DOE DE-FG02-08ER64581; NIMH 1R01-MH072681-01; John Templeton Foundation grant 12456; NIAAA 1P20 AA017068; NINDSR21NS064464 ; NIDA1 R03 DA022435-01A1 ; NIDA1 R03 DA024212-01A1 ; NIDA KO1-DA021632-02 |
PMID:21442040 | nlx_151552 | SCR_008914 | Medical Image Analysis Laboratory - Resting State Data, MIA Laboratory - Resting State Data, Medical Image Analysis Lab - Resting State Data, Medical Image Analysis (MIA) Laboratory - Resting State Data | 2026-02-16 09:47:18 | 10 | ||||||
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Reproducible Brain Charts Resource Report Resource Website |
Reproducible Brain Charts (RRID:SCR_027837) | data set, data or information resource | Open data resource for mapping brain development and its associations with mental health. Integrates data from 5 large studies of brain development in youth from three continents (N = 6,346). Bifactor models were used to create harmonized psychiatric phenotypes, capturing major dimensions of psychopathology. Neuroimaging data were carefully curated and processed using consistent pipelines in a reproducible manner. | Neuroimaging data, curated data, data resource, mapping brain development, mental health, | NIMH R01MH120482; NIMH R37MH125829; NIBIB R01EB022573; NIMH R01MH112847; NIMH R01MH113550; NIMH RF1MH121867; NIMH R01MH123550; NINDS U24NS130411; NIMH P50MH109429; NIMH R01MH123440; NIMH K08MH079364 |
PMID:40987284 | Free, Freely available | SCR_027837 | 2026-02-16 09:51:29 | 0 | |||||||||
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Interagency Modeling and Analysis Group and Multi-scale Modeling Consortium Wiki Resource Report Resource Website 10+ mentions |
Interagency Modeling and Analysis Group and Multi-scale Modeling Consortium Wiki (RRID:SCR_008046) | IMAG | group | Special interest group that brings together program officers who have a shared interest in applying modeling and analysis methods to biomedical systems. The meetings are formatted to facilitate an open discussion of what is currently being supported, and for planning future directions in these areas. At each meeting, time is allotted to hear focused presentations from one or two participants to discuss issues relating to modeling and analysis across the government agencies. Discussions also occur online, and participants are informed of talks, conferences and other activities of interest to the group. IMAG recognized that the modeling community is on the forefront of thinking across the biological continuum, rather than just focusing at one scale or level of resolution. In addition IMAG identified a strong desire among modelers to form multi-disciplinary partnerships across varied research communities. Overall Intent of IMAG through the MSM Consortium is: * To develop new methodologies that span across biological scales * To develop multiscale methodologies applicable to biomedical, biological and behavioral research * To develop methodologies within the local multidisciplinary team and within the larger Framework environment * To further promote multiscale modeling through model sharing This wiki contains information relevant to the IMAG (Interagency Modeling and Analysis Group) and the MSM (Multi-scale Modeling Consortium). | environment, analysis, behavioral, biological, biomedical, continuum, modeling, research, scale, system |
is listed by: 3DVC has parent organization: National Institute of Biomedical Imaging and Bioengineering |
NIBIB ; NIH Blueprint for Neuroscience Research |
nif-0000-10261 | SCR_008046 | IMAG wiki, MSM wiki | 2026-02-14 02:01:37 | 15 | |||||||
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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 | |||||||
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nanoPOTS Resource Report Resource Website 1+ mentions |
nanoPOTS (RRID:SCR_017129) | instrument resource | Nanodroplet processing platform for deep and quantitative proteome profiling of 10 to 100 mammalian cells. It enhances efficiency and recovery of sample processing by downscaling processing volumes. | nanodroplet, processing, platform, quantitative, proteome, profiling, analysis, mammalian, cell, small, volume | has parent organization: Pacific Northwest National Laboratory | NIBIB R21 EB020976; NCI R33 CA225248; NIGMS P41 GM103493; NIDDK UC4 DK104167; NIDDK DP3 DK110844; NIH Office Of The Director S10 OD016350; JDRF |
PMID:29491378 | SCR_017129 | 2026-02-14 02:03:08 | 1 | |||||||||
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flowBin Resource Report Resource Website |
flowBin (RRID:SCR_000051) | software resource | A software package to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them. It establishes common bins across tubes in terms of the common markers, then determines expression within each tube for each bin in terms of the tube-specific markers. | software package, flow cytometry data, r, cell based assay, expression |
is related to: CRAN has parent organization: Bioconductor has parent organization: BC Cancer Agency |
NIBIB R01EB008400; Canadian Cancer Society ; Michael Smith Foundation for Health Research ; International Society for the Advancement of Cytometry |
PMID:25600947 | Free, Available for download, Freely available | OMICS_05593 | SCR_000051 | flowBin - Combining multitube flow cytometry data by binning | 2026-02-14 01:59:35 | 0 |
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