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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
Laser Biomedical Research Center
 
Resource Report
Resource Website
1+ mentions
Laser Biomedical Research Center (RRID:SCR_000106) LBRC access service resource, biomedical technology research center, service resource 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) 2026-10-17 01:36:19 4
Center for EPR Imaging in Vivo Physiology
 
Resource Report
Resource Website
Center for EPR Imaging in Vivo Physiology (RRID:SCR_001410) Center for EPR Imaging in Vivo Physiology biomedical technology research center, training resource Biomedical technology research center that develops instrumentation, analysis techniques, spin probes and spin traps, and methodologies for imaging physiologically relevant aspects of tissue fluids, including high-resolution oxygen maps, with very low frequency electron paramagnetic resonance imaging (EPRI). Novel bridges and high-access, low-field magnet/gradient systems have produced physiologically relevant measurements and accommodate a number of resonant structures. The Center is a consortium between the University of Chicago, the University of Denver, the University of Maryland and Novosibirsk Institute of Organic Chemistry (NIOC), Russia. electron paramagnetic resonance, in vivo, spin probe has parent organization: University of Chicago; Illinois; USA Diseased, Healthy NIBIB 4P41EB002034-17 nlx_152632 SCR_001410 Center for Electron Paramagnetic Resonance (EPR) Imaging in Vivo Physiology, Center for Electron Paramagnetic Resonance Imaging in Vivo Physiology, Very Low Frequency ERP Imaging In Vivo Physiology 2026-10-17 01:36:22 0
Laser Microbeam and Medical Program
 
Resource Report
Resource Website
1+ mentions
Laser Microbeam and Medical Program (RRID:SCR_001409) LAMMP biomedical technology research center, training resource Biomedical technology research center dedicated to the use of lasers and optics in biology and medicine with activities in technological research and development, collaborative research, service, training, and dissemination. One of the primary goals of LAMMP is to facilitate translational research by rapidly moving basic science and technology discoveries from blackboard to benchtop to bedside. This is accomplished by combining state of the art optical technologies with specialized resource facilities for cell and tissue engineering, histopathology, pre-clinical animal models, and clinical care. The resource center has been organized into 3 cores: * Microscopy and Microbeam Technologies (MMT) for high-resolution functional imaging and manipulation of living cells and tissues * Medical Translational Technologies (MTT) for non- and minimally-invasive monitoring, treating, and imaging pre-clinical animal models and human subjects, and * Virtual Photonics Technologies (VPT) for developing computational models and methods that advance the performance of biophotonic technologies, and enhance the information content derived from optical measurements. LAMMP cores contain complementary technologies that are capable of quantitatively characterizing, imaging, and perturbing structure and biochemical function in cells and tissues with scalable resolution and depth sensitivity ranging from micrometers to centimeters. laser, optics, biology, medicine, imaging, microscopy, microbeam, photonics, computational model, cell, tissue has parent organization: University of California at Irvine; California; USA NIBIB P41EB015890 Free, Freely Available nlx_152631 http://lammp.bli.uci.edu/ SCR_001409 2026-10-17 01:34:41 4
Pittsburgh NMR Center for Biomedical Research
 
Resource Report
Resource Website
Pittsburgh NMR Center for Biomedical Research (RRID:SCR_001408) Pittsburgh NMR Center for Biomedical Research biomedical technology research center, training resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 19,2024. Biomedical Technology Research Center that develops methodologies for the acquisition of morphological, biochemical, cellular, and functional information in living animals using nuclear magnetic resonance imaging (MRI) and spectroscopy (MRS). Novel techniques utilizing multidimensional MR imaging, magnetic resonance microscopy (MRM), and multinuclear in vivo spectroscopy are being applied to a wide range of problems in the biomedical sciences. mri, magnetic resonance spectroscopy, imaging, in vivo, nuclear magnetic resonance imaging, magnetic resonance microscopy, multinuclear has parent organization: Carnegie Mellon University; Pennsylvania; USA NIBIB P41 EB001977 THIS RESOURCE IS NO LONGER IN SERVICE nlx_152651 SCR_001408 2026-10-17 01:35:18 0
Hyperpolarized MRI Technology Resource Center
 
Resource Report
Resource Website
Hyperpolarized MRI Technology Resource Center (RRID:SCR_001405) Hyperpolarized MRI Technology Resource Center biomedical technology research center, training resource Biomedical technology research center developing, investigating, and disseminating new hyperpolarized MR techniques, new 13C agents and specialized analysis open-source software for data reconstruction and interpretation. The Technology Research & Development projects will leverage the extensive DNP facilities and experience of the project leaders to develop improved, robust hyperpolarized MRI methods. These technology developments will be driven by Collaborative Projects led by outstanding clinical and basic scientists who aim to use hyperpolarized 13C MRI to accomplish the scientific goals of their funded research. These technical developments will also be disseminated to the Service Project investigators for extramural feedback and then widely to the scientific community via a dedicated website and onsite training. This center will provide state-of-the-art training in this new metabolic imaging field and sponsor a yearly symposium focused on hyperpolarized MR technology development. mri, hyperpolarized, dynamic nuclear polarization, imaging, carbon-13 has parent organization: University of California at San Francisco; California; USA NIBIB P41EB013598 Free, Freely Available nlx_152628 SCR_001405 UCSF Hyperpolarized MRI Technology Resource Center 2026-10-17 01:36:22 0
Radiological Research Accelerator Facility
 
Resource Report
Resource Website
1+ mentions
Radiological Research Accelerator Facility (RRID:SCR_001425) RARAF access service resource, biomedical technology research center, service resource, 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 2026-10-17 01:35:18 1
Center for In Vivo Microscopy
 
Resource Report
Resource Website
10+ mentions
Center for In Vivo Microscopy (RRID:SCR_001426) CIVM biomedical technology research center, training resource Biomedical technology research center dedicated to the development of novel imaging methods for the basic scientist and the application of the methods to important biomedical questions. The CIVM has played a major role in the development of magnetic resonance microscopy with specialized MR imaging systems capable of imaging at more than 500,000x higher resolution than is common in the clinical domain. The CIVM was the first to demonstrate MR images using hyperpolarized 3He which has been moved from mouse to man with recent clinical trials performed at Duke in collaboration with GE. More recently the CIVM has developed the molecular imaging workbench---a system dedicated to multimodality cardiopulmonary imaging in the rodent. Their collaborators are employing these unique imaging systems in an extraordinary range of mouse and rat models of neurologic disease, cardiopulmonary disease and cancer to illuminate the underlying biology and explore new therapies. imaging, magnetic resonance microscopy, magnetic resonance imaging, clinical, mri, ct, x-ray, ultrasound, confocal, optical, spect has parent organization: Duke University; North Carolina; USA Cardiopulmonary disease, Cancer, Neurological disease NIBIB 4P41EB015897-27 Free, Freely Available nlx_152650 SCR_001426 Duke Center for In Vivo Microscopy 2026-10-17 01:34:41 10
RESBIO
 
Resource Report
Resource Website
1+ mentions
RESBIO (RRID:SCR_001424) RESBIO biomedical technology research center, training resource Biomedical technology research center that works to develop integrated tools and technologies that advance the discovery of polymeric biomaterials for regenerative medicine, the delivery of biological agents, and the next generation of medical implants. To achieve its mission, RESBIO's research is focused on the development of combinatorial and computational approaches to biomaterials design and optimization. Within this framework, RESBIO employs and uses: * Advanced multi-photon confocal laser microscopy to explore, understand, and control the response of cells in contact with artificial surfaces * Electron microscopy techniques to study the effect of nano-scale surface morphological features on cell behavior RESBIO research emphasizes the integration of a strong synthetic effort to create new biomaterial candidates with the development of rapid screening techniques for key material and biological properties relevant to the performance of a biomaterial in a given medical application. polymeric biomaterial, regenerative medicine, biological agent, medical implant, biomaterial, design, optimization, delivery, confocal laser microscopy, electron microscopy, cell has parent organization: Rutgers University; New Jersey; USA NIBIB 4P41EB001046-14 Free, Freely Available nlx_152646 http://www.njbiomaterials.org/web/index.php?p=resbio SCR_001424 Polymeric Biomaterials Resource, Integrated Technologies for Polymeric Biomaterials 2026-10-17 01:34:48 1
Center for Magnetic Resonance and Optical Imaging
 
Resource Report
Resource Website
1+ mentions
Center for Magnetic Resonance and Optical Imaging (RRID:SCR_001428) CMROI biomedical technology research center, training resource Biomedical technology research center dedicated to the development and application of innovative, novel magnetic resonance and optical imaging techniques. The facility's core sections provide research and computing resources for numerous user, collaborative, and training projects. The focus of this resource is on developing instrumentation, methodologies, and data analysis techniques for the quantitative assessment of functional, structural, and metabolic parameters in humans with the use of multinuclear magnetic resonance, novel spectral, perfusion, functional, and optical imaging techniques. These technological developments are driven by collaboration with scientists from within and outside University of Pennsylvania, the primary institution. Specifically, the Resource is focused on the development of quantitative, noninvasive MR and optical imaging based biomarkers for studying tissue metabolism and function, with an eye towards clinical translation through early diagnosis. The Center also provides support in the development and evaluation of new therapies in a variety of diseases. magnetic resonance imaging, optical imaging, multinuclear magnetic resonance has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA NIBIB P41 EB015893 Free, Freely Available nlx_152652 http://cmroi.med.upenn.edu/ SCR_001428 2026-10-17 01:36:23 1
National Center for Image-Guided Therapy
 
Resource Report
Resource Website
1+ mentions
National Center for Image-Guided Therapy (RRID:SCR_001419) NCIGT biomedical technology research center, training resource Biomedical Technology Resource Center that serves as a national resource for all aspects of research into medical procedures that are enhanced by imaging. Its common goal is to provide more effective patient care. The center is focused on the multidisciplinary development of innovative image-guided intervention technologies to enable effective, less invasive clinical treatments that are not only more economical, but also produce better results for patients. The NCIGT is helping to implement this vision by serving as a proving ground for some of the next generation of medical therapies. clinical, patient care, imaging, medical procedure has parent organization: Harvard Medical School; Massachusetts; USA NIBIB P41EB015898 Free, Freely Available nlx_152641 SCR_001419 National Center for Image Guided Therapy 2026-10-17 01:34:41 2
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
NCI U01 CA154601;
NCI U24 CA180918;
NCI U24 CA180927;
NIBIB P41 EB015896;
NIBIB T32 EB1680;
NIBI ;
NIDA R90 DA023427;
NIDA T90 DA022759;
NIH Blueprint for Neuroscience Research
PMID:32578020 Free, Available for download, Freely available SCR_016911 2026-10-17 01:34:21 2
3D Developmental Mouse Brain Common Coordinate Framework
 
Resource Report
Resource Website
1+ mentions
3D Developmental Mouse Brain Common Coordinate Framework (RRID:SCR_025544) atlas, data or information resource 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
NIBIB R01EB031722;
NIMH R01MH116176;
NIMH RF1MH12460501;
NINDS R01NS108407
PMID:37745386 Free, Freely available SCR_025544 DevCCF 2026-10-17 01:36:43 2
NeuronUnit
 
Resource Report
Resource Website
1+ mentions
NeuronUnit (RRID:SCR_015634) software resource, software toolkit, source code Software toolkit for data-driven validation of neuron and ion channel models using SciUnit. NeuronUnit implements an interface to several simulators and model description languages, handles test calculations according to domain standards, and enables automated construction of tests based on data from several major public data repositories. ion channel, neuron, validation, simulation, model description language, modeling software uses: SciUnit NIBIB R01EB021711 Tutorial available SCR_015634 2026-10-17 01:35:50 4
LONI Inspector
 
Resource Report
Resource Website
1+ mentions
LONI Inspector (RRID:SCR_004923) LONI Inspector data processing software, software application, software resource A Java application for reading, displaying, searching, comparing, and exporting metadata from medical image files: AFNI, ANALYZE, DICOM, ECAT, GE, Interfile, MINC, and NIFTI. analyze, dicom, java, minc, magnetic resonance, nifti, os independent, win32 (ms windows), workflow is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Laboratory of Neuro Imaging
NIBIB 9P41EB015922-15;
NCRR 2-P41-RR-013642-15
LONI Software License nlx_155785 http://www.nitrc.org/projects/inspector http://www.loni.ucla.edu/Software/LONI-Inspector SCR_004923 2026-10-17 01:31:55 3
Neuroscience Gateway
 
Resource Report
Resource Website
10+ mentions
Neuroscience Gateway (RRID:SCR_008915) NSG data or information resource, portal, project portal, software resource Web portal that allows free access to supercomputing resources for large scale modeling and data processing. Portal facilitates access and use of National Science Foundation (NSF) High Performance Computing (HPC) resources by neuroscientists. Large, scale, modeling, data, computing, neuroscience, neuron, BRAIN Initiative is recommended by: BRAIN Initiative
lists: ModelRun
is related to: XSEDE - Extreme Science and Engineering Discovery Environment
is related to: NEURON
is related to: GENESIS Neural Database and Modelers Workspace
has parent organization: San Diego Supercomputer Center
has parent organization: Neuroscience Information Framework
has parent organization: Yale School of Medicine; Connecticut; USA
BBSRC N005236;
NIBIB R01 EB023297;
NSF 1146949;
NSF 1339856;
NSF 1458495;
NSF 1458840
Free, Freely available nlx_151553, SCR_015767 http://www.nitrc.org/projects/nsg/ SCR_008915 Neuroscience Gateway - A Portal for Computational Neuroscience, Neuroscience Gateway, Neuroscience Gateway (NSG) Portal 2026-10-17 01:32:21 25
Brain Computer Interface 2000 Software Package
 
Resource Report
Resource Website
100+ mentions
Brain Computer Interface 2000 Software Package (RRID:SCR_007346) data processing software, software application, software resource BCI2000 is a general-purpose system for brain-computer interface (BCI) and adaptive neurotechnology research. It can also be used for data acquisition, stimulus presentation, and brain monitoring applications. The mission of the BCI2000 project is to facilitate research and applications in the areas described. Their vision is that BCI2000 will become a widely used software tool for diverse areas of real-time biosignal processing. In order to achieve this vision, BCI2000 system is available for free for non-profit research and educational purposes. BCI2000 supports a variety of data acquisition systems, brain signals, and study/feedback paradigms. During operation, BCI2000 stores data in a common format (BCI2000 native or GDF), along with all relevant event markers and information about system configuration. BCI2000 also includes several tools for data import/conversion (e.g., a routine to load BCI2000 data files directly into Matlab) and export facilities into ASCII. BCI2000 also facilitates interactions with other software. For example, Matlab scripts can be executed in real-time from within BCI2000, or BCI2000 filters can be compiled to execute as stand-alone programs. Furthermore, a simple network-based interface allows for interactions with external programs written in any programming language. For example, a robotic arm application that is external to BCI2000 may be controlled in real time based on brain signals processed by BCI2000, or BCI2000 may use and store along with brain signals behavioral-based inputs such as eye-tracker coordinates. Because it is based on a framework whose services can support any BCI implementation, the use of BCI2000 provides maximum benefit to comprehensive research programs that operate multiple BCI2000 installations to collect data for a variety of studies. The most important benefits of the system in such situations are: - A Proven Solution - Facilitates Operation of Research Programs - Facilitates Deployment in Multiple Sites - Cross-Platform and Cross-Compiler Compatibility - Open Resource Sponsors: BCI2000 development is sponsored by NIH/NIBIB R01 and NIH/NINDS U24 grants. Keywords: General, Purpose, Systems, Brain, Computer, Interface, Research, Application, Brain, Diverse, Educational, Laboratory, Software, Network, Signals, Behavioral, Eye, Tracker, is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: National Institutes of Health
NIBIB P41 EB018783;
NIBIB R01 EB026439;
NINDS U24 NS109103
nif-0000-00251 http://www.nitrc.org/projects/bci2000, http://www.bci2000.org, https://www.neurotechcenter.org/software SCR_007346 BCI2000 2026-10-17 01:31:54 180
LONI Java Image I/O Plugins
 
Resource Report
Resource Website
LONI Java Image I/O Plugins (RRID:SCR_008277) data processing software, software application, software resource Decoders and encoders written in Java for the AFNI, ANALYZE, DICOM, ECAT, GE, MINC, NIFTI and other neuroimaging file formats.The plugins use Java Image I/O interfaces to read and write metadata and image data and can read and write AFNI, ANALYZE 7.5, DICOM, ECAT 7.2, GE 5.0, INTERFILE (including hrrt), MINC, NIFTI, and UCLA PACS file formats. All source code is provided and usage examples are included. plugin, MRI, software, visualization, data processing is related to: Laboratory of Neuro Imaging
has parent organization: University of Southern California; Los Angeles; USA
NIBIB 9P41EB015922-15;
NCRR 2-P41-RR-013642-15
Available for educational and research purposes only nif-0000-23320 SCR_008277 2026-10-17 01:31:54 0
Homer2
 
Resource Report
Resource Website
100+ mentions
Homer2 (RRID:SCR_009586) data processing software, image analysis software, software application, software resource Software matlab scripts used for analyzing fNIRS data to obtain estimates and maps of brain activation. Graphical user interface (GUI) for visualization and analysis of functional near-infrared spectroscopy (fNIRS) data. Analysis, optical, imaging, fnirs, map, brain, activation, BRAIN Initiative is recommended by: BRAIN Initiative
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: NIRx2nirs: A NIRx to .nirs data converter
NCRR P41 RR14075;
NIBIB EB025145;
NIBIB R01 EB006385
Free, Available for download, Freely available nlx_155773 http://www.nitrc.org/projects/homer2, https://homer-fnirs.org/ SCR_009586 HOMER1, Photon Migration Imaging toolbox 2026-10-17 01:33:03 250
TRACULA
 
Resource Report
Resource Website
10+ mentions
TRACULA (RRID:SCR_013152) TRACULA data processing software, software application, software resource Software tool developed for automatically reconstructing a set of major white matter pathways in the brain from diffusion weighted images using probabilistic tractography. This method utilizes prior information on the anatomy of the pathways from a set of training subjects. By incorporating this prior knowledge in the reconstruction procedure, our method obviates the need for manual intervention with the tract solutions at a later stage and thus facilitates the application of tractography to large studies. The trac-all script is used to preprocess raw diffusion data (correcting for eddy current distortion and B0 field inhomogenities), register them to common spaces, model and reconstruct major white matter pathways (included in the atlas) without any manual intervention. trac-all may be used to execute all the above steps or parts of it depending on the dataset and user''''s preference for analyzing diffusion data. Alternatively, scripts exist to execute chunks of each processing pipeline, and individual commands may be run to execute a single processing step. To explore all the options in running trac-all please refer to the trac-all wiki. In order to use this script to reconstruct tracts in Diffusion images, all the subjects in the dataset must have Freesurfer Recons. tractography, white matter tract, white matter pathway, diffusion weighted image, diffusion magnetic resonance imaging, white matter, brain, reconstruct, diffusion tensor imaging is related to: FreeSurfer
has parent organization: Harvard Medical School; Massachusetts; USA
Aging NIH Blueprint for Neuroscience Research ;
Ellison Medical Foundation ;
NIBIB EB008129;
NIMH U01-MH093765;
NCRR P41-RR14075;
NCRR U24-RR021382;
NIBIB R01-EB006758;
NIA R01-AG022381;
National Center for Complementary and Alternative Medicine RC1-AT005728;
NINDS R01-NS052585;
NINDS R21-NS072652;
NINDS R01-NS070963
PMID:22016733 nlx_143919 SCR_013152 TRACULA - TRActs Constrained by UnderLying Anatomy, TRACULA: TRActs Constrained by UnderLying Anatomy, TRActs Constrained by UnderLying Anatomy 2026-10-17 01:33:05 17
DRIFTER
 
Resource Report
Resource Website
10+ mentions
DRIFTER (RRID:SCR_014937) data processing software, image analysis software, software application, software resource Model based Bayesian method for eliminating physiological noise from fMRI data. This algorithm uses image voxel analysis to isolate the cardiac and respiratory noise from the relevant data. bayesian, physiological noise, fMRI, algorithm, cardiac, respiratory, image anaylsis, bold signal has parent organization: Aalto University; Espoo; Finland NICHD R01HD040712;
NINDS R01NS037462;
NINDS R01NS048279;
NCR P41RR014075;
NIMH R01MH083744;
NIDCD R21DC010060;
NIBIB R21EB007298;
National Science Council Taiwan NSC 98-2320-B-002-004-MY3;
National Science Council Taiwan NSC 100-2325-B-002-046;
National Health Research Institute Taiwan NHRI-EX100-9715EC;
Academy of Finland 124698;
Academy of Finland 125349;
Academy of Finland 127624;
Academy of Finland 129670;
Academy of Finland 218054;
Academy of Finland 218248
PMID:22281675 Free, Available for download, Acknowledgement requested SCR_014937 DRIFTER Toolbox 2026-10-17 01:32:26 28

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