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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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HCP Pipelines Resource Report Resource Website 10+ mentions |
HCP Pipelines (RRID:SCR_026575) | software application, software resource, data processing software, image processing software, 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 | 2026-07-28 09:46:42 | 20 | |||||||
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Nested containment list Resource Report Resource Website |
Nested containment list (RRID:SCR_027849) | NCLS, NCList | software resource, software toolkit, software library | Software library for nested containment list data structure for interval overlap queries, like interval tree. It is a static interval-tree that is fast for both construction and lookups. | nested containment list data structure, interval overlap queries, static interval-tree, construction and lookups, | NCRR U54 RR021813; NSF |
PMID:17234640 | Free, Available for download, Freely available | SCR_027849 | , Nested Containment List (NCList), Nested Containment List | 2026-07-28 09:47:04 | 0 | |||||||
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MRQy Resource Report Resource Website 1+ mentions |
MRQy (RRID:SCR_025779) | software application, software resource, data analysis software, data processing software | Software quality assurance and checking tool for quantitative assessment of magnetic resonance imaging and computed tomography data. Used for quality control of MR imaging data. | quantitative assessment, magnetic resonance imaging, computed tomography, imaging data, | NCI U24CA199374; NCI R01CA202752; NCI R01CA208236; NCI R01CA216579; NCI R01CA220581; NCI 1U01CA239055; NCI 1F31CA216935; NCI 1U01CA248226; NHLBI R01HL15127701A1; NIBIB 1R43EB028736; NCRR 1C06RR12463 |
PMID:33176026 | Free, Available for download, Freely available | SCR_025779 | 2026-07-28 09:46:27 | 1 | |||||||||
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OpenSlide Resource Report Resource Website |
OpenSlide (RRID:SCR_028483) | software resource, software toolkit, software library | Software C library that provides a simple interface to read whole-slide images (also known as virtual slides). | read whole-slide images, virtual slides, | NCRR UL1RR024153; NCATS UL1TR000005 |
PMID:24244884 | Free, Available for download, Freely available | SCR_028483 | 2026-07-28 09:47:20 | 0 | |||||||||
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Resource Center for Medical Ultrasonic Transducer Technology Resource Report Resource Website 1+ mentions |
Resource Center for Medical Ultrasonic Transducer Technology (RRID:SCR_001404) | UTRC | training resource | Biomedical technology research center focusing on the development of very high frequency (above 20 MHz) ultrasonic transducers/arrays for applications in medicine and biology that include ophthalmology, dermatology, vascular surgery, and small animal imaging. The research is pursued simultaneously in three directions: novel piezoelectric materials, very high frequency single element transducers and linear arrays, and finite element modeling and material property measurements. The Center also serves the community through collaborative efforts with investigators having a research interest in high-frequency ultrasound imaging. In addition, it performs the function of training and information dissemination by offering conferences, seminars and specialized courses at the University of Southern California. The Center has set forth a number of goals which define its mission: * Conduct novel research and development of very high frequency (>20MHz) ultrasonic transducers, arrays and imaging applications * Collaborate with other academic institutions, non-profit organizations, and small businesses supported by the NIH to further the development of these high-frequency applications and provide the expertise in transducers necessary for project success * Serve as an educational center for training scientists and engineers interested in ultrasonic transducer technology One of the primary goals of the Center is to provide service to outside investigators and small business. Often an investigator or company has a specific application in mind but is without the expertise to develop the necessary ultrasonic device. Investigators at academic institutions, research institutes, or small businesses supported by NIH grants who have a need for medical ultrasound transducers and are interested in a collaborative effort should contact Dr. Hyung Ham Kim or Dr. K. Kirk Shung. Ultrasound transducers and components can be fabricated either completely by center personnel or in a joint effort with other investigators. In addition, collaborators are encouraged to visit the facility for additional training in fabrication and assembly. | ultrasonic transducer, array, ultrasound, imaging | has parent organization: University of Southern California; Los Angeles; USA | NCRR 1S10RR023653-01 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152627 | SCR_001404 | Ultrasonic Transducer Resource Center, USC Resource Center for Medical Ultrasonic Transducer Technology, Resource on Medical Ultrasonic Transducer Technology | 2026-07-25 12:05:02 | 3 | ||||||
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MS-GF+ Resource Report Resource Website 100+ mentions |
MS-GF+ (RRID:SCR_015646) | software resource | Software that performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database. | protein idenitification, peptide sequence, ms, ms spectrum, proteomic, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: Pacific Northwest National Laboratory |
NCRR RR018522; NCRR 1-P41-RR024851; NIAID ; W.R. Wiley Environmental Molecular Science Laboratory |
PMID:25358478 | Free, Available for download, Acknowledgment requested | biotools:ms-gf | https://github.com/sangtaekim/msgfplus, https://bio.tools/ms-gf | SCR_015646 | MSGF+, MSGFPlus | 2026-07-25 12:08:11 | 155 | |||||
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University of Michigan Biorepository Resource Report Resource Website |
University of Michigan Biorepository (RRID:SCR_004643) | MICHER Biorepository | biomaterial supply resource, material resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 24,2025. In 2009, the Medical School and the Michigan Institute for Clinical & Health Research (MICHR) unveiled a new biorepository for U-M researchers in need of a controlled storage environment for biological samples. MICHR is pleased to be able to add to its many services for the research community a centralized biological repository for controlled storage of biological samples, and related services (including DNA, RNA, and other downstream preparation) within the U-M campus. The biorepository, located in the CAP/CLIA-certified Michigan Center for Translational Pathology (MCTP) laboratory at the U-M Traverwood facility on Huron Parkway, will store biologic material, including blood and urine. Sample accessioning and tracking will be accomplished using the caTISSUE suite of programs, and samples will be processed and stored in compliance with CAP/CLIA guidelines. Initially, all samples will be used only with the authorization of the individual investigator who directed the project under which the samples were obtained. Samples will be used in accordance with the relevant informed consent. Long-term plans include federating the database in order to facilitate sharing of data and samples between research teams. | biologic material, blood, urine |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of Michigan Medical School; Michigan; USA |
NCRR UL1RR024986 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_63960 | http://www.michr.umich.edu/biorepository/index.html | SCR_004643 | 2026-07-25 12:12:32 | 0 | ||||||
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STRAP Resource Report Resource Website 100+ mentions |
STRAP (RRID:SCR_005675) | STRAP | software application, software resource, data processing software | Software program that automatically annotates a protein list with information that helps in the meaningful interpretation of data from mass spectrometry and other techniques. It takes protein lists as input, in the form of plain text files, protXML files (usually from the TPP), or Dat files from MASCOT search results. From this, it generates protein annotation tables, and a variety of GO charts to aid individual and differential analysis of proteomics data. It downloads information from mainly the Uniprot and EBI QuickGO databases. STRAP requires Windows XP or higher with at least version 3.5 of the Microsoft .NET Framework installed. Platform: Windows compatible | protein, gene, annotation, mass spectrometry, proteomics, visualization, browser, differential analysis, analysis, ontology or annotation browser, ontology or annotation visualization, differential analysis of proteomics data sets, windows, protein annotation, data visualization, c#, pathway, FASEB list |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: UniProt is related to: QuickGO has parent organization: Boston University School of Medicine; Massachusetts; USA |
NHLBI contract N01 HV28178; NCRR P41 RR10888 |
PMID:19839595 | Open unspecified license, Acknowledgement requested | OMICS_02277, nlx_149115 | SCR_005675 | Software Tool for Rapid Annotation of Proteins, STRAP for GO Annotation, STRAP - Software Tool for Rapid Annotation of Proteins | 2026-07-26 09:03:58 | 120 | |||||
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Autopack Resource Report Resource Website 1+ mentions |
Autopack (RRID:SCR_006830) | autoPack | software application, software resource, data processing software | An open-source general packing algorithm that packs 3D objects onto surfaces, into volumes, and around volumes. It provides a general architecture to allow various packing algorithms to interoperate efficiently in the same model. autoPack can incorporate any packing solution into its modular python program architecture, but is currently optimized to provide a novel solution to the loose packing problem which places objects of discrete size into place (compared to advancing front, popcorn, or other fast tight-packing solutions that allow objects to scale to arbitrary masses.) Most popular 3D software programs now contain robust physics engines based on Bullet that can separate small collections of overlapping objects or allow volumes to be filled by pouring shapes from generators, but these approaches fails for large complex systems and result in either overlapping geometry, crashed software, or non-random gradients. Most packing algorithms are designed to position objects as efficiently as possible, but autoPack allows the user to select from random loose packing to highly organized packing methods����??even to choose both methods at the same time. autoPack positions 3D geometries into, onto, and around volumes with minimal to zero overlap. autoPack mixes several packing approaches and procedural growth algorithms. autoPack can thus place objects with forces and constraints to allow a high degree of control ranging from completely random distributions to highly ordered structures. * zero to minimal overlaps depending on the method used * accuracy vs speed parameters selected by the user * zero edge effects * complete control, from fully random to fully ordered distributions * agent-based interaction, weighting, and collision control | 3d visualization software, modeling software, 3d packing software, packing, 3d object, surface, volume, algorithm |
is related to: Cellpack has parent organization: Google Code has parent organization: Scripps Research Institute is parent organization of: Cellpack |
QB3 at UCSF Fellowship ; NSF 07576; NCRR P41 RR08605 |
GNU Lesser General Public License | nlx_151791 | https://sites.google.com/site/autofill21/, http://code.google.com/p/autofill/ | SCR_006830 | 2026-07-26 09:04:22 | 3 | ||||||
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LONI De-identification Debablet Resource Report Resource Website |
LONI De-identification Debablet (RRID:SCR_009593) | LONI De-identification Debablet | software application, software resource | Software application for removing patient-identifying information from medical image files. Removing this information is often necessary for enabling investigators to share image files in a HIPAA compliant manner. | analyze, console (text based), 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_155784 | http://www.nitrc.org/projects/did | http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=23 | SCR_009593 | 2026-07-26 09:04:53 | 0 | |||||
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BioMesh3D Resource Report Resource Website 1+ mentions |
BioMesh3D (RRID:SCR_009534) | BioMesh3D | software application, software resource | A free, easy to use program for generating quality meshes for use in biological simulations. It is currently integrated with SCIRun and uses the SCIRun system to visualize the intermediate results. The BioMesh3D program uses a particle system to distribute nodes on the separating surfaces that separate the different materials and then uses the TetGen software package to generate a full tetrahedral mesh. | mesh, simulation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SCIRun is related to: SCIRun has parent organization: University of Utah; Utah; USA |
NCRR 5P41RR012553-15; NIGMS 8 P41 GM103545-15 |
PMID:23367171 | MIT License | nlx_155708 | http://www.nitrc.org/projects/biomesh3d | SCR_009534 | 2026-07-26 09:04:52 | 3 | |||||
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ResearchIQ Resource Report Resource Website |
ResearchIQ (RRID:SCR_014304) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented March 14, 2016. Research Integrative Query (ResearchIQ) tool, a semantically anchored resource discovery platform that facilitates semantic discovery of local and publicly available data through a single web portal designed for researchers in the biomedical informatics domain within The Ohio State University. | Platform, Semantic information | has parent organization: Ohio State University; Ohio; USA | NCRR UL1-RR025755 | PMID:26306248 | THIS RESOURCE IS NO LONGER IN SERVICE | http://researchiq.bmi.osumc.edu:8080/#riqview | SCR_014304 | 2026-07-26 09:06:00 | 0 | |||||||
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eXpression2Kinases Resource Report Resource Website 1+ mentions |
eXpression2Kinases (RRID:SCR_016307) | X2K | software application, software resource | Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures. | inferred, network, transcription, factor, protein, kinase, regulate, expression, gene, analysis, combine, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS P50 GM071558; NIDDK R01 DK088541; NLM RC2 LM010994; NIDDK P01 DK056492; NIDDK RC4DK090860; NCRR KL2 RR029885 |
PMID:22080467 | Open source, Free, Freely available, Available for download | biotools:x2k | https://bio.tools/x2k, http://www.maayanlab.net/X2K/ | SCR_016307 | eXpression2Kinases, X2K | 2026-07-26 09:06:37 | 4 | ||||
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LONI Debabeler Resource Report Resource Website |
LONI Debabeler (RRID:SCR_001160) | Debabeler | software application, software resource | Software to manage the conversion of imaging data from one file format and convention to another. It consists of a graphical user interface to visually program the translations, and a data translation engine to read, sort and translate the input files, and write the output files to disk. The data translation engine: (1) Reads metadata from a set of image files on disk to identify the source that produced each file; (2) Groups the image files into user-defined collections using image metadata values; (3) Translates each image file collection by reading metadata and pixel data and mapping the data into the appropriate output file format through a programmable set of connected modules. The Debabeler uses the Java Image I/O Plugin Architecture to read and write a wide variety of common medical image file formats, including ANALYZE, MINC, and most variations of DICOM. | workflow, java, analyze, dicom, minc, nifti-1, neuroimaging, file format, translation, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of California at Los Angeles; California; USA |
NCRR 9P41EB015922-15; NCRR 2-P41-RR-013642-15 |
PMID:15670695 | Free, Available for download, Freely available | nif-0000-00321 | http://www.nitrc.org/projects/debabeler | SCR_001160 | 2026-07-26 09:03:01 | 0 | |||||
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Knowledge Engineering from Experimental Design Resource Report Resource Website 1+ mentions |
Knowledge Engineering from Experimental Design (RRID:SCR_001238) | KEfED | software application, software resource | Knowledge engineering software for reasoning with scientific observations and interpretations. The software has three parts: (a) the KEfED model editor - a design editor for creating KEfED models by drawing a flow diagram of an experimental protocol; (b) the KEfED data interface - a spreadsheet-like tool that permits users to enter experimental data pertaining to a specific model; (c) a "neural connection matrix" interface that presents neural connectivity as a table of ordinal connection strengths representing the interpretations of tract-tracing data. This tool also allows the user to view experimental evidence pertaining to a specific connection. The KEfED model is designed to provide a lightweight representation for scientific knowledge that is (a) generalizable, (b) a suitable target for text-mining approaches, (c) relatively semantically simple, and (d) is based on the way that scientist plan experiments and should therefore be intuitively understandable to non-computational bench scientists. The basic idea of the KEfED model is that scientific observations tend to have a common design: there is a significant difference between measurements of some dependent variable under conditions specified by two (or more) values of some independent variable. | experimental design, observation, interpretation, reasoning, experimental data, observational assertion, knowledge engineering, java |
is listed by: FORCE11 is related to: Bioscholar has parent organization: Biomedical Informatics Research Network |
NIGMS R01-GM083871; NIMH 1R01MH079068-01A2; NCRR 1 U24 RR025736-01 |
PMID:21859449 | Free, Available for download, Freely available | nif-0000-07745 | https://wiki.birncommunity.org/display/NEWBIRNCC/Knowledge+Engineering+from+Experimental+Design+%28%27KEfED%27%29 | SCR_001238 | 2026-07-26 09:03:00 | 1 | |||||
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ImageVis3D Resource Report Resource Website 10+ mentions |
ImageVis3D (RRID:SCR_009566) | ImageVis3D | software application, software resource, data processing software | A new volume rendering program developed by the NIH/NCRR Center for Integrative Biomedical Computing (CIBC). The main design goals of ImageVis3D are: simplicity, scalability, and interactivity. Simplicity is achieved with a new user interface that gives an unprecedented level of flexibility (as shown in the images). Scalability and interactivity for ImageVis3D mean that both on a notebook computer as well as on a high end graphics workstation, the user can interactively explore terabyte sized data sets. Finally, the open source nature as well as the strict component-by-component design allow developers not only to extend ImageVis3D itself but also reuse parts of it, such as the rendering core. This rendering core, for instance, is planned to replace the volume rendering subsystems in many applications at the SCI Institute and with their collaborators. | magnetic resonance, rendering |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: University of Utah; Utah; USA |
NCRR P41-RR12553-15; DOE DEFC0206ER25781 |
Free, Available for download, Freely available | nlx_155776 | http://www.nitrc.org/projects/imagevis3d, https://sources.debian.org/src/imagevis3d/ | SCR_009566 | 2026-07-26 09:04:53 | 10 | ||||||
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LONI Pipeline Processing Environment Resource Report Resource Website 10+ mentions |
LONI Pipeline Processing Environment (RRID:SCR_001161) | LONI Pipeline | software application, workflow software, software resource, data processing software | A free workflow application primarily aimed at neuroimaging researchers that allows users to easily describe their executables in a graphical user interface (ie. create a module) and connect them together to create complex analyses all without having to code a single line in a scripting language. The Pipeline Client runs on your PC/Mac/Linux computer upon which you can create sophisticated processing workflows using a variety of commonly available executable tools (e.g. FSL, AIR, FreeSurfer, AFNI, Diffusion Toolkit, etc). The Distributed Pipeline Server can be installed on your Linux cluster and you can submit processing jobs directly to your own compute systems. Once you����??ve created a module for use in the LONI Pipeline, you can save it into your personal library and reuse it in other workflows you create by simply dragging and dropping it in. Because the LONI Pipeline is written in Java, you can work in whatever operating system suits you best. If there are tools that you need that can only work on another operating system, you can install a Pipeline server on that computer and connect from your client to do processing and analysis remotely. | workflow, neuroscience, afni brik, analyze, bshort, bfloat, computational neuroscience, dicom, imaging genomics, java, linux, macos, microsoft, minc, minc2, nifti, pet, spect, posix/unix-like, sunos/solaris, windows, windows nt/2000, atlas, birn, ccb, functional, na-mic, registration, segmentation, statistical, surface analysis, visual processing environment, volume, warping, image processing |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of California at Los Angeles; California; USA |
NCRR P41 RR013642; NIMH R01 MH71940; NCRR U54 RR021813 |
PMID:12880830 | Free, Available for download, Freely available | nif-0000-00322 | http://www.nitrc.org/projects/pipeline | http://www.loni.ucla.edu/NCRR/Software/Pipeline.html | SCR_001161 | LONI Pipeline Environment | 2026-07-27 09:31:08 | 11 | |||
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Manual Align RTS2000 Resource Report Resource Website |
Manual Align RTS2000 (RRID:SCR_007107) | software application, image processing software, software resource, data processing software | Software program to adjust the alignment of two adjacent images. Allows to correct for any misalignment that may occur during auto-alignment step. Serves as a bootstrap to get the images in approximately the right place. | alignment, process, image, adjust, correct, misalignment |
is affiliated with: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National Center for Microscopy and Imaging Research |
NCRR P41 RR04050 | Free, no longer available | nif-0000-10514 | SCR_007107 | 2026-07-27 09:32:44 | 0 | ||||||||
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Functional Regression Analysis of DTI Tract Statistics Resource Report Resource Website |
Functional Regression Analysis of DTI Tract Statistics (RRID:SCR_002293) | FRATS | software application, image analysis software, software resource, data processing software | Software for the analysis of multiple diffusion properties along fiber bundle as functions in an infinite dimensional space and their association with a set of covariates of interest, such as age, diagnostic status and gender, in real applications. The resulting analysis pipeline can be used for understanding normal brain development, the neural bases of neuropsychiatric disorders, and the joint effects of environmental and genetic factors on white matter fiber bundles. | computational neuroscience, imaging genomics, magnetic resonance, regression analysis, dti, statistics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
NSF BCS-08-26844; NCRR UL1-RR025747-01; NIMH MH086633; NIA AG033387; NIMH MH064065; NICHD HD053000; NIMH MH070890; NINDS R01NS055754; NIBIB U54 EB005149-01 |
PMID:20335089 | Academic Free License | nlx_155629 | SCR_002293 | Functional Regression Analysis of DTI | 2026-07-27 09:31:30 | 0 | |||||
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ArrayQuest Resource Report Resource Website 1+ mentions |
ArrayQuest (RRID:SCR_010935) | ArrayQuest | analysis service resource, service resource, data analysis service, production service resource | A web-accessible program for the analysis of DNA microarray data. ArrayQuest is designed to apply any type of DNA microarray analysis program executable on a Linux system (i.e., Bioconductor statistical and graphical methods written in R as well as BioPerl and C++ based scripts) to DNA microarray data stored in the MUSC DNA Microarray Database, the Gene Expression Omnibus (GEO) or in a password protected private database uploaded to the center point server. ArrayQuest analyses are performed on a computer cluster. |
is listed by: OMICtools is related to: MUSC DNA Microarray Database is related to: Gene Expression Omnibus has parent organization: Medical University of South Carolina; South Carolina; USA |
University Research Resource Foundation ; NCI R24CA095841; NCRR P20RR016434 |
PMID:16321157 | Free, Public | OMICS_00746 | SCR_010935 | ArrayQuest - An On-line DNA Microarray Analysis System | 2026-07-27 09:33:45 | 1 |
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