Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ReproNim: A Center for Reproducible Neuroimaging Computation Resource Report Resource Website 10+ mentions |
ReproNim: A Center for Reproducible Neuroimaging Computation (RRID:SCR_016001) | ReproNim | organization portal, data or information resource, portal | Center to help neuroimaging researchers to find and share data in FAIR fashion, to describe their data and analysis workflows in replicable fashion, to manage their computational resource options so that outcomes of neuroimaging research are more reproducible. | Neuroimaging, share, data, FAIR, analysis, manage, reproducible |
is related to: ABCD-ReproNim Course is related to: SVNTest is parent organization of: ReproIn: The ReproNim image input management system (featuring DataLad) |
NIBIB P41 EB019936 | Restricted | SCR_016005 | http://repronim.org | SCR_016001 | 2026-02-15 09:21:44 | 12 | ||||||
|
Oufti Resource Report Resource Website 10+ mentions |
Oufti (RRID:SCR_016244) | software application, image analysis software, data processing software, software resource | Software designed for analysis of microscopy data. It performs sub-pixel precision detection, quantification of cells and fluorescence signals, as well as other image analysis functions. | microscopy, data, imaging, image, analysis, pixel, fluorescent, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM065835 | PMID:26538279 | biotools:oufti | https://bio.tools/oufti | SCR_016244 | outfi | 2026-02-15 09:21:34 | 13 | ||||||
|
SegAN Resource Report Resource Website 1+ mentions |
SegAN (RRID:SCR_016215) | software application, image analysis software, data processing software, software resource | Image analysis software for medical image segmentation. The software is fueled by an end-to-end adversarial neural network that generates segmentation label maps. | neural, network, segmentation, pixel, spatial, image, medical, analysis, labelling, loss function, segmentor | NIH ; NLM ; LHNCBC HHSN276201500692P |
Free, Available for download | SCR_016215 | Semantic Segmentation with Adversarial Learning (SegAN), Semantic Segmentation with Adversarial Learning, SegAN: Semantic Segmentation with Adversarial Learning | 2026-02-15 09:21:35 | 4 | |||||||||
|
cryoSPARC Resource Report Resource Website 1000+ mentions |
cryoSPARC (RRID:SCR_016501) | software application, image analysis software, data processing software, software resource | Software integrated platform used for obtaining 3D structural information from single particle cryo-EM data. Enables automated, high quality and high-throughput structure discovery of proteins, viruses and molecular complexes for research and drug discovery. | Structura Biotechnology Inc., data, processing, analysis, image, single, particle, cryo-EM, structure, discovery, automated, protein, virus, molecular, complex | is related to: University of Toronto; Ontario; Canada | PMID:28165473 | Available free of charge for academic users with a valid institutional email address, Trail available | SCR_016501 | 2026-02-15 09:21:07 | 2480 | |||||||||
|
Whole Tale Resource Report Resource Website 1+ mentions |
Whole Tale (RRID:SCR_017537) | project portal, data or information resource, portal | Platform for reproducible research. Code base for publishing data. For merging science and cyberinfrastructure pathways. Data Infrastructure Building Block (DIBBS) initiative to build scalable, open source, web-based, multi-user platform for reproducible research enabling creation, publication, and execution of tales – executable research objects that capture data, code, and complete software environment used to produce research findings. To enable researchers to define and create computational environment to manage complete conduct of computational experiments and expose them for analysis and reproducibility. | Reproducible, data, merging, science, cyberinfrastructure, pathway, tale, capture, code, finding, analysis | NSF 1541450 | DOI:10.1016/j.future.2017.12.029 | Free, Freely available | https://github.com/whole-tale/wt-design-docs//blob/stable/README.rst | SCR_017537 | 2026-02-15 09:22:03 | 1 | ||||||||
|
BZ-H3A analyzer software Resource Report Resource Website 10+ mentions |
BZ-H3A analyzer software (RRID:SCR_017375) | software application, image analysis software, data processing software, software resource | Software tool as analysis application BZ-H3A by Keyence, Osaka, Japan for fluorescence microscope BZ-X series. | Analysis, Keyence, Japan, fluorescence, microscope, BZ-X | SCR_017375 | 2026-02-15 09:22:03 | 10 | ||||||||||||
|
Sniffles Resource Report Resource Website 50+ mentions |
Sniffles (RRID:SCR_017619) | software application, data processing software, software resource | Software tool as structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Used to avoid single molecule long read sequencing high error rates. | Structural, variation, caller, third, generation, sequencing, SV, split, read, alignment, mismatch, region, analysis, error, bio.tools |
is listed by: bio.tools is listed by: Debian |
NHGRI R01 HG006677; NHGRI UM1 HG008898 |
PMID:29713083 | Free, Available for download, Freely available | biotools:sniffles | https://bio.tools/sniffles | SCR_017619 | 2026-02-15 09:22:05 | 59 | ||||||
|
UN-SCAN-IT Gel Analysis Software Resource Report Resource Website 1+ mentions |
UN-SCAN-IT Gel Analysis Software (RRID:SCR_017291) | software application, image analysis software, data processing software, software resource | Software package for densitometry measurements of electrophoresis gels by Silk Scientific Inc. Gel analysis software. Turns scanner into gel densitometer. Works with most image formats (TIFF, JPG, BMP, GIF, etc.) from any scanner, digital camera, or other image source. Can quantify Western blots, Agarose gels, PCR gels, TLC. | electrophoresis, gel, image, analysis, density, quantification, Silk Scientific Inc | Restricted | SCR_017291 | 2026-02-15 09:22:01 | 9 | |||||||||||
|
Stereo Investigator - Whole Slide Edition Resource Report Resource Website 1+ mentions |
Stereo Investigator - Whole Slide Edition (RRID:SCR_017667) | software application, image analysis software, data processing software, software resource | Software tool for quantitative analysis using stereology on whole slide images. Used to analyze whole slide image data. Includes number, length, area and volume analyses. | Quantitative, analysis, stereology, whole, slide, image, MBF Bioscience | Restricted | SCR_017667 | 2026-02-15 09:21:24 | 3 | |||||||||||
|
IncuCyte® Chemotaxis Software Resource Report Resource Website 10+ mentions |
IncuCyte® Chemotaxis Software (RRID:SCR_017316) | software application, image analysis software, data processing software, software resource | IncuCyte™ Chemotaxis Cell Migration Software by Essen Bioscience. Add on software module for IncuCyte ZOOM® live cell analysis system. To analyze label free and fluorescently labeled chemotactic cell migration images acquired using ClearView Chemotaxis Plate. | Add-on, module, IncuCyte ZOOM, live-cell, analysis, system, ClearView, Chemotaxis, Plate, Essen Bioscience, Sartorius | is provided by: Sartorius | Restricted | SCR_017316 | IncuCyte Chemotaxis Software | 2026-02-15 09:22:02 | 11 | |||||||||
|
Image Quant TL Resource Report Resource Website 100+ mentions |
Image Quant TL (RRID:SCR_018374) | software application, image analysis software, data processing software, software resource | Software tool for image analysis by Cytiva. Automated image analysis software for general purpose electrophoresis gel, blot, arrays and colony counting. | Image analysis, Cytiva, image, electrophoresis gel image, blot image, array, colony count image, analysis | SCR_018374 | , Image Quant TL array analysis, ImageQuant TL 8.2 | 2026-02-15 09:21:36 | 381 | |||||||||||
|
HALO Resource Report Resource Website 50+ mentions |
HALO (RRID:SCR_018350) | HALO | software application, image analysis software, data processing software, software resource | Software image analysis platform for quantitative tissue analysis in digital pathology by Indica Labs. Used for high-throughput, quantitative tissue analysis in oncology, neuroscience, metabolism, toxicology. | Image analysis platform, digital pathology, quantitative tissue analysis, image, analysis, tissue | is listed by: SoftCite | Restricted | SCR_018350 | Indica Labs HALO software | 2026-02-15 09:22:14 | 77 | ||||||||
|
Spyder Resource Report Resource Website 10+ mentions |
Spyder (RRID:SCR_017585) | software development tool, software application, software development environment, software resource | Interactive scientific development environment package for Python. Used for editing, analysis, debugging, and profiling functionality of comprehensive development tool with data exploration, interactive execution, deep inspection, and visualization. | Python, environment, editing, analysis, debugging, profiling, functionality, development, data, exploration, visualization | is related to: Pythonxy | Free, Available for download, Freely available | SCR_017585 | 2026-02-15 09:21:22 | 49 | ||||||||||
|
Coronavirus Immunotherapy Consortium Resource Report Resource Website 10+ mentions |
Coronavirus Immunotherapy Consortium (RRID:SCR_018258) | CoVIC | organization portal, portal, consortium, data or information resource, topical portal | Consortium to unite efforts and resources from experts across globe to advance effective, antibody based therapies against novel coronavirus, SARS-CoV-2. Represents multidisciplinary convergence of structural biology, virologists, immunologists, clinicians and bioinformaticians from academic and industry settings. Collects antibodies for testing as part of CoVICS. Contributed antibodies are blinded and will only be known as code name. Antibody contributors will be able to see performance of their own molecules and take part in analysis. Contributors retain ownership of their antibodies and may continue to publish on them using original antibody names. Goal is to determine relative in vitro potency and in vivo efficacy using centralized standardized assays to identify best individual mAbs and rational combinations of mAbs. Consortium will recommend ideal therapeutic molecules for human use to protect vulnerable populations from COVID-19 disease. CoVIC database (CoVIC-DB) will serve as clearinghouse for monoclonal antibodies against SARS-CoV-2. Database will catalog contributed antibodies in searchable resource and provide interactive analysis tools for comparisons among them. | COVID-19, antibody, antibody based therapy, coronavirus, SARS-CoV-2, antibody collection, analysis, potency in vitro, efficacy in vivo, standardized assay, identify mAb, therapeutic molecule, vulnerable population protect, database, data |
is related to: La Jolla Institute for Immunology is related to: Duke University; North Carolina; USA is related to: CoVIC-DB Database |
COVID-19 | Free, Freely available | SCR_018258 | 2026-02-15 09:21:34 | 11 | ||||||||
|
University Medical Center Hamburg-Eppendorf Bioinformatics Core Facility Resource Report Resource Website |
University Medical Center Hamburg-Eppendorf Bioinformatics Core Facility (RRID:SCR_017144) | UKE Bioinformatics Core | service resource, production service resource, core facility, access service resource, training service resource, analysis service resource | Core provides bioinformatics services for researchers at University Medical Center Hamburg Eppendorf and related institutions. Focusing on high throughput sequencing data. Services include data analysis, consulting, software development, and bioinformatical training. | bioinformatics, data, analysis, consulting, software, development, training | has parent organization: University Medical Center Hamburg-Eppendorf | Restricted | SCR_017144 | Bioinformatics Core, University Medical Center Hamburg Eppendorf Core, UKE | 2026-02-15 09:21:57 | 0 | ||||||||
|
ClusPro Resource Report Resource Website 500+ mentions |
ClusPro (RRID:SCR_018248) | web service, data access protocol, service resource, software resource | Web tool for protein-protein docking. Server provides removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering data, and location of heparin-binding sites. Six different energy functions can be used, depending on protein type.This protocol describes use of various options, construction of auxiliary restraints files, selection of energy parameters, and analysis of results. | Protein-protein docking, protein structure, energy function, energy parameter selection, analysis, data |
has parent organization: Boston University; Massachusetts; USA has parent organization: Stony Brook University; New York; USA |
NIGMS R35 GM118078; NIGMS R01 GM061867 |
PMID:28079879 | Free, Freely available | SCR_018248 | ClusPro 2.0 | 2026-02-15 09:22:12 | 858 | |||||||
|
Brain Gene Expression Analysis toolbox Resource Report Resource Website 1+ mentions |
Brain Gene Expression Analysis toolbox (RRID:SCR_017438) | software application, data processing software, data analysis software, software resource | Software Matlab toolbox for quantitative analysis of digitized brain wide gene expression data from Allen Atlas of adult mouse brain. | Quantitative, analysis, digitized, brain, gene, expression, data, Allen Atlas, adult, mouse, brain, BRAIN Initiative |
is recommended by: BRAIN Initiative is related to: MATLAB is related to: Allen Institute for Brain Science works with: Allen Mouse Brain Reference Atlas |
Free, Available for download, Freely available | SCR_017438 | , Brain, Gene, Expression, Analysis, toolbox | 2026-02-15 09:22:02 | 1 | |||||||||
|
REDCap Resource Report Resource Website 10000+ mentions |
REDCap (RRID:SCR_003445) | REDCap | web application, software resource | Web application that allows users to build and manage online surveys and databases. Using REDCap's stream-lined process for rapidly developing projects, you may create and design projects using 1) the online method from your web browser using the Online Designer; and/or 2) the offline method by constructing a "data dictionary" template file in Microsoft Excel, which can be later uploaded into REDCap. Both surveys and databases (or a mixture of the two) can be built using these methods. REDCap provides audit trails for tracking data manipulation and user activity, as well as automated export procedures for seamless data downloads to Excel, PDF, and common statistical packages (SPSS, SAS, Stata, R). Also included are a built-in project calendar, a scheduling module, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields. REDCap has a quick and easy software installation process, so that you can get REDCap running and fully functional in a matter of minutes. Several language translations have already been compiled for REDCap (e.g. Chinese, French, German, Portuguese), and it is anticipated that other languages will be available in full versions of REDCap soon. The REDCap Shared Library is a repository for REDCap data collection instruments and forms that can be downloaded and used by researchers at REDCap partner institutions. | online survey, survey, database, translational research, informatics, workflow, clinical research, clinical, metadata, biomedical, online form, data capture, management, analysis, data sharing, data collection, data standard, best practice, data collection instrument, electronic data capture |
is listed by: Biositemaps is listed by: SoftCite is related to: Clinical and Translational Science Awards Consortium has parent organization: Vanderbilt University; Tennessee; USA works with: redcap-completion works with: aux-file-upload |
NIH ; UL1 RR029882 ; UL1 TR000062 ; UL1 RR026314 ; UL1 TR000077 ; UL1 RR024975 ; UL1 TR000445 ; G12 RR003051 ; G12 MD007600 ; UL1 RR024150 ; UL1 TR000135 ; R24 HD042849 ; UL1 RR024989 ; UL1 TR000439 |
PMID:23149159 PMID:18929686 |
Software is available at no cost for REDCap Consortium Partners. If not in the consortium, See the Become a Partner page to find more information about joining our group. | nif-0000-33254 | SCR_003445 | RED Cap, Research Electronic Data Capture, The REDCap Consortium | 2026-02-15 09:18:33 | 20615 | |||||
|
CoVIC-DB Database Resource Report Resource Website 1+ mentions |
CoVIC-DB Database (RRID:SCR_018339) | CoVIC-DB | database, data or information resource, catalog | Serves as clearinghouse for monoclonal antibodies against SARS-CoV-2. Database will catalog contributed antibodies in searchable resource and provide interactive analysis tools for comparisons among them. Most potent antibodies will guide development of vaccines to stop current outbreak and protect against future pandemics. | SARS-CoV-2, monoclonal antibodies, antibody, antibody contribution, analysis, antibody based immunotherapy, COVID-19, COVID-19 data | is related to: Coronavirus Immunotherapy Consortium | COVID-19 | Bill and Melinda Gates Foundation ; Wellcome and MasterCard Impact Fund |
Free, Freely available | SCR_018339 | Coronavirus Immunotherapy Consortium Database | 2026-02-15 09:22:20 | 2 | ||||||
|
Shiny Resource Report Resource Website 500+ mentions |
Shiny (RRID:SCR_001626) | software toolkit, software resource | Open source R package that provides web framework for building web applications using R. Used to create interactive web apps in native R, without needing to use HTML, CSS, or JavaScript. | R, analysis, interactive, web, application |
uses: shinythemes is used by: ClustVis is used by: shinyGEO is used by: PlotsOfData is used by: shinyCircoss is used by: AlloMate is used by: VenomView is used by: bulkAnalyseR is related to: rSPRITE is related to: EHRtemporalVariability is related to: robvis is related to: Omics Data Paper Generator is related to: Mitochondrial Neuron Ubiquitin is related to: chevreul is related to: Click-qPCR is related to: EMImR has parent organization: RStudio works with: BoxPlotR works with: shinyhelper works with: ShinyCell |
PMID:34642739 PMID:26225240 |
Free, Available for download, Freely available | nlx_153894 | SCR_001626 | 2026-02-15 09:18:08 | 522 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on NIF then you can log in from here to get additional features in NIF such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into NIF you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
