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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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SMIA-CUKIE Resource Report Resource Website 1+ mentions |
SMIA-CUKIE (RRID:SCR_014795) | SMIA | data processing software, image analysis software, software application, software resource | Software used to analyze and quantify images stained with multiple fluorophores in vitro or in vivo. It can output both image and value outputs. | immunofluorescence, image analysis software, fluorophore, image output, value output, bulk process, bulk analyze | DOI:10.5772/21699 | Requires Python 2.7 | SCR_014795 | Simultaneous Multichannel Immunofluorescence Digital Imaging Analyzer, Simultaneous Multichannel Immunofluorescence Analysis | 2026-08-21 12:40:29 | 7 | ||||||||
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La Jolla Institute for Immunology Resource Report Resource Website |
La Jolla Institute for Immunology (RRID:SCR_014837) | LJI, | data or information resource, organization portal, portal | Non profit collaborative research organization located in La Jolla, California, UCSD Research Park. Institute researches immunology and immune system diseases to pinpoint specific genes involved, accelerate progress toward development of new treatments and vaccines to prevent and cure type 1 diabetes, cancer and infectious disease. Developer of Immune Epitope Database (IEDB). Provides core facilities with access to equipment, technologies, training and expertise to support innovative research. | Immunology, vaccine, infectious disease, immune system, Immune Epitope Database, sequencing, high throughput, bioinformatics |
is related to: Coronavirus Immunotherapy Consortium is parent organization of: Database of Immune Cell Epigenomes is parent organization of: La Jolla Institute for Immunology Next Generation Sequencing Core Facility is organization facet of: Immune Epitope Database and Analysis Resource (IEDB) |
Type 1 diabetes, Diabetes, Allergy, Alzheimer's disease, Asthma, Atherosclerosis, Atopic dermatitis, Eczema, Autoimmune disease, Cancer, COVID-19, Dengue, Ebola, Fibrosis, Food allergies, HIV, Imflammatory bowel disease, Japanese encephalitis, Lassa fever, Lung cancer, Multiple sclerosis, Nipah, Parkinson's disease, Pneumonia | SCR_014837 | LJI, la jolla, Institute for immunology, La Jolla Institute for Allergy and Immunology | 2026-08-21 12:40:29 | 0 | ||||||||
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ShapePopulationViewer Resource Report Resource Website 1+ mentions |
ShapePopulationViewer (RRID:SCR_014167) | data processing software, image analysis software, software application, software resource | Software that allows users to dynamically interact with multiple surfaces simultaneously. It is very useful for visualisation and comparison of 3D surfaces by also displaying their scalars or vectors attributes stored in the points, and allowing the user to simply modify the colormap. ShapePopulationViewer is available as an extension of 3D Slicer. | 3d surface, colormap, vector, interaction |
is used by: 3D Slicer is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
Available to the research community | SCR_014167 | 2026-08-21 12:40:16 | 3 | ||||||||||
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John Hopkins University, In-Vivo Cellular Molecular Imaging Center Resource Report Resource Website |
John Hopkins University, In-Vivo Cellular Molecular Imaging Center (RRID:SCR_013198) | data or information resource, job resource, organization portal, portal | The vision of the JHU ICMIC is to combine state-of-the-art imaging capabilities with powerful molecular biology techniques to define strategies with intent to cure. It has drawn upon its human resources at JHU to create a center consisting of a multidisciplinary group of premier individuals with diverse skills focused on translating molecular capabilities into imaging possibilities with the single purpose of understanding and curing cancer. Nearly all of the investigators participating in this ICMIC have interactive collaborative projects with one or more of the other investigators. The synergism generated by the collective skills of this unique group of individuals will lead to significant advances in the understanding of cancer and its treatment. The JHU ICMIC structure consists of four interactive and closely related research components focused on hypoxia, HIF-1, and exploiting the hypoxia response element to target cancer cells through choline kinase inhibition. These research components are anchored by the participation of world renowned expertise in HIF-1. The research components utilize MR, PET and Optical Imaging technology to understand cancer vascularization, invasion and metastasis, to achieve effective cancer therapy. The center has selected developmental projects which are highly relevant to the goals of the ICMIC and interactive with the research components. Five resources devoted to adminstration, molecular biology, imaging, probes, and translational application provide the infrastructure to support the research activities of the ICMIC. Research Components in the JHU ICMIC: - Combining Anti-angiogenic therapy with siRNA targeting of choline kinase. - Imaging the Role of HIF-1 in Breast Cancer Progression - Imaging and Targeting Hypoxia in Solid Tumors - Molecular and Functional Imaging of the HER-2/neu Receptor The following are developmental projects currently taking place in ICMIC 1. Receptor imaging using nonparamagnetic MRI contrast agents (2003) 2. New imaging agents for prostate cancer (2003) 3. Non-invasive monitoring of therapeutic effect of siRNA-mediated radiation sensitization in human prostate cancer xenografts (2003) 4. Imaging of the endothelin receptor in cancer (2003) 5. Imaging studies of c-myc regulation of tumor metabolism (2003) 6. Imaging studies of anti-tumorigenic effects of anti-oxidants in vivo (2005) 7. Molecular Imaging with Magnetic Resonance Microsystems (2005) 8. Endogenous angiogenesis inhibitors (2005) 9. MR imaging and spectroscopy in detection and localization of prostate cancer: a prospective trial in patients undergoing cystoprostatectomy and radical prostatectomy. (2005) 10. A versatile visualization system for the analysis of multi-modality and multidimensional cancer imaging (2007) 11. Non-invasive imaging of CXCR4 expression in breast cancer (2007) | endogenous, endothelin, anti-angiogenic, anti-oxidant, anti-tumorigenic, biology, breast, cancer, cell, choline kinase, c-mys, cystoprostatectomy, hif-1, human, hypoxia, inhibition, metabolism, microsystem, molecular, mr, mri, optical imaging, pet, prostate, prostatectomy, radial, receptor, sirna, spectroscopy, technique, technology, tumor, vascularization, xenograft | has parent organization: Johns Hopkins University; Maryland; USA | nif-0000-10273 | SCR_013198 | JHU ICMIC | 2026-08-21 12:40:06 | 0 | |||||||||
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CombineZP Resource Report Resource Website 100+ mentions |
CombineZP (RRID:SCR_014567) | data processing software, image analysis software, software application, software resource | A software used to process stacks of digital images. All of the resulting images are processed to have the same dimensions and then are consolidated into a single image. | digital image, dimension, process stack, digital, dimension modification, image processing, image consolidation | Open Source | SCR_014567 | 2026-08-21 12:40:23 | 137 | |||||||||||
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NIST Mass Spectrometry Data Center Resource Report Resource Website 100+ mentions |
NIST Mass Spectrometry Data Center (RRID:SCR_014680) | data or information resource, organization portal, portal | A data center that develops evaluated mass spectral libraries and provides related software tools that assist compound identification by providing reference mass spectra for GC/MS (by electron ionization) and LC-MS/MS (by tandem mass spectrometry). It also provides gas phase retention indices for GC. Resources include the mass spectral library, the peptide library, and a standard refernece material guide. | metabolomics, metabolomics tool, peptide, mass spectrometry, compound identification, data center, portal | is listed by: Metabolomics Workbench | https://www.nist.gov/mml/biomolecular-measurement/mass-spectrometry-data-center | SCR_014680 | Mass Spectrometry Data Center, NIST MS Data Center, MS Data Center | 2026-08-21 12:40:25 | 108 | |||||||||
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BioParadigms Resource Report Resource Website 10+ mentions |
BioParadigms (RRID:SCR_015494) | data or information resource, portal | Web-based transporter resource that provides access to the TransCure interdisciplinary research network, the Genomic Transporter Database, and the Biomedical Transporter Conferences page. | membrane transporter, membrane transporter portal | has parent organization: University of Bern; Bern; Switzerland | SCR_015494 | Bioparadigms | 2026-08-21 12:40:51 | 23 | ||||||||||
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btrack Resource Report Resource Website 1+ mentions |
btrack (RRID:SCR_013591) | data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. It analyzes and graphs time-lapse imaging data as acquired by a Bio-Rad confocal microscope, for experiments using nonratiometric fluorescent indicator dyes. Btrack can accommodate changes in the positions of imaged cells/tissue regions and can be used for analyzing an unlimited number of areas (cells/tissue regions) in an imaged field. | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00276 | http://ncmir.ucsd.edu/Software/btrack.htm | SCR_013591 | 2026-08-21 12:39:55 | 5 | ||||||||||
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TiltPicker Resource Report Resource Website |
TiltPicker (RRID:SCR_016674) | data processing software, software application, software resource | Software tool to facilitate particle selection in single particle electron microscopy. An interactive graphical interface application designed to streamline the selection of particle pairs from tilted-pair datasets. Designed to work with existing software tools for image processing. | particle, selection, single, electron, microscopy, interactive, graphical, interface, tilted, pair, dataset, image, processing | is listed by: OMICtools | NCRR RR17573; NCRR RR23093 |
PMID:19374019 | Free, Available for download, Freely available | http://emg.nysbc.org/redmine/projects/appion/wiki/Appion_Home | SCR_016674 | 2026-08-21 12:40:59 | 0 | |||||||
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Apache Spark Resource Report Resource Website 10+ mentions |
Apache Spark (RRID:SCR_016557) | data analytics software, data processing software, software application, software resource | Software tool as a unified analytics engine for large scale data processing. An open source distributed general purpose cluster computing framework. | unified, analytics, engine, large, scale, data, processing |
is related to: VariantSpark is related to: spark-xml is related to: spark-xml-utils is related to: SparkFHE has parent organization: University of California at Berkeley; Berkeley; USA |
DOI:10.1145/2934664 | Free, Available for download, Freely available | SCR_016557 | 2026-08-21 12:41:06 | 43 | |||||||||
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docker4seq Resource Report Resource Website 1+ mentions |
docker4seq (RRID:SCR_017006) | data processing software, software application, software resource | Software R package to execute next generation sequencing computing applications, e.g. reads mapping and counting, wrapped in docker containers. | next, generation, sequencing, computing, application, read, mapping, count, docker, container, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: University of Turin;Turin;Italy |
Free, Available for download, Freely available | biotools:docker4seq | https://kendomaniac.github.io/docker4seq/index.html, https://bio.tools/docker4seq | SCR_017006 | 2026-08-21 12:41:01 | 6 | ||||||||
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AfterQC Resource Report Resource Website 10+ mentions |
AfterQC (RRID:SCR_016390) | data processing software, software application, software resource | Software that performs automatic filtering, trimming, error removing, and quality control for fastq data. | fastq, qc, editing, filtering, trimming, dna, rna, seq, sequence, sequencing, poly, pair-end, python | PMID:28361673 | Free, Available for download | SCR_016390 | After QC | 2026-08-21 12:40:47 | 15 | |||||||||
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Prophet Resource Report Resource Website 1+ mentions |
Prophet (RRID:SCR_017083) | data processing software, software application, software resource | Open source software package for producing forecasts for time series data that has multiple seasonality with linear or non linear growth. Implemented in R or Phyton. | data, science, forecast, time, series, multiple, seasonality, linear, non linear, growth, analysis | is listed by: CRAN | DOI:10.7287/peerj.preprints.3190v2 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/prophet/, https://pypi.org/project/fbprophet/ | SCR_017083 | Prophet Automatic Forecasting Procedure | 2026-08-21 12:41:15 | 3 | |||||||
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Data Biosphere Resource Report Resource Website 1+ mentions |
Data Biosphere (RRID:SCR_016154) | data or information resource, portal, project portal | Project whose goal is to provide Data Environments to the biomedical community. The Data Biosphere works to create a user experience around key modular components — each having discrete capabilities and clear rules of interaction, and each served by multiple alternative implementations. | data, environment, biomedicine, standard, module, community | Freely available | https://github.com/databiosphere/ | SCR_016154 | 2026-08-21 12:40:38 | 1 | ||||||||||
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WinRHIZO Resource Report Resource Website 10+ mentions |
WinRHIZO (RRID:SCR_017120) | data processing software, image analysis software, software application, software resource | Software toolbox for image analysis by Regent Instruments Inc. Used for root measurement in different forms like morphology, topology, architecture and color analyses. Automatically or interactively analyses washed roots. | image, analysis, root, measurement, plant, morphology, topology, color, Regent Instruments Inc. | Available for purchase | SCR_017120 | 2026-08-21 12:41:07 | 16 | |||||||||||
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AIMLESS Resource Report Resource Website 500+ mentions |
AIMLESS (RRID:SCR_015747) | data processing software, software application, software resource | Data processing software for x-ray diffraction data. AIMLESS scales together multiple observations of reflections, and merges multiple observations into an average intensity. | xray, differentiation, observation, reflection, scaling, scale | has parent organization: MRC Laboratory of Molecular Biology | PMID:23793146 | Free, Available for download | SCR_015747 | 2026-08-21 12:40:26 | 571 | |||||||||
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autoPROC Resource Report Resource Website 100+ mentions |
autoPROC (RRID:SCR_015748) | data processing software, software application, software resource, software toolkit | Data processing software for X-ray diffraction data. autoPROC is a set of tools and programs to automate steps involved in data processing, such as image analysis, integration, indexing, and determination. | xray, diffraction, data processing, crystallography | European Commission LSHG-CT-2003-503420 | PMID:21460447 | Free for academic use, Available for download | SCR_015748 | 2026-08-21 12:40:47 | 330 | |||||||||
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Science and Technology Facilities Council Resource Report Resource Website 1+ mentions |
Science and Technology Facilities Council (RRID:SCR_016713) | STFS | institution | One of nine Councils within United Kingdom Research and Innovation, an organisation that brings together the UK’s Research Councils, Innovate UK and Research England. Works in partnership with universities, research organisations, businesses, charities, and government to create the environment for research and innovation. | England, research, council, innovation, partnership, United Kingdom |
is parent organization of: CCP4 is parent organization of: CCP4 is parent organization of: Science and Technology Facilities Council Central Laser Facility OCTOPUS Microscopy Core Facility |
, GRID grid.14467.30, Wikidata Q1669366, Crossref Funder ID 501100000271, ISNI 0000 0001 2237 5485 | https://ror.org/057g20z61 | SCR_016713 | Science and Technology Facilities Council, STFC | 2026-08-21 12:40:55 | 2 | |||||||
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Stanford Center for Reproducible Neuroscience Resource Report Resource Website |
Stanford Center for Reproducible Neuroscience (RRID:SCR_016684) | data or information resource, organization portal, portal | Center with the goal of harnessing high-performance computing to make neuroscience research more reliable.Provide researchers with tools to analyze their data in ways that focus on the reproducibility of the results through the OpenfMRI ( OpenNeuro ) and Neurovault projects. | computing, tools, neuroscience, data, analyze, reproducibility, fMRI, OpenfMRI, OpenNeuro, Neurovault |
has parent organization: Stanford University; Stanford; California is parent organization of: OpenNeuro is parent organization of: OpenNeuro is parent organization of: NeuroVault |
SCR_016684 | 2026-08-21 12:40:55 | 0 | |||||||||||
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atacr Resource Report Resource Website 1+ mentions |
atacr (RRID:SCR_016286) | data processing software, software application, software resource | Software that analyzes count data from RNA-capture-seq and ATAC-capture-seq experiments. Using BioConductor RangedSummarizedExperiment objects, atacr implements a set of helper functions and quality control plots specific to the analysis of counts of reads in windows across genomes. | normalization, bootstrap, bayes, factor, test, reference, design, seq, count, capture, data | Gatsby Charitable Foundation ; Marie Curie 656243 |
Free, Available for download, Tutorial available | SCR_016286 | 2026-08-21 12:41:03 | 2 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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