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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Dissect Resource Report Resource Website |
Dissect (RRID:SCR_000058) | Dissect | alignment software, data processing software, image analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions. | Structural events containing transcripts, transcriptome-to-genome alignment, identify and characterize transcriptomic events, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Simon Fraser University; British Columbia; Canada |
PMID:22689759 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01346, biotools:dissect | https://bio.tools/dissect | SCR_000058 | Dissect: DIScovery of Structural Events Containing Transcripts, DIScovery of Structural Events Containing Transcripts | 2026-09-19 12:55:03 | 0 | |||||
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Olympus: IX71 Microscope Resource Report Resource Website 1+ mentions |
Olympus: IX71 Microscope (RRID:SCR_022185) | instrument resource | Research inverted system microscope. Olympus IX2 inverted microscope combined with UIS2 optical system. Used for live cell experiments. | Olympus, live cell imaging, inverted microscope, instrument, equipment, USEDit | is listed by: USEDit | Restricted | Model_Number_IX71 | SCR_022185 | Olympus IX71 | 2026-09-19 12:55:03 | 6 | ||||||||
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Neurolucida Resource Report Resource Website 1000+ mentions |
Neurolucida (RRID:SCR_001775) | data analysis software, data processing software, data visualization software, software application, software resource | Neurolucida is advanced scientific software for brain mapping, neuron reconstruction, anatomical mapping, and morphometry. Since its debut more than 20 years ago, Neurolucida has continued to evolve and has become the worldwide gold-standard for neuron reconstruction and 3D mapping. Neurolucida has the flexibility to handle data in many formats: using live images from digital or video cameras; stored image sets from confocal microscopes, electron microscopes, and scanning tomographic sources, or through the microscope oculars using the patented LucividTM. Neurolucida controls a motorized XYZ stage for integrated navigation through tissue sections, allowing for sophisticated analysis from many fields-of-view. Neurolucidas Serial Section Manager integrates unlimited sections into a single data file, maintaining each section in aligned 3D space for full quantitative analysis. Neurolucidas neuron tracing capabilities include 3D measurement and reconstruction of branching processes. Neurolucida also features sophisticated tools for mapping delineate and map anatomical regions for detailed morphometric analyses. Neurolucida uses advanced computer-controlled microscopy techniques to obtain accurate results and speed your work. Plug-in modules are available for confocal and MRI analysis, 3D solid modeling, and virtual slide creation. The user-friendly interface gives you rapid results, allowing you to acquire data and capture the full 3D extent of neurons and brain regions. You can reconstruct neurons or create 3D serial reconstructions directly from slides or acquired images, and Neurolucida offers full microscope control for brightfield, fluorescent, and confocal microscopes. Its added compatibility with 64-bit Microsoft Vista enables reconstructions with even larger images, image stacks, and virtual slides. Adding the Solid Modeling Module allows you to rotate and view your reconstructions in real time. Neurolucida is available in two separate versions Standard and Workstation. The Standard version enables control of microscope hardware, whereas the Workstation version is used for offline analysis away from the microscope. Neurolucida provides quantitative analysis with results presented in graphical or spreadsheet format exportable to Microsoft Excel. Overall, features include: - Tracing Neurons - Anatomical Mapping - Image Processing and Analysis Features - Editing - Morphometric Analysis - Hardware Integration - Cell Analysis - Visualization Features Sponsors: Neurolucida is supported by MBF Bioscience. | electron microscope, fluorescent, 3d mapping, anatomical, brian, brightfield, camera, confocal, digital, hardware, mapping, microscope, morphometry, neuron, reconstruction, scanning tomographic, software, tissue, virtual, video, image | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:2224829 | Restricted | nif-0000-10294 | http://www.nitrc.org/projects/neurolucida | http://www.mbfbioscience.com/neurolucida/neurolucida | SCR_001775 | MBF Neurolucida | 2026-09-19 12:55:04 | 3396 | |||||
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Zeiss: PALM MicroBeam PALM Resource Report Resource Website 1+ mentions |
Zeiss: PALM MicroBeam PALM (RRID:SCR_020929) | instrument resource | PALM MicroBeam scanning electron microscope for isolating uncontaminated source material simple. | Zeiss, Microlaser Dissection Microscope, Microdissection Microscope, laser microdissection device (aka optical tweezer), Instrument Equipment, USEDit | Commercially available | Model_Number_MicroBeam | SCR_020929 | 2026-09-19 12:54:46 | 4 | ||||||||||
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Zeiss: Axio Scan.Z1 Slide Scanner Resource Report Resource Website 10+ mentions |
Zeiss: Axio Scan.Z1 Slide Scanner (RRID:SCR_020927) | instrument resource | Used to digitize specimens with the Axio Scan.Z1 slide scanner to create high-quality virtual slides. Axio Scan.Z1 tackles the most demanding virtual microscopy research tasks as easily as it handles your routine work. The software module ZEN slidescan is designed specifically for the workflow of capturing virtual slides, while ZEN image analysis tools prepare your data accurately. Organize your virtual slides with ZEN browser, the web-based database, then view your data from any location using any operating system , or share virtual microscopy images online with colleagues and organize your projects, even when you are on the go. | Zeiss, Slide Scanner, Instrument Equipment, USEDit | is related to: Hitachi: 16-bit 3-CCD color camera HV-F203GV / HV-F203SCL | Commercially available | Model_Number_Axioscan | SCR_020927 | 2026-09-19 12:54:46 | 25 | |||||||||
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Zeiss: 2000C Stereomicroscope Resource Report Resource Website 1+ mentions |
Zeiss: 2000C Stereomicroscope (RRID:SCR_020924) | instrument resource | Optical stereomicroscope with 7.7:1 zoom range (pancratic system 0.65x to 5.0x) zooms in continuously or with click stop. It has an object field size of 35mm, with an 0.3x attachment lens system permitting object fields of up to 118mm to be viewed. | Zeiss, Stereomicroscope, Instrument Equipment, USEDit | Commercially available | Model_Number_Zeiss_2000C | SCR_020924 | 2026-09-19 12:54:46 | 1 | ||||||||||
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Wyatt: Optiab Refractometer Resource Report Resource Website |
Wyatt: Optiab Refractometer (RRID:SCR_020897) | instrument resource | Refractometer based on semiconductor photodiode technology and proprietary computer algorithms. Can be used for standard chromatographic applications and measurements such as high concentrations, determination of sample refractive increments dn dc and solvent refractive index. | Wyatt, Refractometer Equipment, USEDit, | Commercially available | Model_Number_Optiab | SCR_020897 | 2026-09-19 12:54:45 | 0 | ||||||||||
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Zeiss: Supra 25 Field Emission Scanning Electron Microscope Resource Report Resource Website 1+ mentions |
Zeiss: Supra 25 Field Emission Scanning Electron Microscope (RRID:SCR_020930) | instrument resource | Field scanning electron microscope with analytical specimen chamber with choice of optional detectors and accessories. It has 5-axes motorised cartesian stage can handle multiple smaller specimens simultaneously. It can image bulky or irregular shaped specimens. | Zeiss, Field Emission Scanning Electron Microscope, Instrument Equipment, USEDit | Commercially available | Model_Number_Supra | SCR_020930 | 2026-09-19 12:54:46 | 1 | ||||||||||
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Wyatt: DynaPro NanoStar Dynamic Light Scattering Detector Resource Report Resource Website |
Wyatt: DynaPro NanoStar Dynamic Light Scattering Detector (RRID:SCR_020898) | instrument resource | Dynamic Light Scattering device that may be utilized to measure not just size, size distributions, particle concentration and weight average molar mass, but also solution properties relevant to sample stability.cuvette-based DLS instrument used for the analysis of proteins, promiscuous inhibitors, micelles, quantum dots, liposomes, metallic nanoparticles and more. | Wyatt, Dynamic Light Scattering Equipment, USEDit, | Commercially available | Model_Number_DynaPro_NanoStar | SCR_020898 | 2026-09-19 12:54:45 | 0 | ||||||||||
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Wyatt: Mobius Dynamic Light Scatterer Resource Report Resource Website 1+ mentions |
Wyatt: Mobius Dynamic Light Scatterer (RRID:SCR_020894) | instrument resource | Dynamic Light Scattering device DLS measures electrophoretic light scattering ELS and DLS simultaneously to determine zeta potential or molecular charge, automated by autosampler or manually, under wide range of solvents. | Wyatt, Dynamic Light Scattering Equipment, USEDit, | Commercially available | Model_Number_Mobius | SCR_020894 | 2026-09-19 12:54:45 | 1 | ||||||||||
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fgsea Resource Report Resource Website 100+ mentions |
fgsea (RRID:SCR_020938) | data analysis software, data processing software, software application, software resource | Software R package for fast preranked gene set enrichment analysis. Allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. | Gene set enrichment analysis, preranked gene set, multiple hypothesis correction, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian |
DOI:10.1101/060012 | Free, Available for download, Freely available | biotools:fgsea | https://github.com/ctlab/fgsea/, https://bio.tools/fgsea | SCR_020938 | fast gene set enrichment analysis, Fast Gene Set Enrichment Analysis, FGSEA | 2026-09-19 12:54:46 | 237 | ||||||
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Common Metabolic Diseases Knowledge Portal Resource Report Resource Website 50+ mentions |
Common Metabolic Diseases Knowledge Portal (RRID:SCR_020937) | CMDKP | data or information resource, data repository, database, disease-related portal, portal, service resource, storage service resource, topical portal | Portal enables browsing, searching, and analysis of human genetic information linked to common metabolic diseases and traits, while protecting integrity and confidentiality of underlying data. Aggregates and analyzes genetic association results, epigenomic annotations, and results of computational prediction methods to provide data, visualizations, and tools in open access portal. | Analyzes genetic association results, aggregates genetic association results, epigenomic annotations, genetic data, epigenomic data |
is listed by: NIDDK Information Network (dkNET) is related to: Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) is related to: Type 1 Diabetes Knowledge Portal is related to: Human Genetics Amplifier is related to: Common Metabolic Disease Genome Atlas |
Metabolic diseases, Type 1 diabetes, Type 2 diabetes, Cardiovascular disease, Cerebrovascular disease, Sleep disorder, Circadian disorder, Diabetes | Accelerating Medicines Partnership | Free, Available for download, Freely available | SCR_020937 | 2026-09-19 12:54:46 | 66 | |||||||
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ez Resource Report Resource Website 1+ mentions |
ez (RRID:SCR_020990) | data analysis software, data processing software, data visualization software, software application, software resource | Software statistical analysis R package used for easy analysis and visualization of factorial experiments. Provides interface to common analysis techniques, including analysis of variance and mixed effects modeling. Visualization functions also include design visualization for pre-analysis data auditing, and correlation matrix visualization. Package includes functions for non-parametric analysis, including permutation tests and bootstrap resampling. | Factorial experiments analysis, factorial experiments, repeated measures, correlation matrix visualization, bootstrap function, variance analysis, mixed effects modeling analysis | is listed by: CRAN | Free, Available for download, Freely available | https://github.com/mike-lawrence/ez | SCR_020990 | 2026-09-19 12:54:47 | 8 | |||||||||
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Beckman Coulter: UniCel DxI 800 Access Immunoassay System Resource Report Resource Website |
Beckman Coulter: UniCel DxI 800 Access Immunoassay System (RRID:SCR_020867) | instrument resource | Immunoassay system analyzer by Beckman Coulter with standardized test menus, assay protocols, instrument processes and reference ranges. Sample types include serum, plasma, urine, amniotic fluid, and whole blood. | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_020867.pdf | Model_Number_DxI 800 Access | SCR_020867 | 2026-09-19 12:54:45 | 0 | ||||||||||
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Wyatt: microViscostar Viscometer Resource Report Resource Website |
Wyatt: microViscostar Viscometer (RRID:SCR_020900) | instrument resource | microViscoStar incorporates multiple novel technologies to provide highest sensitivity, stability and solvent compatibility of any available viscometer for UHPLC. Its ease of use and serviceability make it companion for Wyatt's microDAWN light scattering and microOptilab refractive index detectors for UHPLC. | Wyatt, Viscometer Equipment, USEDit, | Commercially available | Model_Number_microViscostar | SCR_020900 | 2026-09-19 12:54:45 | 0 | ||||||||||
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Thermo Fisher: VaLet Robot; Lab Automation Resource Report Resource Website |
Thermo Fisher: VaLet Robot; Lab Automation (RRID:SCR_020865) | instrument resource | Lab automated tool that automates applications from simple instrument loading to more complex, integrated workflows (with Plate Storage Only) | ThermoFisher, Lab Automation, Instrument, Resource Equipment, Equipment, USEDit, | Commercially available | Model_Number_VaLet Robot | SCR_020865 | 2026-09-19 12:54:44 | 0 | ||||||||||
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Thermo Fisher: Ultra-low Temp G50 AC200 208-230 VOLT 60 HZ; Refrigerated/Heated Bath Circulator Resource Report Resource Website |
Thermo Fisher: Ultra-low Temp G50 AC200 208-230 VOLT 60 HZ; Refrigerated/Heated Bath Circulator (RRID:SCR_020862) | instrument resource | Refirgerated/heated bath circulator that delivers high heating and cooling capacities for rapid heat-up and cool-down times and has electrical requirements of 200/230 V 60 Hz 200 V 50 Hz | ThermoFisher, Refrigerated/Heated Bath Circulator, Instrument, Resource Equipment, Equipment, USEDit, | Commercially available | Model_Number_Ultra-low Temp G50 AC200 208-230 VOLT 60 HZ | SCR_020862 | 2026-09-19 12:54:44 | 0 | ||||||||||
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Turner BioSystems: TBS-380 Fluorometer Resource Report Resource Website |
Turner BioSystems: TBS-380 Fluorometer (RRID:SCR_020863) | instrument resource | TBS-380 Mini-Fluorometer is a dual-channel fluorometer designed for quick, easy, and accurate fluorescence measurements. When properly calibrated with a standard of known concentration, the TBS380 displays the actual concentration of the measured compound. The new Minicell adaptor design enables the user to measure compounds at a low concentration with a low assay volume (e.g. dsDNA at 1ng/mL using PicoGreen, and RNA at 1 ng/mL using RiboGreen). | Turner, Mini Fluorometer, Fluorometer, Instrument Equipment, USEDit | Commercially available | Model_Number_TBS-380 | SCR_020863 | 2026-09-19 12:54:44 | 0 | ||||||||||
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NPSV Resource Report Resource Website 1+ mentions |
NPSV (RRID:SCR_020984) | simulation software, software application, software resource | Software Python tool for standalone genotyping of deletion and insertion structural variants in short read whole genome sequencing data. Implements machine learning based approach for SV genotyping that employs NGS simulation to model the combined effects of the genomic region, sequencer and alignment pipeline. | WGS data, short read, whole genome sequencing data, standalone genotyping, insertion structural variants, deletion structural variants, structural variants, SV genotyping, NGS simulation | Free, Available for download, Freely available | SCR_020984 | Non-Parametric Structural Variant Genotyper, Non-Parametric Structural Variant genotyper | 2026-09-19 12:54:47 | 1 | ||||||||||
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SnapATAC Resource Report Resource Website 10+ mentions |
SnapATAC (RRID:SCR_020981) | data analysis software, data processing software, software application, software resource, software toolkit | Software package for analyzing scATAC-seq datasets.Used to dissects cellular heterogeneity in unbiased manner and map trajectories of cellular states. Can process data from up to million cells. Incorporates existing tools into comprehensive package for analyzing single cell ATAC-seq dataset. | scATAC-seq datasets analysis, dissects cellular heterogeneity, cellular states, map trajectories | NCI K99 CA252020; NIMH U19 MH114831; UCSD School of Medicine |
PMID:33637727 | Free, Available for download, Freely available | https://github.com/r3fang/SnapATAC | SCR_020981 | Single Nucleus Analysis Pipeline for ATAC-seq | 2026-09-19 12:54:47 | 23 |
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