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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.
https://www.gehealthcare.com/products/advanced-visualization/all-applications/volume-viewer
Software tool to provide data 3D visualization and processing. Used for reading and comparing CT, MR, 3D X-ray, PET, and PET/CT datasets.
Proper citation: GE Volume Viewer (RRID:SCR_023417) Copy
One of the largest interdisciplinary research centers in Europe for inspiring science exchange from all over the world. It is member of the Helmholtz Association.
Proper citation: Research Center Jülich; Jülich; Germany (RRID:SCR_023416) Copy
https://broadinstitute.github.io/warp/docs/Pipelines/SlideSeq_Pipeline/README/
Software pipeline developed in collaboration with BRAIN Initiative Cell Census Network and BRAIN Initiative Cell Atlas Network. Supports processing of spatial transcriptomic data generated with Slide-seq commercialized as Curio Seeker assay.
Proper citation: Slide-seq Pipeline (RRID:SCR_023379) Copy
https://github.com/CaT-zTools/CaT-z_Software
Software tool for 3D tracking and automatic classification of rodent behavior. Used for acquisition, annotation, and automatic behavioral profile characterization of laboratory rodents' RGB-D videos. Utilizes video segmentation, tracking of body parts, and automated classification of behaviors through machine learning and computer vision methods. Setup uses low costing RGB-D cameras for tracking behaviors in various environments. Software includes GUI interfaces for video acquisition, annotation, and processing of behavioral data. Software is capable of automated behavior detection with only 30 minutes of annotated video.
Proper citation: CaT-z (RRID:SCR_023399) Copy
https://lookerstudio.google.com/
Former name Google Data Studio, is online tool for converting data into customizable informative reports and dashboards introduced by Google on March 15, 2016 as part of enterprise Google Analytics 360 suite. Online service for graphic data visualization.
Proper citation: Google Looker Studio (RRID:SCR_023549) Copy
https://github.com/Nanostring-Biostats/GeomxTools/
Software package contains tools for analyzing data from NanoString GeoMx Digital Spatial Profiler. Provides functions to read, quality control and normalize starting from Nanostring DCC and PKC files generated from NanoString GeoMx DSP. Contains definition of NanoStringGeoMxSet class which inherits from Biobase’s ExpressionSet class and NanoStringRCCSet class.
Proper citation: NanoString GeoMx Tools (RRID:SCR_023424) Copy
https://choishingwan.gitlab.io/EraSOR/
Software Python tool for removing bias introduced from having overlapped samples between base GWAS data and target genotype data for Polygenic Risk Score analyses. Used for adjusting inflation in PRS prediction and association statistics in presence of sample overlap or close relatedness between GWAS and target samples.
Proper citation: EraSOR (RRID:SCR_023544) Copy
https://non-igg-ab.creative-biolabs.com/non-igg-antibody-application-for-clinical-diagnosis.htm
Provides high quality custom non-IgG antibody services.
Proper citation: Creative Biolabs Non-IgG Antibody Isotypes Services (RRID:SCR_023640) Copy
NanoZoomer series is family of whole slide scanners that rapidly scan glass slides to convert them to digital data. NanoZoomer S360 is ideal for use in hospitals and clinical laboratories.
Proper citation: Hamamatsu: NanoZoomer S360 Digital slide scanner (RRID:SCR_023761) Copy
NanoZoomer series is family of whole slide scanners that rapidly scan glass slides to convert them to digital data. NanoZoomer S210 provides high performance capable of handling large number of slides.
Proper citation: Hamamatsu: NanoZoomer S210 Digital slide scanner (RRID:SCR_023760) Copy
Kinetic plate imager optimized for 96-, 384-, and 1536-well for high throughput screening, enabling whole microplate imaging and simultaneous injections to all wells. System achieves high sensitivity imaging with qCMOS sensor, and highly accurate and repeatable micro-dispensing by adopting 1536 ch dispensing unit capable of dispensing variable volumes. By combining optional parts, robot free semi automation system can be built according to user's purpose.
Proper citation: Hamamatsu: FDSS-GX Kinetic Plate Imager (RRID:SCR_023759) Copy
Web based notebook that enables data driven, interactive data analytics and collaborative documents with SQL, Scala, Python, R and more. Multi purposed web based notebook which brings data ingestion, data exploration, visualization, sharing and collaboration.
Proper citation: Apache Zeppelin (RRID:SCR_023637) Copy
http://www.swisstargetprediction.ch/
Web tool to estimate the most probable macromolecular targets of small molecule, assumed as bioactive. Prediction is founded on combination of 2D and 3D similarity with library of known actives on proteins from three different species.
Proper citation: SwissTargetPrediction (RRID:SCR_023756) Copy
Spatial biology company offering solutions for high parameter tissue analysis from discovery through clinical and translational research, enabling development of more precise therapies for immuno-oncology and other drug development applications.
Proper citation: Akoya Biosciences (RRID:SCR_023774) Copy
https://www.akoyabio.com/phenocycler/instrument/
PhenoCycler-Fusion system is integrated platform combining automated, ultrahigh-plex cycling platform, Akoya PhenoCycler, and its high-speed imaging platform, PhenoImager (formerly Phenoptics), into end-to-end, integrated workflow.
Proper citation: Akoya Biosciences: PhenoCycler-Fusion (RRID:SCR_023773) Copy
Manufacturer of mass spectrometry instrumentation used in biomedical and environmental applications. Originally started by scientists from the University of Toronto Institute for Aerospace Studies, it is now part of Danaher Corporation with the SCIEX R&D division still located in Toronto, Canada.
Proper citation: Sciex (RRID:SCR_023651) Copy
http://naturalscenesdataset.org/
Portal for large scale fMRI dataset conducted at ultra high field strength at Center of Magnetic Resonance Research at University of Minnesota. Dataset consists of whole brain, high resolution fMRI measurements of healthy adult subjects while they viewed thousands of color natural scenes over course of scan sessions. While viewing these images, subjects were engaged in continuous recognition task in which they reported whether they had seen each given image at any point in experiment. These data constitute massive benchmark dataset for computational models of visual representation and cognition, and can support wide range of scientific inquiry.
Proper citation: Natural Scenes Dataset (RRID:SCR_023648) Copy
https://www.intelligent-imaging.com/slidebook.php
Digital microscopy software for research microscopy. It comes standard with drivers to control numerous instruments in and around the microscope. When online, data is acquired in a native-3D format over time, color and specimen locations in customizable experiment protocols. Data can be analyzed by a wide variety of tools for image processing including mathematical operations, statistics functions, analysis scripting and import to/export from MATLAB. Additional modules are available for special applications ranging from deconvolution to photomanipulation to multiphoton.
Proper citation: SlideBook (RRID:SCR_014423) Copy
High throughput Surface Plasmon Resonance system with high quality interaction data for better informed decision making in antibody selection, drug discovery and more., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Cytiva: Biacore 4000 (RRID:SCR_023766) Copy
Fluorescence activated cell analyzing instrument by BD Biosciences. Allows for the simultaneous detection of up to 30 parameters and 28 colors.
Proper citation: BD Biosciences: FACSymphony A3 Cell Analyzer (RRID:SCR_023644) Copy
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