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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Macrogen Resource Report Resource Website 5000+ mentions |
Macrogen (RRID:SCR_014454) | analysis service resource, biomaterial analysis service, material analysis service, production service resource, service resource | A company that provides a variety of next generation sequencing services. The company provides researchers with whole genome resequencing, exome sequencing, targeted sequencing, transcriptomics, and epigenome sequencing. | sequencing assay, sequencing analysis software, next generation sequencing | is affiliated with: Axeq Technologies | Commercial entity | SCR_014454 | SciCrunch Registry | Macrogen Inc. | 2026-10-10 12:39:18 | 6322 | |||||||||
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SCRATCH Resource Report Resource Website 100+ mentions |
SCRATCH (RRID:SCR_014291) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web protein structure and structural feature prediction server.Software suite includes predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts and tertiary structure. User provides amino acid sequence and selects desired predictions, then submits to the server. | Protein predictor, secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts, tertiary structure prediction, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:15980571 | Free, Freely available | biotools:scratch | https://bio.tools/scratch | http://www.igb.uci.edu/servers/psss.html | SCR_014291 | SciCrunch Registry | Scratch Protein Predictor | 2026-10-10 12:39:16 | 141 | |||||
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NNcon Resource Report Resource Website 1+ mentions |
NNcon (RRID:SCR_014292) | prediction, software tool | Protein contact map prediction is useful for protein folding rate prediction, model selection and 3D structure prediction. Here we describe NNcon, a fast and reliable contact map prediction server and software. NNcon was ranked among the most accurate residue contact predictors in the Eighth Critical Assessment of Techniques for Protein Structure Prediction (CASP8), 2008. | text mining objective, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:19420062 | biotools:nncon | https://bio.tools/nncon | http://casp.rnet.missouri.edu/nncon.html | SCR_014292 | SciCrunch Registry | 2026-10-10 12:39:26 | 2 | |||||||
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SAP Visual Enterprise Author Resource Report Resource Website 1+ mentions |
SAP Visual Enterprise Author (RRID:SCR_014293) | authoring tool, software application, software resource | A desktop application used to create and manage 2D and 3D animation and video and audio assets. SAP Visual Enterprise Author can be used to render visual content into common desktop documents, file formats, and business applications for secure downstream use. A variety of tools allows users to view, transform, optimize, animate, and publish in different formats. | authoring tool, image, animation, 2d, 3d, audio, video | Pay for product | SCR_014293 | SciCrunch Registry | SAP 3D Visual Enterprise Author | 2026-10-10 12:39:45 | 2 | ||||||||||
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Biobserve Viewer Resource Report Resource Website 10+ mentions |
Biobserve Viewer (RRID:SCR_014337) | data acquisition software, data analysis software, data processing software, software application, software resource | Software that provides subject tracking with body axis alignment and angle of view, which is then used to track body, nose and tail movements without marking the animal. Users may create the scoring system used by the software, as well as zones to observe, quantify, and compare the behavior of an animal in one or more areas. The software features several data acquisition and analysis tools to gather and interpret the data. | mouse, animal tracking, behavior, data acquisition software, data analysis software | Pay for product | SCR_014337 | SciCrunch Registry | Bio Observe Viewer | 2026-10-10 12:39:27 | 12 | ||||||||||
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Andor iQ Resource Report Resource Website 100+ mentions |
Andor iQ (RRID:SCR_014461) | data processing software, image analysis software, image processing software, software application, software resource | A live cell imaging software that allows for control of iXon EMCCD and sCMOS cameras in synchronized combination with a number of additional imaging hardware devices. iQ can be used to run experiments to investigate dynamic processes in both single cells and multicellular systems, image fixed samples, and generate 3 dimensional image volumes for analysis. | image acquisition and analysis, iXon, sCMOS, EMCCD, live cell, 3d image | Public | SCR_014461 | SciCrunch Registry | 2026-10-10 12:39:48 | 255 | |||||||||||
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ClinProTools Resource Report Resource Website 100+ mentions |
ClinProTools (RRID:SCR_014341) | data acquisition software, data analysis software, data processing software, software application, software resource | Biomarker detection and evaluation software which provides an advanced basis for mining unknown potential biomarkers in complex protein profiles. Visualization tools such as stack plots and box-and-whiskers plots can be used to interactively inspect and compare large data sets originating from samples that contain different clinical diagnoses. ClinProTools also supplies sophisticated mathematical algorithms for the discovery of complex biomarker pattern models. Besides validation, class-prediction tools are also integrated to allow the implementation of the whole biomarker detection and evaluation process. | biomarker detection, biomarker evaluation, mining, visualization tools, large data set, biomarker pattern model | Pay for product | SCR_014341 | SciCrunch Registry | 2026-10-10 12:39:25 | 274 | |||||||||||
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LSM Image Examiner Resource Report Resource Website 1000+ mentions Rating or validation data |
LSM Image Examiner (RRID:SCR_014344) | data management software, software application, software resource | Software used to compile images obtained from the Zeiss LSM 510 confocal microscope. The browser can be used for general image archiving and handling and interactive measurement in labs and workgroups. Features include orthogonal sectioning, 3D cut function, 3D view with calculation of single projections, and interactive measurement functions in the overlay dialog, such as scale bar, distance, and area. | data management software, image archive, image management, interactive measurement | is listed by: SoftCite | Available for download | http://www.zeiss.com/microscopy/en_us/website/downloads/lsm-image-browser.html http://lsm-image-examiner.software.informer.com | SCR_014344 | SciCrunch Registry | LSM Image Browser | 2026-10-10 12:39:27 | 1520 | ||||||||
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ScanImage Resource Report Resource Website 500+ mentions |
ScanImage (RRID:SCR_014307) | data acquisition software, data processing software, signal processing software, software application, software resource | Open source software application for laser scanning microscopy, electrophysiology, laser scanning photostimulation, and other physiological methods focused on neurobiology. Used to control laser scanning microscopes without need for custom data acquisition hardware. Standard data acquisition boards are used to acquire data and control laser scanning. The tasks of signal integration and image processing are placed on the computer CPU. Multiple versions of ScanImage are available, each with their own features. | Laser, scanning, microscopy, electrophysiology, photostimulation, neurobiology, control, data, acquisition, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: Cold Spring Harbor Laboratory has parent organization: Northwestern University; Illinois; USA |
PMID:12801419 | Restricted | http://scanimage.vidriotechnologies.com/display/SIH/ScanImage+Home | SCR_014307 | SciCrunch Registry | Scan Image, ScanImage | 2026-10-10 12:39:26 | 876 | |||||||
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TurboReg Resource Report Resource Website 50+ mentions |
TurboReg (RRID:SCR_014308) | data processing software, image processing software, software application, software resource | An ImageJ plugin for the automatic alignment of a source image (or a stack) to a target image. Manual, automatic, and batch alignment modes are available. Users may specify some landmarks to establish the initial correspondence between images. In automatic and batch modes, the landmarks are automatically refined to match the landmarks of the target image. After registration, the plugin creates a warped image using the final position of the source image and the target landmarks. The plugin can be called by a macro or by another plugin. Technical guidance is available on the website. | image processing software, imagej, plugin, image alignment, automatic alignment, landmark | has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland | PMID:18267377 | Available for download, Freely available for research purposes, Acknowledgement requested | SCR_014308 | SciCrunch Registry | 2026-10-10 12:39:45 | 83 | |||||||||
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FreezeFrame Resource Report Resource Website 500+ mentions |
FreezeFrame (RRID:SCR_014429) | data acquisition software, data processing software, software application, software resource | A video-based system to detect animal movement in fear conditioning experiments, as well as movements in learned helplessness experiments. FreezeFrame can detect animal movements (as small as 1mm) and actions, including grooming, sniffing, turning, and rearing. It can also collect and process data for learned helplessness experiments, such as Tail Suspension and the Porsolt Forced Swim Test. This software can monitor animals for up to 15 times per second. | learned helplessness, fear conditioning, animal, movement, video system | is related to: Limelight | Public, Commercial | SCR_014429 | SciCrunch Registry | FreezeView | 2026-10-10 12:39:26 | 508 | |||||||||
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AnimalTracker Resource Report Resource Website 10+ mentions |
AnimalTracker (RRID:SCR_014397) | data analysis software, data processing software, software application, software resource | A universal tracking application specifically designed to support animal behavioral analysis. AnimalTracker consists of three main modules which can be used independently: Tracker is responsible for image processing and providing the coordinates of the identified object; Zone Designer provides tools to create custom-made investigation areas in order to design a maze-setup; and Tracking Analyzer module serves to define and obtain the parameters needed for the evaluation. | animal, tracking system, universal, animal behavior, analysis | Hungarian Brain Research Program | Acknowledgment required, Available for download, Open source | SCR_014397 | SciCrunch Registry | Animal Tracker | 2026-10-10 12:39:28 | 22 | |||||||||
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SPOT Basic Resource Report Resource Website 10+ mentions |
SPOT Basic (RRID:SCR_014313) | authoring tool, software application, software resource | Image capture software which creates publication quality images. SPOT allows users to view the live image and a preview of the captured image side by side, enabling image editing before capture. Enhancements such as calibration marks and measurements can be applied after image capture. An advanced version is also available. | image capture, authoring tool, software, publication quality image | Basic and Advanced versions are available, Commercially available | SCR_014313 | SciCrunch Registry | SPOT Basic software | 2026-10-10 12:39:45 | 21 | ||||||||||
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Mastrave modelling library Resource Report Resource Website |
Mastrave modelling library (RRID:SCR_014399) | software library, software resource, software toolkit | A software library written to perform vectorized scientific computing and oriented to ease complex modelling tasks such as those typically needed within environmental models, even when involving irregular and heterogeneous data series. The Mastrave project attempts to allow a more effective, quick interoperability between GNU Octave and Matlab users by using a well documented wrap around the main incompatibilities between those computing environments and by promoting a general idiom based on their common, stable syntagms. | free software, array programming, semantics, mathematics, statistics, semantic array programming, library, environmental modelling, environmental modeling |
is related to: GNU Octave is related to: MATLAB |
Free, Available for download | SCR_014399 | SciCrunch Registry | Mastrave modeling library, Mastrave | 2026-10-10 12:39:47 | 0 | |||||||||
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Surveyor with Turboscan Resource Report Resource Website 1+ mentions |
Surveyor with Turboscan (RRID:SCR_014433) | data acquisition software, data processing software, image acquisition software, software application, software resource | Automated scanning software used in conjunction with the Leica DM6000B microscope to obtain whole-slide image mosaics of histological slides. When performing a scan, Turboscan or the standard scan may be used. | scan, data acquisition software, hardware management software, microscope software, image mosaic, histological slide | Freely available online | http://www.objectiveimaging.com/download/files/Surveyor%20User%20Guide.pdf | SCR_014433 | SciCrunch Registry | 2026-10-10 12:39:26 | 5 | ||||||||||
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ReBuilding a Kidney Resource Report Resource Website 1+ mentions |
ReBuilding a Kidney (RRID:SCR_014442) | RBK | data or information resource, funding resource, organization portal, portal, resource | A consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function. Their goal is to coordinate and integrate research to support the development and implementation of strategies such as de novo repair of nephrons, the re-generation of nephrons, and the in vitro engineering of a biological kidney to enhance renal repair and promote the generation of new nephrons in the postnatal organ. Investigators may apply for funding of a kidney-related project through the RBK Partnership Project. Funded projects would join the consortium. | consortium, kidney, rebuild, kidney cell type, human, kidney function, nephron, engineer, renal repair | is listed by: NIDDK Information Network (dkNET) | NIDDK | PMID:28096308 | Available to the research community, Account needed to view data | SCR_014442 | SciCrunch Registry | (Re)Building a Kidney | 2026-10-10 12:39:26 | 3 | ||||||
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Ventana Image Viewer Resource Report Resource Website 1+ mentions |
Ventana Image Viewer (RRID:SCR_014446) | data processing software, image processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 12,2024. A digital slide image software that is used with the VENTANA iScan Coreo Au slide scanner. This software helps facilitate viewing high quality images with little latency. The image view software can also support the viewing of multiple images simultaneously. | ventana, image software, ventana iscan coreo, hardware management software, image processing, digital slide image, slide scanner | THIS RESOURCE IS NO LONGER IN SERVICE | http://www.ventana.com/product/page?view=dpusecases | SCR_014446 | SciCrunch Registry | 2026-10-10 12:39:18 | 1 | ||||||||||
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ANY-maze Resource Report Resource Website 1000+ mentions |
ANY-maze (RRID:SCR_014289) | data acquisition software, data processing software, image acquisition software, software application, software resource | Video tracking system used to automate testing in a variety of behavioral apparatus. ANY-maze can automatically track the tail, head, or body of a test animal in up to 16 pieces of apparatus. The software can record live images or digital files with different camera types and save the data in multiple formats. ANY-maze contains built in statistical tests and standard measures for distance, speed, mobility, duration, etc., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | video tracking system, automated video tracking, behavioral apparatus, data acquisition software, record live image | is related to: IITC Life Sciences: Rotarod Test | THIS RESOURCE IS NO LONGER IN SERVICE | http://www.anymaze.co.uk/ | SCR_014289 | SciCrunch Registry | ANY-MAZE, ANY-Maze, any maze | 2026-10-10 12:39:24 | 1337 | ||||||||
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Definiens Developer XD Resource Report Resource Website 10+ mentions |
Definiens Developer XD (RRID:SCR_014283) | software resource | A development environment designed to create automated image analysis solutions for segmentation and classification tasks. It delivers quantitative and consistent data for any type of image (e.g., IHC, ISH, IF images in different formats). Developer XD also contains a large library of image analysis algorithms, which users can add to, for whole slide images and tissue microarrays (TMAs). It can be integrated with an existing Tissue Studio installation. | development environment, image analysis solution, segmentation, classification, image analysis algorithm library, tissue microarray, whole slide image, tissue studio | is listed by: SoftCite | SCR_014283 | SciCrunch Registry | 2026-10-10 12:39:16 | 11 | |||||||||||
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Seahorse Wave Resource Report Resource Website 100+ mentions |
Seahorse Wave (RRID:SCR_014526) | data analysis software, data management software, data processing software, software application, software resource | Software to manage Seahorse XFe24 Analyzer, which measures OCR and ECAR of live cells in a 24-well plate format. Users can create and modify assay templates and analyze and manage data. | hardware management software, seahorse, xf data analysis, live cells | has parent organization: Agilent Technologies | http://www.agilent.com/cs/pubimages/misc/User_Guide_Wave_Desktop_2-3.pdf | SCR_014526 | SciCrunch Registry | 2026-10-10 12:39:49 | 104 |
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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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