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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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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 | 2026-10-24 12:47:15 | 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 | 2026-10-24 12:47:15 | 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 | 2026-10-24 12:47:15 | 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 | 2026-10-24 12:47:19 | 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 | 2026-10-24 12:47:16 | 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 | 2026-10-24 12:47:15 | 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 | 2026-10-24 12:47:16 | 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 | 2026-10-24 12:47:19 | 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 | 2026-10-24 12:47:19 | 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 | 2026-10-24 12:47:17 | 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 | 2026-10-24 12:47:17 | 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 | 2026-10-24 12:47:15 | 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 | 2026-10-24 12:47:17 | 104 | ||||||||||
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pyLMM Resource Report Resource Website 10+ mentions |
pyLMM (RRID:SCR_014525) | data analysis software, data processing software, software application, software resource, standalone software | A Python package for doing linear mixed model associations in genome wide association studies (GWAS). The software corrects for population structure using EMMA. | python, data analysis software, linear mixed model, genome wide association studies, gwas, lmm, emma | DOI:10.1534/genetics.107.080101 | Install using pip | SCR_014525 | SciCrunch Registry | 2026-10-24 12:47:17 | 12 | ||||||||||
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ENIGMA-DTI Pipeline Resource Report Resource Website 50+ mentions |
ENIGMA-DTI Pipeline (RRID:SCR_014649) | protocol | Pipeline which provides tools to extract whole-brain average and regional measurements from DTI images including FA, AD, RD and MD. Protocols for preprocessing, ENIGMA-DTI processing (skeletonization and ROI extraction), and GWAS analysis are available. Software tools used for each process are listed within the protocols. | dti, enigma, protocol, pipeline |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Southern California; Los Angeles; USA has parent organization: ENIGMA |
NIBIB U54 EB020403 | Available for download from NITRC | http://www.nitrc.org/projects/enigma_dti | SCR_014649 | SciCrunch Registry | ENIGMA-DTI protocol, ENIGMA DTI pipeline, ENIGMA DTI protocol | 2026-10-24 12:47:19 | 50 | |||||||
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NCBI Virus Resource Report Resource Website 50+ mentions |
NCBI Virus (RRID:SCR_018253) | data access protocol, data or information resource, portal, software resource, topical portal, web service | Community portal for viral sequence data from RefSeq, GenBank and other NCBI repositories. Integrative, value added resource designed to support retrieval, display and analysis of curated collection of virus sequences and large sequence datasets. Used to increase usability of data archived in GenBank and other NCBI repositories. | Viral sequence data, viral data retrival, viral data analysis, viral data display, curated virus sequence, data set |
is related to: RefSeq is related to: GenBank |
PMID:27899678 | Free, Freely available | SCR_018253 | SciCrunch Registry | National Center for Biotechnology Information Virus | 2026-10-24 12:49:15 | 76 | ||||||||
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Creative Biogene Pelodictyon Cultivation Service Resource Resource Report Resource Website |
Creative Biogene Pelodictyon Cultivation Service Resource (RRID:SCR_022244) | service resource | Service for Pelodictyon cultivation. | Creative Biogene, biomedical service, Pelodictyon, bacteria cultivation. | has parent organization: Creative Biogene | Restricted | SCR_022244 | SciCrunch Registry | Pelodictyon Cultivation | 2026-10-24 12:49:17 | 0 | |||||||||
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Creative Biogene Mitochondrial Biomarkers and Therapeutic Targets Service Resource Resource Report Resource Website 1+ mentions |
Creative Biogene Mitochondrial Biomarkers and Therapeutic Targets Service Resource (RRID:SCR_022240) | service resource | Creative Biogene service for discovery of disease specific proteins associated with mitochondrial epigenetic products, which can be used as molecular targets for new drug design and provide molecular markers for early diagnosis of diseases. | Creative Biogene, biomedical service, disease specific proteins discovery, mitochondrial epigenetic product, molecular targets, new drug design, molecular markers | has parent organization: Creative Biogene | Restricted | SCR_022240 | SciCrunch Registry | Mitochondrial Biomarkers and Therapeutic Targets | 2026-10-24 12:49:17 | 6 | |||||||||
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triku Resource Report Resource Website 1+ mentions |
triku (RRID:SCR_020977) | data analysis software, data processing software, software application, software resource | Software tool as feature selection method based on nearest neighbors for single-cell data. | Selection method, nearest neighbors, single cell data, data analysis | uses: scanpy | Free, Available for download, Freely available | https://triku.readthedocs.io/en/latest/ | SCR_020977 | SciCrunch Registry | 2026-10-24 12:49:16 | 2 | |||||||||
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3DOC Resource Report Resource Website |
3DOC (RRID:SCR_021547) | data or information resource, instrument resource, portal, project portal | Project related to animals learned perform action in order to achieve reward. Fully 3D printable chamber able to perform operant conditioning using off-the-shelf, low-cost optical and electronic components, that can be reproduced rigorously in any laboratory equipped with 3D printer. | Instrument, operant conditioning, 3D printable chamber, OpenBehavior | is listed by: OpenBehavior | DOI:10.1523/eneuro.0502-19.2020 | Commercially available | SCR_021547 | SciCrunch Registry | 2026-10-24 12:49:16 | 0 |
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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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