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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Neuronexus: Neural Probe A1x16-3mm-100-703 Resource Report Resource Website |
Neuronexus: Neural Probe A1x16-3mm-100-703 (RRID:SCR_016678) | instrument resource | Instrument as a 16 channel linear electrode array from NeuroNexus Technologies, Ann Arbor, Michigan. Used to map brain function, detect neural activity, and stimulate or modulate neural circuits when brain function is impaired. Used for small and large animal models for neuroscience and clinical applications. | NeuroNexus, Matrix Array, neural, probe, 16 channel, linear, electrode, array, map, brain, function | Commercially available | http://neuronexus.com/electrode-array/a1x16-3mm-100-703/ | SCR_016678 | SciCrunch Registry | 2026-09-26 02:15:50 | 0 | ||||||||||
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A-M SYSTEMS: Model 2100 Isolated Pulse Stimulator Resource Report Resource Website 1+ mentions |
A-M SYSTEMS: Model 2100 Isolated Pulse Stimulator (RRID:SCR_016677) | instrument resource | Instrument used for a variety of physiological stimulation protocols, including behavioral feedback, LTP/LTD, lesion making, electrode marking, ultrafast timing applications, orthodromic/antidromic stimulation, and kindling. Used in a neurophysiological and physiological experiment protocols. | A-M Systems, stimulation, instrument, neurophysiological, physiological, experiment, protocol | Commercially available | https://drive.google.com/file/d/1sN9NYzMciABPPgk09f3cVZDrhiJfak24/view?usp=drivesdk | https://www.a-msystems.com/pub/manuals/2100manual.pdf | SCR_016677 | SciCrunch Registry | 2026-09-26 02:15:50 | 6 | |||||||||
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Suite2P Resource Report Resource Website 50+ mentions |
Suite2P (RRID:SCR_016434) | data analysis software, data processing software, image processing software, software application, software resource, software toolkit | Software package for processing two-photon recordings. Available together with a graphical user interface that allows manual curation of the results. Used in two-photon microscopy for the analysis of data from two-photon imaging. Registers raw movies, detects active cells, extracts their calcium traces and infers their spike times. | two, photon, microscopy, processing, image, data, record |
is related to: MATLAB has parent organization: University College London; London; United Kingdom |
Free, Available for download, Freely available | SCR_016434 | SciCrunch Registry | 2026-09-26 02:15:47 | 84 | ||||||||||
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User Friendly Functional Connectivity - UF²C Resource Report Resource Website 1+ mentions |
User Friendly Functional Connectivity - UF²C (RRID:SCR_016550) | UF²C | data analysis software, data processing software, image analysis software, software application, software resource, software toolkit | Software tool to standardize and facilitate connectivity studies through a graphical user interface and validated preset parameters. | standardize, functional, connectivity, brain, magnetic, resonance, imaging, graphical, user, interface, parameter |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: MATLAB |
FAPESP | Free, Available for download, Freely available | SCR_016550 | SciCrunch Registry | User Friendly Functional Connectivity | 2026-09-26 02:15:48 | 1 | |||||||
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Sleep Heart Health Study Resource Report Resource Website 50+ mentions |
Sleep Heart Health Study (RRID:SCR_016559) | SHHS | data or information resource, disease-related portal, portal, topical portal | Portal for a multi-cohort study focused on sleep-disordered breathing and cardiovascular outcomes implemented by the National Heart Lung and Blood Institute. Recorded signals are: EEG, ECG, EOG, SaO2, HR, EOG, EMG, respiratory inductance plethysmography, respiration (thermistor), position, light. | dataset, analysis, sleep, apnea, breathing, disorder, cardiovascular, disease, EEG, ECG, respiration, PSG | is listed by: National Sleep Research Resource (NSRR) | sleep disorder, sleep apnea, cardiovascular disease | NHLBI U01 HL53916; NHLBI U01 HL53931; NHLBI U01 HL53934; NHLBI U01 HL53937; NHLBI U01 HL53938; NHLBI U01 HL53941; NHLBI U01 HL64360 |
PMID:9493915 | Free, Freely available, Registration required for membership | SCR_016559 | SciCrunch Registry | Sleep Heart Health Study | 2026-09-26 02:15:49 | 84 | |||||
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Praat Resource Report Resource Website 100+ mentions |
Praat (RRID:SCR_016564) | data analysis software, data processing software, software application, software resource | Software tool for phonetics research to analyse, synthesize, and manipulate speech. | phonetics, analyse, systhetize, speech | Free, Available for download, Freely available, Tutorial available | http://www.praat.org, https://github.com/praat/praat/blob/master/fon/manual_tutorials.cpp | SCR_016564 | SciCrunch Registry | 2026-09-26 02:15:48 | 123 | ||||||||||
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SINCERA Pipeline Resource Report Resource Website 1+ mentions |
SINCERA Pipeline (RRID:SCR_016563) | SINCERA | data analysis software, data analytics software, data processing software, software application, software resource | Software tool implemented in R S4 as an analytic pipeline for processing single-cell RNA-seq data from a whole organ or sorted cells. Used for Single Cell RNA-Seq profiling analysis. | single, cell, RNA seq, data, sorted, whole, organ, profiling, analysis | NHLBI R01 HL105433; NHLBI U01 HL110964; NHLBI U01 HL122642 |
PMID:26600239 | Free, Available for download, Freely available | https://research.cchmc.org/pbge/sincera.html | SCR_016563 | SciCrunch Registry | SINCERA, SINgle CEll RNA seq profiling Analysis | 2026-09-26 02:15:49 | 5 | ||||||
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Stitching Resource Report Resource Website 1+ mentions |
Stitching (RRID:SCR_016568) | data processing software, image analysis software, image processing software, image reconstruction software, software application, software resource | Software package available through Fiji to image large biological specimen at high resolution. Comes with 2 different plugins to reconstruct big images/stacks : Pairwise Stitching to stitch two 2d-5d images, and Grid/Collection Stitching to stitch an arbitrary amount of 2d-5d input images. | biological, speciment, resoultion, reconstruct, big, image, stack, stitching | Free, Available for download, Freely available | https://github.com/fiji/Stitching/releases/tag/Stitching_-3.1.3 | SCR_016568 | SciCrunch Registry | 2026-09-26 02:15:49 | 4 | ||||||||||
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Docker Desktop Resource Report Resource Website 10+ mentions |
Docker Desktop (RRID:SCR_016445) | DD | software application, software development environment, software development tool, software resource | Software development environment that helps users build containerized software using Docker and Kubernetes softwares. It is executable on desktop and cloud, and allows access to a vast library of community containerized content in Docker Hub. | software, container, build, code, coding, containerize, develop, development, environment, application | Free, Commercially available, Requires account to download, Available for download | SCR_016445 | SciCrunch Registry | Docker, DockerDesktop | 2026-09-26 02:15:47 | 26 | |||||||||
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Microscopy Image Browser Resource Report Resource Website 100+ mentions |
Microscopy Image Browser (RRID:SCR_016560) | MIB | data analysis software, data processing software, data visualization software, image processing software, software application, software resource, standalone software | Software package for advanced image processing, analysis, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets. | segmentation, analysis, multidimentional, dataset, light, electron, microscopy, image, processing, visualization, data, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: MATLAB |
Biocenter Finland ; Biological Imaging Network Academy of Finland ; University of Helsinki |
PMID:26727152 | Free, Available for download, Freely available | biotools:mib | https://www.youtube.com/watch?v=I9FWmJX_nl0&index=1&list=PLGkFvW985wz8cj8CWmXOFkXpvoX_HwXzj, https://bio.tools/mib | SCR_016560 | SciCrunch Registry | MIB, Microscopy Image Browser | 2026-09-26 02:15:48 | 160 | ||||
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SMI BeGaze Resource Report Resource Website 1+ mentions |
SMI BeGaze (RRID:SCR_016648) | SMI BeGaze | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit, standalone software | Software package for eye tracking studies by New Bio Technology Ltd. Used for designing eye movement studies and recording, analyzing, visualizing data of eye tracking results. | eye, tracking, study, New Bio Technology Ltd, recording, analyzing, visualizing, data | Commercially available | SCR_016648 | SciCrunch Registry | SMI BeGaze™, SMI BehavioralGaze, SMI Behavioral and Gaze Analysis | 2026-09-26 02:15:49 | 7 | |||||||||
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MCTrace Resource Report Resource Website 1+ mentions |
MCTrace (RRID:SCR_016532) | data analysis software, data processing software, image analysis software, software application, software resource | Software tool as a program for building skeletonized models of 3D structures with a graphical user interface. GUI based neuronal network model building. | build, skeletonized, model, 3D structure, neuronal, network | Free, Available for download, Freely available | SCR_016532 | SciCrunch Registry | 2026-09-26 02:15:48 | 3 | |||||||||||
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metaPocket Resource Report Resource Website 10+ mentions |
metaPocket (RRID:SCR_016653) | analysis service resource, production service resource, service resource, simulation software, software application, software resource | Software tool to identify pockets on protein surface to predict ligand-binding sites. | protein, surface, prediction, ligand, binding, site, identify, pocket | is listed by: OMICtools | EU 7th Framework Marie Curie Actions of International Research Staff Exchange Scheme (IRSES) ; Ministry of Science and Technology (MOST) China |
PMID:19645590 PMID:21636590 |
Free for academic users, Freely available | http://sysbio.zju.edu.cn/metapocket | SCR_016653 | SciCrunch Registry | metaPocket, metaPocket 2.0 | 2026-09-26 02:15:49 | 41 | ||||||
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fermi Resource Report Resource Website |
fermi (RRID:SCR_016652) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software assembler and analysis tool for whole-genome short-gun sequencing for Illumina reads. Provides tools for error correction, sequence-to-read alignment and comparison between read sets. Used for large genomes. | assembler, analysis, whole, genome, short, gun, sequencing, error, correction | is listed by: OMICtools | NHGRI U01 HG005208 | PMID:22569178 | Free, Available for download, Freely available | SCR_016652 | SciCrunch Registry | 2026-09-26 02:15:49 | 0 | ||||||||
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Human Cell Atlas Resource Report Resource Website 100+ mentions |
Human Cell Atlas (RRID:SCR_016530) | atlas, catalog, data or information resource, database, image, map, portal | Software tool as a catalog of comprehensive reference of human cells based on their stable properties, transient features, locations and abundances. Map to show the relationships among its elements. Open data international collaborative project involving diverse scientific communities to provide a framework for understanding cellular dysregulation in human disease. | human, cell, line, atlas, catalog, map, open, data, international, project, FASEB list |
is listed by: NIDDK Information Network (dkNET) is related to: Optimus Pipeline is related to: Smart-seq2 Multi-Sample Pipeline is related to: Broad Institute Genomics Platform |
PMID:29206104 | Free, Available for download, Freely available | SCR_016530 | SciCrunch Registry | 2026-09-26 02:15:48 | 127 | |||||||||
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circular statistics Resource Report Resource Website 10+ mentions |
circular statistics (RRID:SCR_016651) | CircStat | data analysis software, data processing software, software application, software resource | Software toolbox for MATLAB for the descriptive and inferential statistical analysis of directional data. | circular, inferential, statistics, directional, data |
has parent organization: Max Planck Institute for Biological Cybernetics; Tubingen; Germany works with: MATLAB |
German Ministry of Education ; Science ; Research and Technology ; German National Academic Foundation |
DOI:10.18637/jss.v031.i10 | Free, Available for download, Registration required to MathWorks Account, | https://github.com/circstat/circstat-matlab | SCR_016651 | SciCrunch Registry | Matlab Circular Statistics Toolbox, , circstat-matlab, circular statistics, Circular Statistics, CircStat for Matlab | 2026-09-26 02:15:50 | 47 | |||||
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Cardiovascular Disease Knowledge Portal Resource Report Resource Website 10+ mentions |
Cardiovascular Disease Knowledge Portal (RRID:SCR_016536) | data or information resource, database, disease-related portal, portal, topical portal | Platform for analysis of the genetics of cardiovascular disease.Used for searching and analysis of human genetic information linked to myocardial infarction, atrial fibrillation and related traits while protecting the integrity and confidentiality of the data. | genetic, data, cardiovascular, disease, human | is listed by: NIDDK Information Network (dkNET) | cardiovascular disease, myocardial infarction, atrial fibrillation | Accelerating Medicines Partnership in Type 2 Diabetes ; National Institute of Cardiovascular Diseases and Stroke |
Free, Available for download, Google ID required, Tutorial available | SCR_016536 | SciCrunch Registry | 2026-09-26 02:15:48 | 31 | ||||||||
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jPerfusionModule Resource Report Resource Website 1+ mentions |
jPerfusionModule (RRID:SCR_016534) | data analysis software, data processing software, image analysis software, software application, software resource | Software tool written in Java that reads DICOM-files from Dynamic Susceptibility Contrast (DSC) Magnetic Resonance Imaging (MRI) and calculates standardized Time-to-Peak (stdTTP) parameter. Maps from this calculation are provided as RGB- and Monochrom2-Dicom files and may be sent to a PACS automatically. Works on windows® platforms on PC’s (Intel® CPUs from Pentium I up to the I7-octo cores) together with the Philips 1.5T ACS-NT up to the Ingenia Systems (n> 20.000), with the Philips 3.0T Systems (n ~ 1.000), the Siemens 1.5T Avanto (SQ-machine) (n> 10.000) and the Siemens 3.0T TimTrio (n ~ 200) so far. Works with uncompressed DICOM-standard files. | dictom, file, read, dynamic, susceptibility, constrast, mangentic, resonance, imaging, calculate, standardized, stdTTP, parameter, | Commercially available | SCR_016534 | SciCrunch Registry | 2026-09-26 02:15:48 | 1 | |||||||||||
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MetaXpress Resource Report Resource Website 500+ mentions |
MetaXpress (RRID:SCR_016654) | data acquisition software, data processing software, image acquisition software, image analysis software, software application, software resource | Software tool for multi level analysis of applications optimized for ImageXpress instruments. High-content image analysis software featuring time lapse analysis. Used for 2D and 3D imaging. | Molecular Devices, ImageXpress, high, content, image, analysis, acquisition, time, lapse, 2D, 3D, cellular, imaging | Commercially available | SCR_016654 | SciCrunch Registry | 2026-09-26 02:15:49 | 657 | |||||||||||
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nonparametricGGC_toolbox Resource Report Resource Website 1+ mentions |
nonparametricGGC_toolbox (RRID:SCR_016539) | nonparametricGGC | data analysis software, data processing software, software application, software resource | Software package for simulation framework and codes for estimating nonparametric Granger causality. Used to study brain functions. | nonparametric, Granger, causality, simulation, framework, code, estimate, brain, function | is related to: MATLAB | the Swiss National Science Foundation | Free, Available for download, Freely available | SCR_016539 | SciCrunch Registry | nonparametric Granger Geweke Causality | 2026-09-26 02:15:48 | 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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