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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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GuPPy Resource Report Resource Website 10+ mentions |
GuPPy (RRID:SCR_022353) | data analysis software, data processing software, software application, software resource | Software Python toolbox that makes fiber photometry data analysis intuitive and light on programming.Used to measure neural activity of freely behaving animals. | OpenBehavior, photometry analysis, neural activity measure, freely behaving animals |
is listed by: OpenBehavior has parent organization: Northwestern University Feinberg School of Medicine; Illinois; USA |
DOI:10.1038/s41598-021-03626-9 | https://github.com/LernerLab/GuPPy | SCR_022353 | SciCrunch Registry | Guided Photometry Analysis in Python | 2026-09-26 02:17:19 | 18 | ||||||||
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Adaptive Immune Receptor Repertoire Software Guidelines Resource Report Resource Website |
Adaptive Immune Receptor Repertoire Software Guidelines (RRID:SCR_022595) | data or information resource, narrative resource, portal, standard specification, topical portal | AIRR Software Guidelines were created by AIRR Software Working Group to promote standards for AIRR software tools and resources in order to enable rigorous and reproducible immune repertoire research at largest scale possible.Established standards for software tools. Authors whose tools comply with this standard will, subject to ratification from AIRR Software WG, be permitted to advertise their tools as being AIRR compliant. Guidelines include compliance checklist, list of compliant tools, and recommended software evaluation data sets. | standards for AIRR software tools and resources, AIRR compliant, compliance checklist, list of compliant tools, recommended software evaluation data sets | is related to: AIRR Data Commons | Free, Freely available | https://fairsharing.org/FAIRsharing.eNSzPf | SCR_022595 | SciCrunch Registry | 2026-09-26 02:17:21 | 0 | |||||||||
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Pain Assessment at Withdrawal Speeds Resource Report Resource Website |
Pain Assessment at Withdrawal Speeds (RRID:SCR_022350) | PAWS | data analysis software, data processing software, software application, software resource | Statistical software platform for automated scoring of pain in mice.Software R package takes paw trajectory data in response to stimulus and provides automated scoring of pain. | OpenBehavior, behavior measurement, freely moving mice, behavioral data analysis, scoring of reflexive paw withdrawal | is listed by: OpenBehavior | DOI:10.7554/eLife.57258 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/paws/ | SCR_022350 | SciCrunch Registry | 2026-09-26 02:17:19 | 0 | |||||||
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Adaptive Immune Receptor Repertoire Rearrangement Schema Resource Report Resource Website 1+ mentions |
Adaptive Immune Receptor Repertoire Rearrangement Schema (RRID:SCR_022592) | data or information resource, narrative resource, portal, standard specification, topical portal | Part of AIRR Data Model, defines annotations needed for rearrangements, which are sequences describing rearranged adaptive immune receptor chain (e.g., antibody heavy chain or TCR beta chain). Data for Rearrangement objects are stored as rows in tab delimited file and should be compatible with any TSV reader. Dataset is defined in this context as: TSV file, TSV with companion YAML file containing metadata, or directory containing multiple TSV files and YAML files. | AIRR Data Model, annotations needed for rearrangements, rearranged adaptive immune receptor chain sequences, | is related to: AIRR Data Commons | PMID:29144493 | Free, Freely available | https://fairsharing.org/FAIRsharing.zwjNAh | SCR_022592 | SciCrunch Registry | 2026-09-26 02:17:21 | 1 | ||||||||
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Mouse Action Recognition System Resource Report Resource Website 1+ mentions |
Mouse Action Recognition System (RRID:SCR_022347) | MARS | data analysis software, data processing software, software application, software resource | Software Python pipeline for automated detection, pose estimation, and behavior classification in socially interacting mice.Used for pose estimation and behavior quantification in pairs of freely behaving mice. | OpenBehavior, behavior measurement, video analysis, real time recording and analysis, pose estimation and behavior quantification, freely behaving mice |
is listed by: OpenBehavior is related to: MARS Developer has parent organization: Northwestern University; Illinois; USA |
DOI:10.7554/eLife.63720 | Free, Available for download, Freely available | https://github.com/neuroethology/MARS | SCR_022347 | SciCrunch Registry | 2026-09-26 02:17:19 | 8 | |||||||
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Artec 3D: Eva Fast 3D scanner Resource Report Resource Website |
Artec 3D: Eva Fast 3D scanner (RRID:SCR_022589) | instrument resource | 3D scanner for making quick, textured, and accurate 3D models of medium sized objects such as human bust, alloy wheel, or motorcycle exhaust system. Used for capturing objects of almost any kind, including objects with black and shiny surfaces. | Artec3D, 3D scanner, 3D models, medium sized objects, capturing objects, instrument, equipment, USEDit |
is listed by: USEDit is listed by: MfN Berlin Micro-CT Laboratory Core Facility |
Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_022589.pdf | SCR_022589 | SciCrunch Registry | 2026-09-26 02:17:21 | 0 | |||||||||
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Artec 3D: Space Spider Resource Report Resource Website 1+ mentions |
Artec 3D: Space Spider (RRID:SCR_022588) | instrument resource | 3D scanner based on blue light technology. Precision instrument for CAD users and engineers. Used for capturing small objects or intricate details of large industrial objects in high resolution, with accuracy and brilliant color. | Artec3D, 3D scanner, blue light technology, capturing small objects, intricate details of large industrial objects, instrument, equipment, USEDit |
is listed by: USEDit is listed by: MfN Berlin Micro-CT Laboratory Core Facility |
Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_022588.pdf | SCR_022588 | SciCrunch Registry | 2026-09-26 02:17:21 | 2 | |||||||||
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SIPEC Resource Report Resource Website |
SIPEC (RRID:SCR_022364) | SIPEC | data analysis software, data processing software, software application, software resource | Software pipeline for video analysis. Deep learning Swiss knife for behavioral data analysis.Performs segmentation, identification, pose-estimation and classification of complex behaviour. Used for analysis of behavior of multiple animals in complex environments. | OpenBehavior, video analysis, behavioral data analysis |
is listed by: OpenBehavior has parent organization: ETH Zurich; Zurich; Switzerland |
DOI:10.1038/s42256-022-00477-5 | Free, Available for download, Freely available | https://github.com/SIPEC-Animal-Data-Analysis/SIPEC | SCR_022364 | SciCrunch Registry | SIPEC project | 2026-09-26 02:17:20 | 0 | ||||||
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Timed pressure control hardware and software for delivery of air mediated distensions in animal models Resource Report Resource Website 1+ mentions |
Timed pressure control hardware and software for delivery of air mediated distensions in animal models (RRID:SCR_022363) | data or information resource, instrument resource, portal, project portal | System uses Arduino microcontroller to control relay module that operates solenoid valve which all sit in 3D printed housing. Solenoid works in conjunction with flowmeter regulator to allow for controlled flow of pressurized air into target. Timing of distensions is controlled via either custom Python based UI, or by triggered TTL pulse.Timed pressure control hardware and software used for delivery of air mediated distensions in animal models. | OpenBehavior, Instrument, behavior apparatus, delivery of air mediated distensions, animal models | is listed by: OpenBehavior | DOI:10.1016/J.OHX.2022.E00271 | Free, Freely available | https://osf.io/rs5p4 | SCR_022363 | SciCrunch Registry | Timed pressure control hardware and software for delivery of air mediated distensions in animal models project | 2026-09-26 02:17:19 | 1 | |||||||
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OpenPose Resource Report Resource Website 10+ mentions |
OpenPose (RRID:SCR_022362) | data analysis software, data processing software, software application, software resource | Software tool as multi subject keypoint detection library for real time pose estimation.Used to track behavior of monkeys in natural environments, without disrupting their typical pattern of behavior. Deep learning software system for body, face, hands, and foot estimation in monkeys. | OpenBehavior, tracking limb orientation, behavior measurement, freely moving, realtime recording and analysis, video analysis | is listed by: OpenBehavior | DOI:10.1101/2021.01.28.428726 | Free, Available for download, Freely available | https://github.com/CMU-Perceptual-Computing-Lab/openpose | SCR_022362 | SciCrunch Registry | 2026-09-26 02:17:19 | 13 | ||||||||
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TRex Resource Report Resource Website 1+ mentions |
TRex (RRID:SCR_022361) | data analysis software, data processing software, software application, software resource | Open source animal tracking software tool. Used to visually track movement of multiple animals at once. | OpenBehavior, animal tracking, visually track movement | is listed by: OpenBehavior | DOI:10.7554/eLife.64000 | https://github.com/mooch443/trex | SCR_022361 | SciCrunch Registry | 2026-09-26 02:17:19 | 2 | |||||||||
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DLStream Resource Report Resource Website 1+ mentions |
DLStream (RRID:SCR_022359) | data analysis software, data processing software, software application, software resource | Software tool enables closed loop behavioral experiments using deep learning based markerless, real time posture detection.Closed loop behavioral experiment toolkit using pose estimation of body parts. | OpenBehavior, video analysis, behavioral experiment, pose estimation, body parts | is listed by: OpenBehavior | Projekt DEAL | DOI:10.1038/s42003-021-01654-9 | Free, Available for download, Freely available | https://github.com/SchwarzNeuroconLab/DeepLabStream | SCR_022359 | SciCrunch Registry | DeepLabStream | 2026-09-26 02:17:19 | 1 | ||||||
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Variational Embedding of Animal Motion Resource Report Resource Website 1+ mentions |
Variational Embedding of Animal Motion (RRID:SCR_022477) | VAME | data processing software, data visualization software, software application, software resource | Software Python tool to cluster behavioral signals obtained from pose estimation tools. Unsupervised probabilistic deep learning framework capable of finding behavioral motifs in pose estimation data. Capable of augmenting quantitative behavioral analyses of data derived from standard pose-estimation software packages. Written based on core functions from DeepLabCut, and readily works with pose data from that package. Can also work with data from other pose estimation packages such as SLEAP. | OpenBehavior, vame, variational embedding of animal motion, pytorch, pose estimation |
is listed by: OpenBehavior is related to: DeepLabCut is related to: SLEAP, LEAP and MotionMapper project |
Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/vame/ | SCR_022477 | SciCrunch Registry | Variational Animal Motion Embedding, VAME: Variational Embedding of Animal Motion | 2026-09-26 02:17:20 | 3 | |||||||
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AIRR Community Resource Report Resource Website |
AIRR Community (RRID:SCR_022598) | data or information resource, narrative resource, portal, standard specification | Research driven group that is organizing and coordinating stakeholders in use of next generation sequencing technologies to study antibody/B-cell and T-cell receptor repertoires. Develops and promotes standards and recommendations for obtaining, analyzing, curating and comparing/sharing AIRR-seq datasets;using and validating tools for analyzing AIRR-seq data;relating AIRR-seq datasets to other “big data” sets, such as microarray, flow cytometric, and MiSeq and single-cell gene-expression data; legal and ethical issues involving use and sharing of AIRR-seq data sets derived from human sources. | next generation sequencing technologies use, study antibody, B-cell and T-cell receptor repertoires, standards and recommendations for AIRR-seq datasets | is related to: AIRR Data Commons | Free, Freely available | SCR_022598 | SciCrunch Registry | Adaptive Immune Receptor Repertoire Community, Adaptive Immune Receptor Repertoire Community of The Antibody Society | 2026-09-26 02:17:21 | 0 | |||||||||
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Pyneal Resource Report Resource Website |
Pyneal (RRID:SCR_022333) | data analysis software, data processing software, software application, software resource | Open source software package to support rt-fMRI via data in formats generated by Siemens, Philips, and GE. Used to support real time functional magnetic resonance imaging. | OpenBehavior, real time functional magnetic resonance imaging | is listed by: OpenBehavior | DOI:10.3389/fnins.2020.00900 | Free, Available for download, Freely available | https://github.com/jeffmacinnes/pyneal | SCR_022333 | SciCrunch Registry | 2026-09-26 02:17:19 | 0 | ||||||||
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OORTT Resource Report Resource Website |
OORTT (RRID:SCR_022331) | software resource | Software Pyton scripts to run computerised task of Reaction Time. Scripts, together with their instructions and scoresheets.Used for assessment of RTs that is freely available, compatible with all operating systems, without license and activation costs, and based on open source software platform. | OpenBehavior, behavioral measurment, reaction time, assessment of reaction times, OpenSesame 3.1.9 | is listed by: OpenBehavior | DOI:10.1007/s10072-020-04839-y | Free, Available for download, Freely available | https://osf.io/xvcg6/ | SCR_022331 | SciCrunch Registry | Open source Open access Reaction Time Test | 2026-09-26 02:17:19 | 0 | |||||||
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AutoStereota Resource Report Resource Website 1+ mentions |
AutoStereota (RRID:SCR_022330) | data or information resource, instrument resource, portal, project portal | Automated surgical instrument for brain tissue aspiration.Instrument for microendoscope implantation. Utilizes robotic control of needle connected to vacuum pump to aspirate brain tissue. System consists of robotic surgical instrument built around commercially available stereotaxic instrument and open source MATLAB-based GUI for control. | OpenBehavior, Instrument, brain tissue aspiration, microendoscope implantation | is listed by: OpenBehavior | DOI:10.1016/j.jneumeth.2018.10.013 | Free, Freely available | https://github.com/liang-bo/AutoStereota | SCR_022330 | SciCrunch Registry | 2026-09-26 02:17:19 | 3 | ||||||||
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learnMSA Resource Report Resource Website 1+ mentions |
learnMSA (RRID:SCR_022572) | alignment software, data processing software, image analysis software, software application, software resource | Software tool as multiple sequence alignment formulated as statistical machine learning problem, where optimal profile hidden Markov model for potentially very large family of protein sequences is searched and alignment is decoded. | Multiple sequence alignment, protein sequences, statistical machine learning problem, hidden Markov model | Free, Available for download, Freely available | SCR_022572 | SciCrunch Registry | 2026-09-26 02:17:20 | 2 | |||||||||||
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sei Resource Report Resource Website 10+ mentions |
sei (RRID:SCR_022571) | data access protocol, software resource, web service | Web server for systematically predicting sequence regulatory activities and applying sequence information to human genetics data. Provides global map from any sequence to regulatory activities, as represented by sequence classes, and each sequence class integrates predictions for chromatin profiles like transcription factor, histone marks, and chromatin accessibility profiles across wide range of cell types. | systematically predicting sequence regulatory activities, applying sequence information, human genetics data, sequence class predictions | National Science Foundation Graduate Research Fellowship Program ; NHGRI R01HG005998; NHLBI U54HL117798; NIGMS R01GM071966 |
PMID:35817977 | Free, Available for download, Freely available | https://hb.flatironinstitute.org/sei | SCR_022571 | SciCrunch Registry | 2026-09-26 02:17:20 | 10 | ||||||||
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pMAT Resource Report Resource Website 1+ mentions |
pMAT (RRID:SCR_022570) | pMAT | data analysis software, data processing software, software application, software resource | Open source software suite for analysis of fiber photometry data. | fiber photometry data analysis, fiber photometry | NIDA DA043572 | PMID:33385438 | SCR_022570 | SciCrunch Registry | Photometry Modular Analysis Tool | 2026-09-26 02:17:20 | 8 |
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