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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ULTRA-DD Resource Report Resource Website |
ULTRA-DD (RRID:SCR_018995) | data or information resource, portal, project portal | Project aim is to identify and validate novel targets in auto immune and inflammatory diseases. Used to create and profile target directed chemical and antibody probes in patient cell derived assays, provide biomarker and phenotypic read outs in more disease relevant context. | Novel target identification, auto immune disease, inflammatory disease, profile target, target directed chemical, chemical probe, antibody probe, patient cell derived assay, biomarker, phenotypic read out, drug discovery | Auto immune and inflammatory diseases. | EFPIA companies ; European Union Seventh Framework Programme ; Innovative Medicines Initiative Joint Undertaking |
Free, Freely available | SCR_018995 | Unrestricted Leveraging of Targets for Research Advancement and Drug Discovery | 2026-08-29 11:29:00 | 0 | ||||||||
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Wave Surfer project Resource Report Resource Website |
Wave Surfer project (RRID:SCR_021476) | data or information resource, portal, project portal | Project related to neurophysiology data acquisition and analysis.Included open source software application for neurophysiology data acquisition and analysis is provided by Howard Hughes Medical Institute Janelia Research Campus scientists. Program is based in MatLab, and evolved from earlier open source software package called Ephus. | Neurophysiology data acquisition, neurophysiology data analysis, neurophysiology data, MATLAB, OpenBehavior |
is listed by: OpenBehavior is related to: Wave Surfer |
Free, Freely available | SCR_021476 | Wave Surfer | 2026-08-29 11:29:02 | 0 | |||||||||
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Calcium Imaging data Analysis project Resource Report Resource Website 1+ mentions |
Calcium Imaging data Analysis project (RRID:SCR_021477) | CaImAn | data or information resource, portal, project portal | Project related to calcium imaging.Provides software library, CaImAn, for one and two-photon Calcium Imaging data Analysis. | calcium imaging analysis, movie handling, motion correction, source extraction, spike deconvolution, result visualization, OpenBehavior |
is listed by: OpenBehavior is related to: Calcium Imaging data Analysis |
DOI:10.7554/elife.38173 | Free, Freely available | SCR_021477 | Calcium Imaging data Analysis | 2026-08-29 11:28:52 | 2 | |||||||
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ARTS biomarker Resource Report Resource Website 10+ mentions |
ARTS biomarker (RRID:SCR_019288) | data processing software, software application, software resource | Software tool as automated biomarker that outputs score linked to likelihood person sufferring from arteriolosclerosis based on brain MRI data and basic demographic information. MRI data processing pipeline and classifier are packaged into software container.Users do not need to perform any image processing, and are only required to install Singularity to run ARTS. | Automated biomarker, score output, arteriolosclerosis, brain MRI data, demographic information, | Restricted | SCR_019288 | ARTS | 2026-08-29 11:28:50 | 29 | ||||||||||
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DecodingDynamic Resource Report Resource Website 1+ mentions |
DecodingDynamic (RRID:SCR_021099) | data or information resource, software resource, source code | Data, code, and notebooks for replicating analyses reported in Rogers et al., Evidence for deep, distributed and dynamic semantic code in human ventral anterior temporal cortex. | ECoG, neural networks, semantics, replicating analyses, data, code, notebooks, human ventral anterior temporal cortex, semantic code | European Research Council ; Medical Research Council Programme |
DOI:10.1101/695049 | Free, Freely available | SCR_021099 | 2026-08-29 11:28:55 | 1 | |||||||||
|
BonVision project Resource Report Resource Website |
BonVision project (RRID:SCR_021491) | data or information resource, portal, project portal | Project related to creating and controlling visual environments.Provided open source software package for creating and controlling visual environments was developed by University College London scientists. | Creating visual environments, controlling visual environments, Bonsai, 2D environment, 3D environments, OpenBehavior |
is listed by: OpenBehavior is related to: BonVision has parent organization: University College London; London; United Kingdom |
DOI:10.1101/2020.03.09.983775 | Free, Freely available | SCR_021491 | BonVision | 2026-08-29 11:29:02 | 0 | ||||||||
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Smart-seq2 Multi-Sample Pipeline Resource Report Resource Website 1+ mentions |
Smart-seq2 Multi-Sample Pipeline (RRID:SCR_018920) | data processing software, software application, software resource, software toolkit | The Smart-seq2 Single Nucleus Multi-Sample (Multi-snSS2) pipeline was developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) to process single-nucleus RNAseq (snRNAseq) data generated by Smart-seq2 assays. | Single cell data, Smart seq2 technology, scRNAseq data, Smart-seq2 assay data, data processing | is related to: Human Cell Atlas | Free, Available for download, Freely available | https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/smartseq2_multisample | SCR_018920 | 2026-08-29 11:29:00 | 4 | |||||||||
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Open Source Whisking Video Database portal Resource Report Resource Website |
Open Source Whisking Video Database portal (RRID:SCR_021404) | data or information resource, portal, project portal | Portal provides shared database of videos featuring juvenile and adult male rats and adult male mice exploring stationary objects.This dataset includes wide variety of experimental conditions including genetic, pharmacological, and sensory deprivation interventions to explore how active sensing behavior is modulated by different factors. Database of high speed videos of whisking behavior in freely moving rodents.Open source high speed infrared videography database to study principles of active sensing in freely navigating rodents. | High speed videos, whisking behavior, freely moving rodents, infrared videography database, active sensing, OpenBehavior |
is listed by: OpenBehavior is related to: Open Source Whisking Video Database |
DOI:10.1093/gigascience/giy134 | Free, Freely available | SCR_021404 | 2026-08-29 11:29:02 | 0 | |||||||||
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DeepFly3D Resource Report Resource Website 1+ mentions |
DeepFly3D (RRID:SCR_021402) | data processing software, image analysis software, software application, software resource | Software tool as PyTorch and PyQT5 implementation of 2D-3D tethered Drosophila pose estimation. Image annotation tool used for pose estimation and appendage tracking. Provides interface for pose estimation and to permit further correction of 2D pose estimates, which are automatically converted to 3D pose. | Image annotation, pose tracking, pose estimation, motor circuit, behavioral measure, accurate 3D pose estimation, OpenBehavior |
is listed by: OpenBehavior is related to: DeepFly3D project |
DOI:10.7554/elife.48571 | Free, Available for download, Freely Available | https://edspace.american.edu/openbehavior/project/deepfly3d/ | SCR_021402 | 2026-08-29 11:28:51 | 1 | ||||||||
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CloudReg Resource Report Resource Website |
CloudReg (RRID:SCR_022795) | data processing software, image analysis software, software application, software resource | Software automated, terascale, cloud based image analysis pipeline for preprocessing and cross modal, nonlinear registration between volumetric datasets with artifacts. Automatic terabyte scale cross modal brain volume registration. | brain volume, nonlinear registration, automatic terabyte scale, cross modal brain volume registration, image analysis pipeline, volumetric datasets with artifacts | is used by: BICCN | AP Giannini Foundation ; Johns Hopkins University Kavli Neuroscience Discovery Institute Postdoctoral Fellowship ; Karen Toffler Charitable Trust ; Kavli Neuroscience Discovery Institute ; Microsoft Research ; NIA P01AG009973; NIA R01 AG066184; NIDA 1K99DA050662; NIMH K08MH113039; NIMH R01 MH099647; NIMH U19MH114821; NINDS K99 NS116122; NSF EEC 1707298 |
PMID:34253927 | Free, Available for download, Freely available | https://github.com/neurodata/CloudReg/ | SCR_022795 | 2026-08-29 11:28:54 | 0 | |||||||
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Argus Resource Report Resource Website 1+ mentions |
Argus (RRID:SCR_021585) | data or information resource, portal, project portal, software resource | Portal provides software tool for analysis and quantification of both single and socially interacting zebrafish. Software data extraction and analysis tool built in open source R language for tracking zebrafish behavior. | Analysis, quantification, socially interacting zebrafish, OpenBehavior |
is listed by: OpenBehavior is listed by: SoftCite is related to: Argus |
DOI:10.3758/s13428-018-1083-y | Free, Freely available | SCR_021619 | SCR_021585 | 2026-08-29 11:28:57 | 1 | ||||||||
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xHLA Resource Report Resource Website 1+ mentions |
xHLA (RRID:SCR_022277) | data processing software, software application, software resource | Software tool for fast and accurate HLA typing from short read sequence data. Iteratively refines mapping results at amino acid level to achieve four digit typing accuracy for both class I and II HLA genes, taking only 3 min to process 30× whole genome BAM file on desktop computer. | HLA typing, short read sequence data, refines mapping results, amino acid level, four digit typing accuracy | Health Resources and Services Administration ; NCI 5U24CA076518; NHLBI 5U10HL069294; Office of Naval Research Grants |
PMID:28674023 | Free, Available for download, Freely available | SCR_022277 | 2026-08-29 11:28:58 | 2 | |||||||||
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BRAIN Initiative Cell Atlas Network Resource Report Resource Website 10+ mentions |
BRAIN Initiative Cell Atlas Network (RRID:SCR_022794) | BICAN | data or information resource, portal | Provides molecular and anatomical foundational framework for study of brain function and disorders.Comprehensive Center on Human and Non-Human Primate Brain Cell Atlases with goal to build reference brain cell atlases that will be used throughout research community. | Cell Atlas Network, study of brain function and disorders, build reference brain cell atlases |
uses: NIH NeuroBioBank uses: NeMOarchive uses: Terra uses: Brain Image Library uses: SpinalJ uses: Cell Annotation Platform uses: Connectome Workbench uses: BALSA uses: Cytosplore Viewer uses: Cellarium is related to: BICCN is related to: Brain Cell Data Viewer is related to: CZ CELLxGENE Discover is related to: CATlas is related to: Epi-Retro-Seq is related to: NeMO Analytics is related to: UCSC Cell Browser is related to: MetaMarkers is related to: Brain Knowledge Platform is related to: Human Brain Variation Project has parent organization: Allen Institute has parent organization: Allen Institute for Brain Science has organization facet: Slide-seq Pipeline has organization facet: ATAC Pipeline has organization facet: Multiome Pipeline has organization facet: Whole Mouse Brain Cell and Genome Atlas has organization facet: snm3C Pipeline has organization facet: Paired-Tag Pipeline has organization facet: NIMP: Neuroanatomy-anchored Information Management Platform for Collaborative BICAN Data Generation has organization facet: NHash Identifier has organization facet: Atlas Ontology Model has organization facet: Allen Brain Map BICCN Data Catalog has organization facet: Atlas Ontology Model has organization facet: Early Postnatal Developmental Mouse Brain Atlas has organization facet: BRAINCELL-AID has organization facet: JOSA has organization facet: Annotation Comparison Explorer has organization facet: Brain Image Library has organization facet: DELAY has organization facet: chromograph has organization facet: fetal_brain_multiomics has organization facet: CBI BrAinPI has organization facet: bkbit has organization facet: BuildIndices has organization facet: HOMBA Macaque Reference Atlas has organization facet: HOMBA Adult Marmoset Basal Ganglia Atlas has organization facet: SlideTags.wdl has organization facet: storm-control has organization facet: PIANO:Probabilistic Inference Autoencoder Networks for multi-Omics has organization facet: BICAN Basal Ganglia Epigenome Explorer has organization facet: Brain Initiative Cell Atlas Network Data Catalog has organization facet: BrainKB has organization facet: CrossExpression has organization facet: bican-mccarroll-manuscript1 has organization facet: HMBA Adult Human Brain Atlas has organization facet: Harmonized Ontology of Mammalian Brain Anatomy (HOMBA) has organization facet: NIMP Analytics has organization facet: Human Striatum Slide-tags Viewer |
NIH MH130918; NIH MH130968 |
Free, Freely available | https://www.braininitiative.org/funding-opportunity/brain-initiative-cell-atlas-network-bican-comprehensive-center-on-human-and-non-human-primate-brain-cell-atlases-um1-clinical-trial-not-allowed/, https://braininitiative.nih.gov/funding-opportunies/brain-initiative-cell-atlas-network-bican-specialized-collaboratory-human-non | SCR_022794 | 2026-08-29 11:28:58 | 33 | |||||||
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Tissue Studio Resource Report Resource Website 1+ mentions |
Tissue Studio (RRID:SCR_023001) | data processing software, image analysis software, software application, software resource | Software to detect regions of interests and distinguishes cells and sub-cellular objects within these target regions from immunohistochemistry specimen. Used for digital pathology image analysis. | Definiens Inc., detect target regions, immunohistochemistry specimen, distinguishes cells and sub-cellular objects | PMID:30930117 | Restricted | SCR_023001 | Definiens Tissue Studio | 2026-08-29 11:28:59 | 2 | |||||||||
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Neocortical Microcircuit Portal Resource Report Resource Website 1+ mentions |
Neocortical Microcircuit Portal (RRID:SCR_022032) | data or information resource, portal, project portal | Neocortical microcircuit collaboration portal is resource for rat somatosensory cortex. NMC portal allows users to access experimental data used in reconstruction process, download cellular and synaptic models, and analyze predicted properties of microcircuit. | rat somatosensory cortex, reconstruction process, cellular and synaptic models, microcircuit, microcircuit predicted properties | Cajal Blue Brain project ; EPFL Hebrew University Collaborative Grant ; EPFL ; European Union Seventh Framework Program ; Gatsby Charitable Foundation ; Ministerio de Economia y Competitividad Spanish Ministry of Education and Science |
DOI:10.3389/fncir.2015.00044 | Free, Freely available | SCR_022032 | Blue Brain Neocortical Microcircuit Portal, NMC portal | 2026-08-29 11:29:03 | 5 | ||||||||
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QCAlign Resource Report Resource Website 1+ mentions |
QCAlign (RRID:SCR_023088) | data processing software, image analysis software, software application, software resource | Software tool to detect regions that are affected by tissue damage, labelling defects, artifacts or errors in image acquisition, regions that are poorly registered, or where registration cannot be verified. Makes it easier for the user to explore the atlas hierarchy and decide on customized hierarchy level for investigation. QCAlign was developed to support QUINT workflow which supports spatial analysis of labelling in series of brain sections from mouse and rat based on registration to reference atlas. | QUINT, supports spatial analysis, labelling in series, detect tissue damage regions, detect errors in image acquisitionbrain sections, mouse, rat, reference atlas, | has parent organization: University of Oslo; Oslo; Norway | European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA). | Free, Available for download, Freely available | https://qcalign.readthedocs.io; https://github.com/Neural-Systems-at-UIO/QCAlign | SCR_023088 | 2026-08-29 11:28:59 | 4 | ||||||||
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MouseMove project Resource Report Resource Website |
MouseMove project (RRID:SCR_021581) | data or information resource, portal, project portal | Portal provides MouseMove software system used to analyze Open Field behavior of mice after experimental stroke to show reduced locomotor activity and to quantify laterality deficits. System is used in combination with open source program ImageJ and MTrack2 plugin to analyze pre recorded Open Field test video. System has two downloadable components, ImageJ macro and separate program with custom built MouseMove GUI. ImageJ is used to subtract background video from experiment and create image of animals total trajectory. MouseMove GUI then completes detailed analysis of movement patterns, measuring fractional time spent stationary, distance traveled, speed mean and various details of laterality. | Open Field behavior analysis, mice after experimental stroke, reduced locomotor activity, quantify laterality deficits, OpenBehavior |
is listed by: OpenBehavior is related to: MouseMove |
DOI:10.1038/srep16171 | Free, Freely available | SCR_021581 | MouseMove system | 2026-08-29 11:29:03 | 0 | ||||||||
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Generative Diffeomorphic Mapping Resource Report Resource Website |
Generative Diffeomorphic Mapping (RRID:SCR_022825) | data or information resource, portal | Web portal that explains technique of Diffeomorphic Mapping and Shape Analysis. | Diffeomorphic Mapping and Shape Analysis, mapping, diffeomorphic | is used by: BICCN | Free, Freely available | SCR_022825 | 2026-08-29 11:28:59 | 0 | ||||||||||
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Pittsburgh Supercomputing Center Resource Report Resource Website 1+ mentions |
Pittsburgh Supercomputing Center (RRID:SCR_022823) | PSC | data or information resource, organization portal, portal | Joint computational research center with Carnegie Mellon University and University of Pittsburgh. Provides university, government and industrial researchers with access to several systems for high performance computing, communications and data storage available to scientists and engineers nationwide for unclassified research. | computational research center, high performance computing, communications and data storage, |
is used by: BICCN is related to: Carnegie Mellon University; Pennsylvania; USA is related to: University of Pittsburgh; Pennsylvania; USA |
open | SCR_022823 | 2026-08-29 11:29:04 | 2 | |||||||||
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SparkAn Resource Report Resource Website 1+ mentions |
SparkAn (RRID:SCR_022028) | data processing software, image analysis software, software application, software resource | Software tool for custom calcium imaging analysis. | custom software, calcium imaging analysis | Free, Freely available | SCR_022028 | 2026-08-29 11:28:58 | 5 |
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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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