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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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larvalign Resource Report Resource Website 1+ mentions |
larvalign (RRID:SCR_015815) | data analysis software, data or information resource, data processing software, data set, sequence analysis software, software application, software resource, software toolkit | Software package including computational methods for aligning gene expression patterns from the larval brain of Drosophila melanogaster. Its method includes evaluation of the registration framework involved in template generation and mapping. | drosophila melanogaster, computational method, gene expression, alignment, larval brain, larvae, template generation, mapping, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download | biotools:larvalign | https://bio.tools/larvalign | SCR_015815 | SciCrunch Registry | 2026-11-07 11:58:29 | 1 | ||||||||
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CluePedia Cytoscape plugin Resource Report Resource Website 100+ mentions |
CluePedia Cytoscape plugin (RRID:SCR_015784) | data analysis software, data processing software, data visualization software, software application, software resource | Data analysis software and search tool for new markers potentially associated to pathways. CluePedia calculates linear and non-linear statistical dependencies from experimental data and investigates interrelations within each pathway to reveal associations through gene/protein/miRNA enrichments. | cytoscape, cluepedia, search tool, marker, pathway, experimental data, in silico data, linear dependence, gene, protein, miRNA | is a plug in for: Cytoscape | INCa ; Canceropole Ile de France ; INSERM ; MedImmune ; Qatar National Research Fund NPRP09-1174-3-291; European Commission 7FP Geninca 202230); LabEx Immuno-Oncology |
PMID:23325622 | Free for non-profits, Free for academic use, Available for download, Commercially available, Available for purchase | SCR_015784 | SciCrunch Registry | CluePedia: A ClueGO plugin, CluePedia: A ClueGO plugin for pathway insights using integrated experimental and in silico data | 2026-11-07 11:58:32 | 193 | |||||||
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Flowing Software 2.5.1 Resource Report Resource Website 100+ mentions |
Flowing Software 2.5.1 (RRID:SCR_015781) | data analysis software, data processing software, software application, software resource | Software for flow cytometry data analysis. Flowing Software has many common analysis tools, such as dot plots, histograms, quadrants, statistics, overlay histograms etc. | cytometry, flow cytometry, flow cytometry data, data analysis, box plot, histogram, quadrant, statistic, overlay histogram | Free, Available for download | http://www.flowingsoftware.com/, https://en.freedownloadmanager.org/users-choice/Flowing_Software_2.5.1.html | SCR_015781 | SciCrunch Registry | Flowing Software | 2026-11-07 11:58:28 | 134 | |||||||||
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BICCN Resource Report Resource Website 100+ mentions |
BICCN (RRID:SCR_015820) | BICCN | consortium, data or information resource, organization portal, portal | Consortium for the cell census in the brain. Integrated network of data generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate brains. | cell census, neuroscience, brain, brain initiative cell census network, whole mouse brain, |
uses: QuickNII uses: HistoloZee uses: CellLocator uses: Semi-Manual Alignment to Reference Templates uses: LoomPy uses: Cytosplore Viewer uses: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) uses: Blue Brain Cell Atlas uses: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas uses: Hippocampome.org uses: Neuron Phenotype Ontology uses: Brain Image Library uses: Distributed Archives for Neurophysiology Data Integration uses: NeuroMorpho.Org uses: Azimuth uses: Brain Observatory Storage Service and Database (BossDB) uses: Optimus Pipeline uses: scATAC Pipeline uses: Smart-seq2 Single Nucleus Multi Sample Pipeline uses: CEMBA MethylC Seq Pipeline uses: Brain Architecture Project uses: Single Cell Portal uses: MorphoHub uses: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas uses: Mouse Connectome Project uses: Allen Mouse Brain Reference Atlas uses: Allen Mouse Brain Common Coordinate Framework uses: Allen Human Reference Atlas, 3D, 2020 uses: NeMO Analytics uses: ANTS - Advanced Normalization ToolS uses: CloudReg uses: Brainome portal uses: CATlas uses: MetaNeighbor uses: Cell Annotation Platform uses: cellxgene uses: Neuroglancer uses: Vaa3D uses: QuickNII and VisuAlign uses: Hi5App uses: CloudVolume uses: neuroXiv uses: Brain Data Standards Ontology uses: Pittsburgh Supercomputing Center uses: Molecular Biosensor and Imaging Center uses: Generative Diffeomorphic Mapping uses: NIH NeuroBioBank uses: NeMOarchive lists: ccf_streamlines is related to: Mouse Connectome Project is related to: BarensLab Mini-Atlas is related to: Cumulus is related to: Pegasus is related to: Cirrocumulus is related to: Gene functional conservation across cell types and species is related to: BRAIN Initiative Cell Atlas Network is related to: ATAC Pipeline is related to: Slide-seq Pipeline is related to: Brain Knowledge Platform has parent organization: Allen Institute has parent organization: Allen Institute for Brain Science provides: mBrainAligner provides: BICCN Cell Registry provides: Cell Type Knowledge Explorer provides: Epiviz has organization facet: BICCN Anatomy and Morphology Project has organization facet: Cell Type Knowledge Explorer has organization facet: mBrainAligner has organization facet: Terra has organization facet: Allen Brain Cell Atlas has organization facet: Multiome Pipeline has organization facet: Allen Software Development Kit has organization facet: BICCN Imaging and analysis Techniques to Construct Cell Census Atlas of Human Brain has organization facet: Allen Brain Map BICCN Data Catalog has organization facet: snm3C Pipeline has organization facet: Paired-Tag Pipeline has organization facet: BuildIndices has organization facet: MapMyCells has organization facet: Smart-seq2 Multi-Sample Pipeline |
NIMH U19 MH114821; NIMH U19 MH114830; NIMH U19 MH114831 |
PMID:37390046 | Restricted | SCR_017266 | SCR_015820 | SciCrunch Registry | BICCN 2.0, BRAIN Initiative Cell Census Network, BRAIN Initiative Cell Census Network (BICCN) | 2026-11-07 11:58:16 | 234 | |||||
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Piggy Resource Report Resource Website 10+ mentions |
Piggy (RRID:SCR_015941) | data analysis software, data processing software, software application, software resource | Pipeline for analyzing intergenic regions in bacteria. It is designed to be used in conjunction with Roary (https://github.com/sanger-pathogens/Roary). | intergenic, region, bacterial, analysis, gene, genome, assembly | Medical Research Council | Free, Available for download | SCR_015941 | SciCrunch Registry | 2026-11-07 11:58:30 | 32 | ||||||||||
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Feeding Experimentation Device project Resource Report Resource Website 1+ mentions |
Feeding Experimentation Device project (RRID:SCR_015942) | FED | data or information resource, portal, topical portal | Flexible open-source device for measuring feeding behavior. FED measures food intake in mice. It is battery powered and designed to be used in rodent colony caging.Home cage-compatible feeding system that measures food intake with high accuracy and temporal resolution. FED offers alternative to commercial feeders, with convenience of use in tradition colony rack caging. | Feeding, food intake, optogenetic, behavioral data analysis, data analysis software, behavior apparatus, behavior rig, reward delivery, behavior measurement, homecage, Instrument, OpenBehavior |
is listed by: OpenBehavior has parent organization: Washington University in St. Louis; Missouri; USA |
NIH | PMID:27060385 | Commercially available | https://github.com/KravitzLab/FED1, https://edspace.american.edu/openbehavior/project/feeding-experimentation-device/, https://hackaday.io/project/72964-feeding-experimentation-device-fed-20 | SCR_015942 | SciCrunch Registry | , FED1, FED2, Feeding Experimentation Device system, Feeding Experimentation Device | 2026-11-07 11:58:36 | 1 | |||||
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BeatBox Resource Report Resource Website 10+ mentions |
BeatBox (RRID:SCR_015780) | simulation software, software application, software resource | Simulation environment that combines flexible script language user interface with computational tools in order to setup cardiac electrophysiology in-silico experiments without re-coding at low-level. It aims to include cell excitation, tissue/anatomy models, and stimulation protocols in BeatBox scripts so that simulation run either sequentially or in parallel (MPI) without re-compilation. | simulation, cardiac electrophysiology, computation, script language, c, ecg, heart, cardiology, simulation protocol | EPSRC EP/I029664; EPSRC EP/N014391/1; EPSRC EP/P008690/1 |
PMID:28467407 | Free, Available for download | https://github.com/beatbox-heart/beatbox-public/tree/v1.7.982 | SCR_015780 | SciCrunch Registry | BeatBox—HPC simulation environment for biophysically and anatomically realistic cardiac electrophysiology. | 2026-11-07 11:58:15 | 11 | |||||||
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BioVoxxel Toolbox Resource Report Resource Website 10+ mentions |
BioVoxxel Toolbox (RRID:SCR_015825) | data processing software, image analysis software, software application, software resource, software toolkit | Software toolkit for analyzing tool for microscopic images. It contains plugins and some macros dealing with image filtering, image segmentation and binary image processing and analysis. | microscopic image analysis, image filtering, image segmentation, binary processing, binary analysis, particle analysis |
is related to: ImageJ is a plug in for: ImageJ is a plug in for: Fiji/ImageJ is a plug in for: Fiji |
Free, Available for download | https://imagej.net/BioVoxxel_Toolbox, https://github.com/biovoxxel/BioVoxxel_Toolbox | SCR_015825 | SciCrunch Registry | BioVoxxel, BioVoxxel Toolbox (ImageJ/Fiji) | 2026-11-07 11:58:16 | 33 | ||||||||
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DiPDE Resource Report Resource Website 1+ mentions |
DiPDE (RRID:SCR_015822) | data analysis software, data processing software, simulation software, software application, software resource, source code | Simulation platform for numerically solving the time evolution of coupled networks of neuronal populations. DiPDE can facilitate the fast exploration of mesoscale (population-level) network topologies, where large populations of neurons are treated as homogeneous with random fine-scale connectivity. | simulation, time evolution, coupled network, neuron population, neural network, mesoscale network topology, fine-scale connectivity | Allen Institute for Brain Science | Free, Available for download | https://github.com/AllenInstitute/dipde | SCR_015822 | SciCrunch Registry | DiPDE (Integro-partial differential equation with displacement), dipde | 2026-11-07 11:58:33 | 3 | ||||||||
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Bpod Resource Report Resource Website 10+ mentions |
Bpod (RRID:SCR_015943) | software resource | Software for a measurement and control system for behavior research, most often used to implement operant (Go/NoGo, 2AFC) tasks. This software controls a hierarchy of hardware modules, each powered by an Arduino-programmable microcontroller. | sanworks, rodent, behavior, experiment, control, software, hardware, arduino, measurement | is listed by: OpenBehavior | Open source, Free, Available for download | https://github.com/sanworks/Bpod | SCR_015943 | SciCrunch Registry | 2026-11-07 11:58:07 | 42 | |||||||||
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FiberApp Resource Report Resource Website 10+ mentions |
FiberApp (RRID:SCR_015826) | data analysis software, data processing software, software application, software resource | Software for tracking and analysis based on algorithms describing structural and topological features of fiber-like objects. The program operates on images from any microscopic source (atomic force or transmission electron microscopy, optical, fluorescence, confocal, etc.), acquiring the spatial coordinates of objects. | semiflexible polymer, neurodegenerative disease, fiber-like object, topography, tracking, analysis, microscopic image analysis | Swiss National Science Foundation SNF 2-77002-11 | Open source, Available for download | SCR_015826 | SciCrunch Registry | FiberApp: An Open-Source Software for Tracking and Analyzing Polymers, Biomacromolecules, Filaments, and Fibrous Objects | 2026-11-07 11:58:29 | 28 | |||||||||
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LI-COR Image Studio Software Resource Report Resource Website 100+ mentions |
LI-COR Image Studio Software (RRID:SCR_015795) | data acquisition software, data processing software, image analysis software, software application, software resource | Image analysis software that acquires, analyzes, and archives research data without altering raw findings. It integrates data and changes how pixels are mapped to the screen for clearer display, rather than altering the pixels of the image data itself. | image studio, image analysis, raw data, image acquisition, pixel mapping, image viewer | Commercially available, Available for purchase, Free version available, Runs on Windows, Runs on MAC OS | https://www.licor.com/bio/products/software/image_studio | SCR_015795 | SciCrunch Registry | LI-COR Image Studio, Image Studio™ Software | 2026-11-07 11:58:29 | 223 | |||||||||
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Sigma: Millicell Cell Culture Inserts Resource Report Resource Website 10+ mentions |
Sigma: Millicell Cell Culture Inserts (RRID:SCR_015799) | instrument resource | Equipment that provides physical support for cell cultures. These cell culture inserts feature attachment and suspension cells that can access media from both their apical and basolateral sides. | cell culture, culture insert, hardware, attachment, suspension cell, apical side, basolateral side, instrument, equipment | Commercially available, Available for purchase | https://drive.google.com/file/d/1iKvbwq8VXv1PtD0ItetDiDk8tUv0RwlR/view?usp=drivesdk | https://www.emdmillipore.com/US/en/product/Millicell-Cell-Culture-Inserts, MM_NF-C10504?amp%3Bbd=1&bd=1#documentation | http://www.merckmillipore.com/ES/es/product/Millicell-Cell-Culture-Inserts, MM_NF-C10504?ReferrerURL=https%3A%2F%2Fwww.google.es%2F&bd=1 | SCR_015799 | SciCrunch Registry | Millicell® Cell Culture Inserts | 2026-11-07 11:58:29 | 10 | |||||||
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Adobe Audition Resource Report Resource Website 1+ mentions |
Adobe Audition (RRID:SCR_015796) | authoring tool, data analysis software, data processing software, software application, software resource, software toolkit | Software for sound analysis, audio editing, and audio recording. It features multitrack, waveform, and spectral display for creating, mixing, editing, and restoring audio content for research or non-research purposes. | audio, editing, recording, sound analysis, audio analysis, audio editing, adobe | Commercially available, Available for purchase | SCR_015796 | SciCrunch Registry | Adobe Audition CC | 2026-11-07 11:58:32 | 8 | ||||||||||
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NAPR: Neuroanatomical Age Prediction using R Resource Report Resource Website 1+ mentions |
NAPR: Neuroanatomical Age Prediction using R (RRID:SCR_015759) | NAPR | data repository, service resource, storage service resource | Cloud-based framework that allows users to estimate the age of individual subjects using cortical thickness maps derived from their own locally processed T1-weighted whole brain MRI scans. The provided age prediction models were trained using (i) relevance vector machines and (ii) Gaussian processes machine learning methods applied to cortical thickness surfaces obtained using Freesurfer v5.3. | neuroanatomy, prediction, r, neuroimaging, mri scan, cortical thickness, relevance vector | DOI:10.1101/099309 | Free, Available for download | http://www.cloudneuro.org/ | SCR_015759 | SciCrunch Registry | Neuroanatomical Age Prediction using R | 2026-11-07 11:58:15 | 1 | |||||||
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Real time localization system for autonomous robots Benchmark Dataset Resource Report Resource Website |
Real time localization system for autonomous robots Benchmark Dataset (RRID:SCR_015756) | Dataset that can be used to analyze cyber-attacks to an indoor real time localization system for autonomous robots. Data have been gathered in an indoor mock-up apartment using an autonomous robot with an on-board Real Time Location System (RTLS). | benchmark, neural network, machine learning, autonomous robot, real time location system, rtls, training data, cyber-attack | is related to: Range-based people tracker classifiers Benchmark Dataset | Freely available, Available for download | SCR_015756 | SciCrunch Registry | Benchmark dataset for analysis of cyber-attacks to an indoor real time localization system for autonomous robots | 2026-11-07 11:58:31 | 0 | ||||||||||
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Brain-CODE Resource Report Resource Website 10+ mentions |
Brain-CODE (RRID:SCR_015877) | data repository, service resource, storage service resource | Brain-CODE is a large-scale informatics platform that manages the acquisition and storage of multidimensional data collected from participants with a variety of brain disorders. | informatics, data storage, brain disorder | brain disorder, neurological disorder, informatics platform, data repository, data storage service, neuroscience | Public, Freely available, The research community can contribute to this resource | r3d100012181 | https://doi.org/10.17616/R3CK9G | SCR_015877 | SciCrunch Registry | 2026-11-07 11:58:29 | 49 | ||||||||
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Emory Epithelial Pathobiology Research Development Center Resource Report Resource Website |
Emory Epithelial Pathobiology Research Development Center (RRID:SCR_015916) | data or information resource, disease-related portal, organizational portal, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th,2023. Center for pathobiology research development. | pathobiology, research, development | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015916 | SciCrunch Registry | 2026-11-07 11:58:07 | 0 | |||||||||||
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Antha Resource Report Resource Website |
Antha (RRID:SCR_015761) | software resource | Software language for methods to simplify protocols into reusable components that can be exchanged or removed to produce simple, reproducible, and scalable workflows. It allows users to develop, execute, and analyse biological experiments faster, while also introducing standardization and modularity to bioengineering. | software language, programming language, method, protocol, bioengineering, standardization, robot, robotics software | Freely available | https://github.com/antha-lang/antha | SCR_015761 | SciCrunch Registry | Synthace Antha | 2026-11-07 11:58:31 | 0 | |||||||||
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MetaNetX Resource Report Resource Website 50+ mentions |
MetaNetX (RRID:SCR_015882) | data access protocol, software resource, web service | Web application to perform automated model construction and genome annotation for large-scale metabolic networks. Platform for accessing, analyzing and manipulating genome-scale metabolic networks (GSM) as well as biochemical pathways. | automated model construction, genome annotation, model, construction, genome, annotation, metabolic network, repository, gsm, biochemical, pathway | SIB Swiss Institute of Bioinformatics ; Swiss Federal Government ; Swiss National Science Foundation |
PMID:26527720 PMID:23357920 PMID:23172809 |
Free, Freely available | SCR_015882 | SciCrunch Registry | MNXref, MetaNetX: Automated Model Construction and Genome Annotation for Large-Scale Metabolic Networks | 2026-11-07 11:58:30 | 94 |
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