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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://edspace.american.edu/openbehavior/project/nose-poke-device/
Portal provides arduino based, 3D-printed nose poke device for rats. Includes set of instructions on how to build this device using arduino, some 3D printed parts and some off-the-shelf electronic components.
Proper citation: Nose Poke Device (RRID:SCR_021568) Copy
https://github.com/strawlab/freemovr_engine
Software tool as virtual reality engine built on ROS and OpenSceneGraph.Perspective correct Virtual Reality for freely moving animals engine. Used for multicomputer realtime tracking and display with goal of being useful for scientific studies of vision and behavior.Part of FreemoVR system.
Proper citation: FreemoVR (RRID:SCR_021601) Copy
https://github.com/HanLabBU/micro-control-final
Teensy microcontroller based interface for optical imaging camera control during behavioral experiments.
Proper citation: Teensy-Based Interface (RRID:SCR_021602) Copy
https://edspace.american.edu/openbehavior/project/syringe-pump/
Open source syringe pump apparatus developed by scientists from Michigan Technological University. Syringe pump is designed using freely available open source computer aided design (CAD) software and manufactured using open source RepRap 3-D printer and readily available parts.
Proper citation: Pearce Lab Syringe Pump project (RRID:SCR_021566) Copy
https://github.com/FlySorterLLC
Software tool to automate various fly handling tasks.Control software for Drosophila handling robot MAPLE.
Proper citation: Modular Automated Platform for Large Scale Experiments (RRID:SCR_021600) Copy
https://edspace.american.edu/openbehavior/project/operant-box-auditory-tasks-obat/
Portal provides operant box designed to train small primates in auditory tasks.Device is based on computer and Arduino Mega 2560 board, named OBAT (Operant Box for Auditory Tasks), designed to present two different auditory stimuli to small primates.All schematics and software source code are available.
Proper citation: Operant Box for Auditory Tasks project (RRID:SCR_021564) Copy
https://edspace.american.edu/openbehavior/project/robucket/
Portal for open source operant chamber, based on Arduino microcontroller platform, that can be used to train mice to respond for reward. Designed by NIDDK scientists.Apparatus contains two nose pokes, drinking well, and solenoid controlled sucrose delivery system. Chamber can run magazine training, fixed ratio and progressive ratio training schedules, and can be programmed to run more complicated behavioral paradigms.
Proper citation: Rodent Operant Bucket project (RRID:SCR_021565) Copy
https://github.com/amchagas/poke_device_arduino
Software tool as script to test if IR led, IR photodiode, arduino and 3D printed nose poke device work properly. Part of Nose Poke Device system.
Proper citation: poke device arduino (RRID:SCR_021608) Copy
https://github.com/delcasso/hope
Softwre tool as part of Hybrid-drive combining Optogenetics, Pharmacology, and Electrophysiology project for brain implant.
Proper citation: Hybrid-drive combining Optogenetics, Pharmacology, and Electrophysiology (RRID:SCR_021606) Copy
https://github.com/bioinfo-biols/CIRIquant
Software Python package for accurate circRNA quantification and differential expression analysis. Comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data. Accurate quantification of circular RNAs identifies extensive circular isoform switching events.
Proper citation: CIRIquant (RRID:SCR_021661) Copy
https://github.com/kostkalab/scds
Software R package for computational doublet annotation of single cell RNA sequencing data. Software tool for in silico identification of doublets in scRNA-seq data.
Proper citation: Single Cell Doublet Scoring (RRID:SCR_021541) Copy
https://www.nanostring.com/products/geomx-digital-spatial-profiler/geomx-dsp-overview/
Integrated commercial system comprising hardware, software and nCounter chemistry that enables simultaneous, highly multiplex spatial profiling of proteins or RNA in FFPE tissues. DSP platform quantifies abundance of protein or RNA by counting unique indexing oligonucleotides assigned to each target of interest. Used to rapidly and quantitatively assess biological implications of heterogeneity within tissue samples.
Proper citation: NanoString: GeoMx Digital Spatial Profiler (RRID:SCR_021660) Copy
https://meyerinst.com/library/NanoZoomer_RS_Brochure_Catalog.pdf
High speed, high resolution digital scanner with network features. User friendly full slide scanner designed to process up to 210 slides automatically.
Proper citation: Hamamatsu: NanoZoomer 2.0-HT (RRID:SCR_021658) Copy
https://pypi.org/project/ontquery/
Software tool as framework querying ontology terms within SciCrunch and SciCrunch SciGraph endpoints.
Proper citation: ontquery (RRID:SCR_021659) Copy
Public university in Florianópolis, the capital city of Santa Catarina in southern Brazil.
Proper citation: Federal University of Santa Catarina; Santa Catarina; Brazil (RRID:SCR_021535) Copy
System includes automated cell counter for trypan blue viability for cell lines and bright field imaging and pattern recognition software to quickly and accurately identify and count individual cells. Cell count, concentration, diameter, and % viability are automatically calculated and reported.
Proper citation: McKinley: Cellometer Auto T4 (RRID:SCR_021656) Copy
https://github.com/flatironinstitute/CaImAn
Open source software tool for scalable calcium imaging data analysis. Used for large scale calcium imaging analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
Proper citation: Calcium Imaging data Analysis (RRID:SCR_021533) Copy
https://hackaday.io/project/181604-mri-stereoscope
Project provides miniature mirror stereoscope system for MRI-scanner. System takes advantage of commonly used display equipment, MRI head coil, and display screen. Miniature Wheatstone stereoscope is used for human neuroimaging.
Proper citation: MRI-stereoscope project (RRID:SCR_021655) Copy
https://spikeforest.flatironinstitute.org/about
Open source and reproducible software suite that benchmarks performance of automated spike sorting algorithms across extensive, curated database of ground truth electrophysiological recordings, displaying results interactively on continuously updating website.
Proper citation: Spike Forest (RRID:SCR_021532) Copy
https://edspace.american.edu/openbehavior/project/openfeeder/
Project related to studying reward and feeding behavior. Provides open source automatic feeding system that can be customized for food types from seeds to pellets.System integrates plexiglass tubes, Arduino Uno, motor driver, and piezo sensor to reliably deliver accurate amounts of food, and can also be built using 3D printed parts.
Proper citation: OpenFeeder (RRID:SCR_021552) Copy
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