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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://ufsc.br/

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   

•   Source: SciCrunch Registry

https://www.nexcelom.com/nexcelom-products/automated-cell-counters/cellometer-auto-t4-automated-cell-counter/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/tonebox-system-automated-auditory-operant-conditioning/

Project related to auditory behavioral task data collection.Provided high throughput operant conditioning in mouse homecage system was developed by University of Maryland,College Park, scientists.Automated system for training up to hundreds of mice in auditory behavioral task features custom Matlab GUI running on desktop which connects to Raspberry Pi to administer auditory stimuli from USB soundcard and collects auditory data as well as licking data from water spout with commercially available capacitive sensors. Parts list and build instructions are readily available from paper and associated GitHub repository.

Proper citation: ToneBox (RRID:SCR_021548) Copy   

•   Source: SciCrunch Registry

https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md

Software tool for accurate, fast and versatile mapping/quantification of single cell and single nucleus RNA-seq data. Used for mapping, demultiplexing and quantification for single cell RNA-seq. Comprehensive turnkey solution for quantifying gene expression in single-cell/nucleus RNA-seq data, built into RNA-seq aligner STAR.

Proper citation: STARsolo (RRID:SCR_021542) Copy   

•   Source: SciCrunch Registry

https://circexplorer2.readthedocs.io/en/latest/

Software package for comprehensive and integrative circular RNA analysis. It is the successor of CIRCexplorer with plenty of new features to facilitate circular RNA identification and characterization. Used to annotate circRNAs, de novo assemble novel circular RNA transcripts and chracterize various of alternative (back-)splicing events of circular RNAs.

Proper citation: CIRCexplorer2 (RRID:SCR_021664) Copy   

•   Source: SciCrunch Registry

https://github.com/ratcave/ratcave

Software 3D graphics python package for cognitive psychology experiments. Open source, cross platform Python library that adds 3D stimulus support to all OpenGL-based 2D Python stimulus libraries. These libraries include VisionEgg, Psychopy, Pyglet, and PyGam.

Proper citation: Ratcave (RRID:SCR_021599) Copy   

•   Source: SciCrunch Registry

https://sourcemd.toolforge.org/index_old.php

Web tool as prototype service to automatically generate Wikidata items using metadata from scholarly publications. Citation lookup tool in Wikipedia platform. Takes persistent identifier for scholarly article and processes it by importing bibliographic metadata into Wikidata items. In August 2018, it was merged with ORCIDator into single tool that allows for fully automated batch processing based on ISBN-13, DOI, ORCID iD, PubMed ID, PMCID identifiers.

Proper citation: SourceMD (RRID:SCR_021633) Copy   

•   Source: SciCrunch Registry

https://github.com/mne-tools/mne-cpp

Software tool for real time processing of electrophysiological data.

Proper citation: MNE Scan (RRID:SCR_021530) Copy   

•   Source: SciCrunch Registry

https://services.healthtech.dtu.dk/service.php?NetMHC-4.0

Web tool for binding prediction of peptides to MHC class I molecules. The newest version NetMHC- 4.0 is used for prediction of peptide MHC class I binding affinity using gapped sequence alignment that allows insertions and deletions in alignment.

Proper citation: NetMHC (RRID:SCR_021651) Copy   

•   Source: SciCrunch Registry