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https://github.com/cihga39871/Atria
Open source software tool as adapter and quality trimmer for Next-Generation Sequence data.
Proper citation: Atria (RRID:SCR_021313) Copy
https://edspace.american.edu/openbehavior/project/actifield/
Project related to measuring locomotor activity.System includes infrared motion detection and arduino to record activity in variety of chamber set ups. Provides actimeter and software tool to measure and record locomotor activity.
Proper citation: Actifield project (RRID:SCR_021452) Copy
https://github.com/gordonberman/MotionMapper
Software tool to work on videos (not poses).Uses image analysis and multivariate statistical methods to find stereotyped behaviors in flies, mice, and other species.
Proper citation: MotionMapper (RRID:SCR_021384) Copy
https://github.com/YttriLab/B-SOID
Software pipeline that pairs unsupervised pattern recognition with supervised classification to achieve fast predictions of behaviors that are not predefined by users.Unsupervised learning algorithm that discovers and classifies actions based on inherent statistics of data points provided.
Proper citation: Behavioral Segmentation of Open-field in DeepLabCut (RRID:SCR_021385) Copy
Software tool as real time position tracker for behavioral research. Used for processing images, extracting object position information, and streaming data to disk and/or the network in real time.
Proper citation: Online Animal Tracker (RRID:SCR_021412) Copy
https://github.com/ngaggion/ChronoRoot
System which combines 3D printed open hardware with deep segmentation networks for high temporal resolution phenotyping of plant roots in agarized medium. Deep learning based root extraction method which leverages the latest advances in convolutional neural networks for image segmentation, and incorporates temporal consistency into the root system architecture reconstruction process.
Proper citation: ChronoRoot (RRID:SCR_021259) Copy
https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification
Software package as collection template and associated materials for SARS-CoV-2 metadata. Contains metadata collection template based on data standard designed to harmonize genomic surveillance contextual data (sample metadata, epidemiological/clinical/laboratory data, methods information) across datasets, laboratories and databases during pandemic, and beyond. Template contains standardized fields, terms and formats for structuring information, and is accompanied by field level reference guide which provides definitions, guidance and examples for populating fields. Fields have been prioritized using colour coding system as required (yellow), recommended (purple), and optional (white). Users can use as much or as little of specification as they wish, according to their needs, and need not share information unless permitted to do so. SOP and protocols for submitting to public repositories are also included.
Proper citation: Public Health Alliance for Genomic Epidemiology SARS-CoV-2 Contextual Data Specification (RRID:SCR_021378) Copy
https://edspace.american.edu/openbehavior/project/locowhisk/
Portable behavioural set up that incorporates both gait analysis (using pedobarograph) and whisker movements (using high speed video camera and infrared light source).Automatically records both whisker and gait information and provides added statistical tools to analyse data. LocoWhisk system includes ARTv2 software for simultaneous measurement of locomotion behaviours and whisker movements.
Proper citation: LocoWhisk project (RRID:SCR_021430) Copy
Software tool for fitting kinetic and equilibrium data based on numerical integration of rate equation from any model input user. Simulation and data-fitting software for research and education designed specifically for the field of chemical kinetics.
Proper citation: KinTek Explorer (RRID:SCR_021274) Copy
https://edspace.american.edu/openbehavior/project/2abt/
Project related to training mice on task that requires continued updating of action/outcome relationships. Behavioral project includes task protocol and corresponding build instructions.Open source behavioral box used to train mice on task that requires continued updating of action/outcome relationships. Permits investigation of motivated behavior that requires flexible relationships between sensory stimuli and motor action. Project provided by Harvard Medical School scientists.
Proper citation: Two Armed Bandit Task project (RRID:SCR_021483) Copy
Open source software tool as library for implementation of gradient boosting with various machine learning algorithms.Optimized distributed gradient boosting library designed to be highly efficient, flexible and portable.Supports regression, classification, ranking and user defined objectives.
Proper citation: XGBoost (RRID:SCR_021361) Copy
https://edspace.american.edu/openbehavior/project/ucla-miniscope/
Project related to fluorescence imaging to record neural activity in awake, freely behaving mice.Provided system is developed by UCLA scientists. Miniscope system includes Miniscope with single, flexible coaxial cable to carry power, control signals, and imaging data to open source Data Acquisition hardware and software. Open source miniature fluorescence microscope uses wide-field fluorescence imaging to record neural activity in awake, freely behaving mice.
Proper citation: UCLA Miniscope project (RRID:SCR_021480) Copy
https://github.com/MouseLand/facemap
Software toolbox for unsupervised video analysis of rodent behavior.Used for videographic processing of head fixed rodent behavior.
Proper citation: FaceMap (RRID:SCR_021513) Copy
Software tool as JavaScript 3D Library.Used to create and display animated 3D computer graphics on Web browser. Three.js scripts may be used in conjunction with HTML5 canvas element, SVG or WebGL.
Proper citation: three.js (RRID:SCR_021357) Copy
https://tomopy.readthedocs.io/en/1.5.2/ipynb/tomopy.html
Software tool for tomographic reconstruction.
Proper citation: Gridrec (RRID:SCR_021358) Copy
https://github.com/bonsai-rx/bonsai
Software tool as event based framework for processing and controlling data streams. Open source software tool as visual language for reactive programming.Used for composing reactive and asynchronous data streams coming from video cameras, microphones, electrophysiology systems or data acquisition boards.
Proper citation: Bonsai (RRID:SCR_021512) Copy
https://corybrunson.github.io/ggalluvial/
Software tool as ggplot2 extension for alluvial plots. Used to visualize frequency distributions over time or frequency tables involving several categorical variables. Requires user to specify dimensions, either as separate aesthetics or as key-value pairs, relies on separate layers (stats and geoms) to produce strata, alluvia, and alluvial segments called lodes and flows.
Proper citation: ggalluvial (RRID:SCR_021253) Copy
Software tool as macro for SPSS, SAS, and R that conducts observed variable mediation, moderation, and conditional process analysis.Observed variable OLS and logistic regression path analysis modeling tool. Used for estimating direct and indirect effects in single and multiple mediator models parallel and serial, two and three way interactions in moderation models along with simple slopes and regions of significance for probing interactions, and conditional indirect effects in moderated mediation models with single or multiple mediators or moderators. Operates on Windows and Mac versions of SPSS and SAS.
Proper citation: PROCESS (RRID:SCR_021369) Copy
https://pypi.org/project/fuzzywuzzy/
Software pacakge that uses Levenshtein Distance to calculate differences between sequences for string matching.
Proper citation: FuzzyWuzzy (RRID:SCR_021699) Copy
https://edspace.american.edu/openbehavior/project/chendoscope/
Portal provides open source Compact Head Mounted Endoscope for imaging in freely behaving mouse. Includes accessible and flexible set of calcium imaging tools for neuroscience research community.
Proper citation: CHEndoscope (RRID:SCR_021587) Copy
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