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https://edspace.american.edu/openbehavior/project/mousemove/

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.

Proper citation: MouseMove project (RRID:SCR_021581) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/ratcave/

Portal provides open source, cross platform Python library that adds 3D stimulus support to all OpenGL based 2D Python stimulus libraries. Ratcave comes with resources including basic 3D object primitives and wide range of 3D light effects. Intuitive object oriented interface allows for all objects, which include meshes, lights, and cameras, can be repositioned, rotated, and scaled.

Proper citation: Ratcave project (RRID:SCR_021555) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/brainglobe/

Project is related to working with atlas data from multiple species on common platform.Provides collection of Python tools for working with atlas data from multiple species on common platform and for morphological analyses in systems neuroscience.

Proper citation: BrainGlobe project (RRID:SCR_021481) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/toolboxes-ephys-analysis/

Portal includes compared several toolboxes for spike and LFP analysis, connectivity analysis, dimensionality reduction, and generalized linear modeling. Discussion about major features of software available for Python and MATLAB including Brainstorm, Chronux, Elephant, FieldTrip, gramm, Spike Viewer, and SPIKY. They include succinct tables for assessing system and program requirements, quality of documentation and support, and data types accepted by each toolbox.

Proper citation: Toolboxes for Spike and LFP Analysis project (RRID:SCR_021478) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/scintillate/

Project related to time series calcium imaging evaluation and pre-processing. Included open source graphical viewer for time series calcium imaging evaluation and pre-processing is provided by Swedish University scientists .

Proper citation: Scintillate project (RRID:SCR_021479) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/self-grooming-mice/

Portal provides protocol that implements JAABA, open source machine learning based behavior detection system; motr, open-source mouse trajectory tracking software; and bonsai, open source system capable of streaming and recording video. Together they use these tools to process videos of mice performing grooming behaviors in variety of behavioral setups.

Proper citation: Automated Classification of Self-grooming in Mice project (RRID:SCR_021597) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/bonvision/

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.

Proper citation: BonVision project (RRID:SCR_021491) 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://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/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   

•   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://edspace.american.edu/openbehavior/project/cap-touch-sensor/

Project related to accurately counting and monitoring the behavior of organisms.Provides open source capacitive touch sensing system.Capacitive sensors are positioned to readily detect direct physical touches from rodent under investigation. Device,designed around capacitive touch sensor MPR121,accurately counts and monitors behavior of organisms.

Proper citation: Capactive Touch Sensor project (RRID:SCR_021486) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/finchscope/

Project related to fluorescent imaging. Provides single photon fluorescent imaging microscope systems. System includes modular in vivo all optical neurophysiology rigs with transparent hardware, and acquisition and analysis software.Provide designs for 3D printed, lightweight, wireless capable microscope and motorized commutator, designed for multi month monitoring neural activity of zebra finches while they sing their courtship songs. Adapted for rodents and birds such as canaries.

Proper citation: FinchScope project (RRID:SCR_021484) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/cMadan/stl-toolbox

Software toolbox for visualizing and quantifying movement from pre-recorded videos.Used for summarizing animal movement data as single image ( spectral time lapse algorithm) as well as automate analysis of animal movement data.

Proper citation: Quantifying Animal Movement from Pre-recorded Videos (RRID:SCR_021515) Copy   

•   Source: SciCrunch Registry

https://github.com/ikodvanj/ratPASTA/

Software package for processing and visualising data from startle experiments in rodents or experiments measuring grip strength in rodents.

Proper citation: Platform for Acoustic STArtle (RRID:SCR_021516) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/kscottz/SkinnerBox

Software tool for data logging and analysis.

Proper citation: Skinner Box (RRID:SCR_021514) Copy   

•   Source: SciCrunch Registry