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

Project related to distraction free behavioral acquisition. Provides imaging setup for distraction free behavioral acquisition with automated tracking using open source ImageJ software and workflow for extraction of behavioral endpoints of zebrafish. Used for online tracking of larval zebrafish at high framerates.Provides user interface to run experiments as well as flexible design to allow definition of arbitrary open- and closed- loop experiments.

Proper citation: ZebraTrack project (RRID:SCR_021429) Copy   

•   Source: SciCrunch Registry

https://github.com/BrettHewitt/ART

Software tool to automatically track rodent position and movement.Used to track head movements, body movements and also aspects of body size. It is able to identify certain behaviours from video footage too, such as rotations, moving forwards, interacting with objects and staying still.

Proper citation: Automated Rodent Tracker (RRID:SCR_021510) Copy   

•   Source: SciCrunch Registry

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

Project about synchronizing video and neural signals. Provides software Python toolbox for interactive characterization in neuroscience.Software tool used to review and annotate signal data synchronized with video, performs simple initial analyses including signal filtering and spike detection, supports variety of file formats.

Proper citation: neurotic project (RRID:SCR_021403) Copy   

•   Source: SciCrunch Registry

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

Project features single board real time input/output system including touch sensing joysticks to quantify mouse forelimb trajectories with micron millisecond spatiotemporal resolution, which resolves mouse forelimb kinematics and further allows extraction of primitives. Joystick increases spatial precision, and reduces displacement force. Joystick is then integrated into automated home cage system to train mice in center out reach task.

Proper citation: RodentJoystick (RRID:SCR_023482) Copy   

•   Source: SciCrunch Registry

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

Software tool to extract relevant features from images and use time series of these features to classify whether given behavior is present in each frame of video recording.machine learning pipeline for supervised behavior classification from raw pixels. Performs action recognition ,automated behavior classification, over frames. Used for automated behavior classification to detect and track behavior over time.

Proper citation: DeepEthogram (RRID:SCR_022355) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/mri-compatible-microdrive/

MRI compatible microdrive that can precisely position electrodes without causing significant imaging artifacts.

Proper citation: MRI Compatible Microdrive (RRID:SCR_022352) Copy   

•   Source: SciCrunch Registry

https://github.com/SunGL001/DeepBhvTracking

Software tool as novel tracking algorithm that combines deep learning and background subtraction.

Proper citation: DeepBhvTracking (RRID:SCR_022351) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/neonatal-stereotax/

3D printed device for stereotaxic viral delivery into brains of neonatal mice.Used for stable and precise stereotaxic surgery in neonatal mice.

Proper citation: Neonatal Stereotaxic Mouse Adaptor (RRID:SCR_022349) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/neuroethology-tools/

Software Matlab based tool to visualize and analyze multimodal datasets.

Proper citation: Behavior Ensemble and Neural Trajectory Observatory (RRID:SCR_022348) Copy   

•   Source: SciCrunch Registry

https://github.com/neuroethology/MARS_Developer

Software MARS based Python pipeline used for detection, pose estimation and behavior classification in experiments of any format. Repository contains all the code you'll need to train your own version of MARS.

Proper citation: MARS Developer (RRID:SCR_022346) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/led-matrix-stimuli/

Open source device consists of three LED matrices that can be independently controlled via open source Arduino Uno microcontroller. Matrices of LEDs are mounted above nose pokes to examine perceptual decision making in rats. Highly modifiable LED matrices for visual stimulus presentation in behavioral studies.Designs for printing these accessory devices are available in GitHub account for the project.

Proper citation: LED Matrix Stimuli (RRID:SCR_022345) Copy   

•   Source: SciCrunch Registry

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

Closed loop automated reaching apparatus for interrogating complex motor behaviors.Mechanical components include behavior box, series of cameras, and food pellet dispenser. Single workstation computer manages cameras, communicates with microcontroller, and analyzes mouse behavior in real time using modules extracted from DeepLabCut. Integrates fully automated, markerless kinematic tracking of multiple features to classify animal behavior and delivers neural stimulation based on behavioral outcomes. CLARA is compatible with advanced neurophysiological tools, enabling testing of neurostimulation devices and identification of novel neurological biomarkers.System fully automates trial initiation and pellet delivery and is capable of accurately delivering stimulation in response to trial outcome with short latency.

Proper citation: Closed Loop Automated Reaching Apparatus (RRID:SCR_022365) Copy   

•   Source: SciCrunch Registry

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

Software tool as single neural network model that learns how to segment spectrograms of birdsong into annotated syllables.

Proper citation: TweetyNet (RRID:SCR_022360) Copy   

•   Source: SciCrunch Registry

https://cellexplorer.org/

Open source framework for single cell characterization and visualization.Graphical user interface, standardized processing module and data structure for exploring and classifying single cells acquired using extracellular electrodes.

Proper citation: CellExplorer (RRID:SCR_022358) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/pycro-manager/

Open source software for customized and reproducible microscope control. Software Python package that enables control of micro-manager as well as development of customized experiments integrated with real-time image processing.

Proper citation: Pycro Manager (RRID:SCR_022356) Copy   

•   Source: SciCrunch Registry

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

Software tool as generalist algorithm for cell and nucleus segmentation.

Proper citation: Cellpose (RRID:SCR_022332) Copy   

•   Source: SciCrunch Registry

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

Non invasive, infrared activity and sleep measurement system that uses passive infrared sensors and Arduino microprocessor. Publication provides protocol for assembling COMPASS as well as provides support protocols and python scripts for data analysis, best practices for optimum results, troubleshooting, and alternative protocols for different use scenarios.

Proper citation: COMPASS (RRID:SCR_022329) Copy   

•   Source: SciCrunch Registry

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

Software Python package for visualizing and interacting with datasets registered to brain atlases. Used for visualization of neuroanatomical and morphological data.

Proper citation: Brainrender (RRID:SCR_022328) Copy   

•   Source: SciCrunch Registry

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

3D printed microdrive for electrophysiology and optophysiology. Consists of main body and head. Used for in vivo tetrode recording, optical imaging, and optogenetic manipulation in freely moving mice.Design files and build instructions for this device can be found on TetrODrive GitHub.Microdrive can be assembled in 15 min and price for all materials, including 3D printer, is lower than single commercial microdrive.

Proper citation: TetrODrive (RRID:SCR_022326) Copy   

•   Source: SciCrunch Registry

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

Open source system built around Arduino based microcontroller for analog and digital input and synchronization combined with custom printed circuit board. Hardware and Arduino-based firmware used to synchronize experimental and electrophysiological data.

Proper citation: Florida research open source synchronization tool (RRID:SCR_022344) Copy   

•   Source: SciCrunch Registry