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

Project related to videographic processing of head fixed rodent behaviors. Provides software toolbox for unsupervised video analysis of rodent behavior.

Proper citation: FaceMap project (RRID:SCR_021428) Copy   

•   Source: SciCrunch Registry

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://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/deepfly3d/

Project related to deep learning based pose estimator for studying how neural circuits control limbed behaviors in tethered Drosophila. Includes Deep Fly image annotation tool for pose estimation and to permit further correction of 2D pose estimates, which are automatically converted to 3D pose.

Proper citation: DeepFly3D project (RRID:SCR_021400) 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/spikeforest/

Project related to neural data analysis. Provides 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 project (RRID:SCR_021472) Copy   

•   Source: SciCrunch Registry

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

Project related to preprocessing of images. Provieds software Python tool to processes raw macaque fMRI images using algorithms embedded in automatic pipeline.

Proper citation: Pypreclin project (RRID:SCR_021473) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/mne-scan/

Project related to real time acquisition and processing of electrophysiological data.Provides software tool for acquisition and processing of electrophysiological data.

Proper citation: MNE Scan project (RRID:SCR_021470) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/3dtracker/, http://www.3dtracker.org/

Project related to markerless computerized behavioral analysis for laboratory animals.Provides open source 3D video based behavioral analysis system for neuroscience. System includes open source software tool for 3D-video based markerless computerized behavioral analysis.

Proper citation: 3DTracker project (RRID:SCR_021440) Copy   

•   Source: SciCrunch Registry

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

Project related to animal behavior in complex mazes.Provides software MATLAB package for linearization of place fields in complex mazes.

Proper citation: LinCoM project (RRID:SCR_021438) Copy   

•   Source: SciCrunch Registry

https://github.com/oculomatic/oculomatic-release

Software tool for high speed eye tracking for Point Gray USB3.0 cameras.Oculomatic software tracks eye position within acquired image frame at frame rate dictated by image sensor.

Proper citation: Oculomatic (RRID:SCR_021525) 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://www.dropbox.com/s/wx7aicjh4is81om/HomeCageForelimbTask.py?dl=0

Software Python tool running on Raspberry Pi computer. Used for trial timing and data logging. Part of Autonomous Training of Forelimb Motor Task system.

Proper citation: Autonomous Training of a Forelimb Motor Task (RRID:SCR_021603) Copy   

•   Source: SciCrunch Registry

https://github.com/mauriciowr/OBAT

Software tool as part of Operant Box for Auditory Tasks system.

Proper citation: Operant Box for Auditory Tasks (RRID:SCR_021604) Copy   

•   Source: SciCrunch Registry

https://github.com/PTMonteiro/GoFish_Ajuwon_etal_2022

Bonsai code for running GOFish platform for behavioural experiments in fish.

Proper citation: GoFish Ajuwon etal 2022 (RRID:SCR_022511) Copy   

•   Source: SciCrunch Registry

https://github.com/mmgxw3/pipetteFindingCNN

Software application for convolutional neural network that assesses pipette positioning before patch clamp is begun to minimize patch clamping errors in electrophysiology experiments. Used for detecting pipette positioning and making patch clamping procedures.

Proper citation: Pipette Finding CNN (RRID:SCR_024992) Copy   

•   Source: SciCrunch Registry

https://github.com/ZuAh/Custom-fitting-of-implants

Tutorial to custom-design and -fit implants to continuous and discontinuous skull surfaces. Universal Guide for Skull Extraction and Custom-Fitting of Implants to Continuous and Discontinuous Skulls.

Proper citation: Custom-fitting-of-implants (RRID:SCR_025270) Copy   

•   Source: SciCrunch Registry

https://github.com/MaSoMoTr/MaSoMoTr

Markerless video-based tool to simultaneously track two interacting mice of the same appearance in controlled settings for quantifying behaviors such as different types of sniffing, touching, and locomotion to improve tracking accuracy under these settings without increased human effort. It incorporates conventional handcrafted tracking and deep-learning-based techniques. The tool is trained on small number of manually annotated images from basic experimental setup and outputs body masks and coordinates of the snout and tail-base for each mouse.

Proper citation: Markerless Mouse Tracking for Social Experiments (RRID:SCR_025368) Copy   

•   Source: SciCrunch Registry

https://github.com/AdaptiveMotorControlLab/Camera_Control

Open source software package that allows video to be recorded in sync with behavior. Python GUI and scripts allows investigators to record from multiple imaging source camera feeds with associated timestamps for each frame. Python API to record video system timestamps from Imaging Source USB cameras. Package requires Windows 10, Anaconda, and Git, and is compatible with Imaging Source USB3 cameras. Part of Camera Control project.

Proper citation: Camera Control (RRID:SCR_021614) Copy   

•   Source: SciCrunch Registry

https://github.com/jellen44/AutomaticSleepScoringTool

Software pipeline for sleep researchers to perform automatic sleep scoring for rodents. Artificial neural network for automated behavioral state classification in rats.

Proper citation: AutomaticSleepScoringTool (RRID:SCR_022300) Copy   

•   Source: SciCrunch Registry