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

Project to detect spatial navigation behavior in animals.Provides open source software for analyzing spatial navigation search strategies developed by University of British Columbia scientists.

Proper citation: Pathfinder project (RRID:SCR_021447) Copy   

•   Source: SciCrunch Registry

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

Project related to behavioral experiments.Provides software Python framework for running behavioral experiments designed by University of Oregon scientists.

Proper citation: AutoPilot project (RRID:SCR_021448) 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/wave-surfer/

Project related to neurophysiology data acquisition and analysis.Included open source software application for neurophysiology data acquisition and analysis is provided by Howard Hughes Medical Institute Janelia Research Campus scientists. Program is based in MatLab, and evolved from earlier open source software package called Ephus.

Proper citation: Wave Surfer project (RRID:SCR_021476) 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/caiman/

Project related to calcium imaging.Provides software library, CaImAn, for one and two-photon Calcium Imaging data Analysis.

Proper citation: Calcium Imaging data Analysis project (RRID:SCR_021477) 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/LaubachLab/MedParse

Software tool to read MedPC data into Python and Matlab. MedPC code for saving precise times of behavioral events and MatLab and Python functions to convert MedPC data into time event codes.

Proper citation: MedParse (RRID:SCR_021528) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/jonnew/Oat

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   

•   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/jpgill86/neurotic

Software Python toolbox for interactive characterization in neuroscience.Users can read in variety of file formats for neural data and video, which they can then process, filter, analyze, annotate and plot.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.Facilitates collaborations by using portable specification for loading and processing data and retrieving data files from online sources.App for Windows, macOS, and Linux to review and annotate electrophysiology data and simultaneously captured video.

Proper citation: neurotic (RRID:SCR_021406) Copy   

•   Source: SciCrunch Registry

https://github.com/olivierfriard/BORIS

Open source event logging software for video/audio coding and live observations.Multiplatform standalone program that allows user specific coding environment for computer based review of previously recorded videos or live observations.

Proper citation: Behavioral Observation Research Interactive Software (RRID:SCR_021509) Copy   

•   Source: SciCrunch Registry

https://github.com/lapphe/raspberry_rat

Software Python platform for recording, converting, and uploading videos to cloud and for performing scheduled video recordings. Repository also includes wiki section with comprehensive guide to setting up Raspberry Pis for this purpose. Raspberry Pis are often cheaper than camcorder and can produce HD video. They are also equipped with infrared camera, making them ideal for recordings of animals that are active in low light conditions.

Proper citation: Rasberry rat (RRID:SCR_023467) Copy   

•   Source: SciCrunch Registry

https://github.com/chenxinfeng4/ArControl

Software tool as Arduino UNO/Mega based, visual programming and real-time behavioral platform for neuroscience. It can run Go/No-Go, 2AFPC and Optogenetic stimulation tasks. Stand alone and intuitive Gaphical User Interface application.Part of ArControl system.

Proper citation: ArControl (RRID:SCR_021605) Copy   

•   Source: SciCrunch Registry

https://www.eneuro.org/content/10/5/ENEURO.0127-22.2023

Open source, adaptable tracking system for multiple rodents. Scalable and customizable system for tracking and behavior assessment consists of Raspberry Pi based video and RFID acquisition. Maximum of six rodents of any coat color can be tracked simultaneously in any user defined arena with few restrictions. For pose estimation and travel trajectory analysis, PyMouseTracks supports interfacing with open source packages such as DeepLabCut and Traja.

Proper citation: PyMouseTracks (RRID:SCR_024453) Copy   

•   Source: SciCrunch Registry

https://github.com/EwellNeuroLab?tab=repositories

Low cost platform for multianimal chronic Local Field Potential video monitoring with Graphical User Interface for seizure detection and behavioral scoring. Enables chronic monitoring of several animals simultaneously, synchronizes bilateral local field potential and video streams in real time, and parses recorded data into manageable file sizes. Hardware solution leverages Intan and Open Ephys acquisition systems and software solution is implemented in Bonsai. Data are synchronized and parsed in Bonsai, allowing for flexibility and scalability of up to 128 channels per animal. The use of Intan adapter board for LFP video recordings allows compatibility with large variety of recording devices. Custom made electrodes and cables were components for the chronic LFP recordings. Used as acquisition system for long term video neurophysiology recordings.

Proper citation: LFP Monitoring (RRID:SCR_024428) Copy   

•   Source: SciCrunch Registry

https://github.com/bkntr/brainways

Open source software that automatically registers coronal slices and quantifies fluorescent markers. Python based, AI registration algorithm for slice matching to the Waxholm rat atlas. Slice quantification can be trained on any atlas, which allows use for other subjects such as mice, zebrafish, and humans. AI-based software for registration and analysis of fluorescent markers on coronal brain slices.

Proper citation: Brainways (RRID:SCR_024402) Copy   

•   Source: SciCrunch Registry