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https://www.eneuro.org/content/9/5/ENEURO.0099-22.2022

Open source modular apparatus to produce guide cannulas exploiting 3D printing technology. Step by step procedure to realize hippocampal guide cannulas. 3D-printed guide cannula implant, as well as rotary tool based cutting station for fabrication of cannulae. Useful to conduct research in all the fields where access to brain areas is needed.

Proper citation: Customized Guide Cannulas (RRID:SCR_023941) 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
  

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://www.eneuro.org/content/10/8/ENEURO.0212-23.2023

Simple, lightweight, and low cost customizable multielectrode array for Local Field Potential recordings. Used to collect LFP data from different brain regions simultaneously in rats. Can be modified to record single unit and multiunit activity in addition to LFP activity using both wired and wireless neural data acquisition systems.

Proper citation: Customizable Multielectrode Array (RRID:SCR_024551) 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/danbider/lightning-pose

Software video centric package for direct video manipulation. Semi supervised animal pose estimation algorithm, Bayesian post processing approach and deep learning package. Improved animal pose estimation via semi-supervised learning, Bayesian ensembling, and cloud-native open-source tools.

Proper citation: Lightning Pose (RRID:SCR_024480) Copy   

•   Source: SciCrunch Registry
  

https://edspace.american.edu/openbehavior/project/eco-hab/

Portal provides open source, RFID-based system for automated measurement and analysis of social preference and in-cohort sociability in mice. System was developed by Nencki Institute of Experimental Biology scientists.

Proper citation: Eco-HAB (RRID:SCR_021588) Copy   

•   Source: SciCrunch Registry
  

https://github.com/KravitzLab/fed/wiki

Flexible open-source device for measuring feeding behavior. FED measures food intake in mice. It is battery powered and designed to be used in rodent colony caging.Home cage-compatible feeding system that measures food intake with high accuracy and temporal resolution. FED offers alternative to commercial feeders, with convenience of use in tradition colony rack caging.

Proper citation: Feeding Experimentation Device project (RRID:SCR_015942) Copy   

•   Source: SciCrunch Registry
  

https://github.com/sanworks

Software for a measurement and control system for behavior research, most often used to implement operant (Go/NoGo, 2AFC) tasks. This software controls a hierarchy of hardware modules, each powered by an Arduino-programmable microcontroller.

Proper citation: Bpod (RRID:SCR_015943) Copy   

•   Source: SciCrunch Registry
  

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

Project related to individual mice positions analysis, specifically their nose positions. Includes software tool for analysis of mouse position data designed by Hebrew University scientists. Provides open source software to analyze positions of individual mice, specifically their nose positions, in behavioral arena with the goal of minimizing error.

Proper citation: Optimouse project (RRID:SCR_021463) Copy   

•   Source: SciCrunch Registry
  

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

Project related to mouse tracking and analysis of mouse movements during computerized lab experiments. Provides open source software plugin to record and analyze mouse movements.

Proper citation: Mousetrap project (RRID:SCR_021456) Copy   

•   Source: SciCrunch Registry
  

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

Project related to saving precise times of behavioral events.Provides software tool to read MedPC data into Python and Matlab.

Proper citation: MedParse project (RRID:SCR_021455) Copy   

•   Source: SciCrunch Registry
  

https://edspace.american.edu/openbehavior/project/offline-behavior-video-analysis/

Project related to visualizing and quantifying movement from pre-recorded videos. Provides software toolbox for visualizing and quantifying movement.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 project (RRID:SCR_021436) Copy   

•   Source: SciCrunch Registry
  

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

Project related to computer based review of previously recorded videos or live observations. Related to study of animal and human behavior. Provides open source, multiplatform standalone program that allows user specific coding environment for computer based review of previously recorded videos or live observations.Developed by scientists from University of Turin.

Proper citation: Behavioral Observation Research Interactive Software project (RRID:SCR_021434) 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/m-track/

Project related to tracking movement of labelled paws in grooming and freely behaving mice. Provides software toolbox for automated detection of forepaw trajectories in mice.

Proper citation: M-Track project (RRID:SCR_021433) Copy   

•   Source: SciCrunch Registry
  

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/bonsai/

Project related to composing reactive and asynchronous data streams coming from video cameras, microphones, electrophysiology systems or data acquisition boards. Provides open source software tool as visual language for reactive programming.

Proper citation: Bonsai project (RRID:SCR_021443) Copy   

•   Source: SciCrunch Registry
  

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

Project related to behavior tracking and analysis. Provides deep learning toolbox that automates taking high speed quality video to track behavior in rodents and humans.

Proper citation: DeepBehavior project (RRID:SCR_021387) Copy   

•   Source: SciCrunch Registry