Tools   Select Another Resource Report Type

https://github.com/LINCellularNeuroscience/VAME

Software Python tool to cluster behavioral signals obtained from pose estimation tools. Unsupervised probabilistic deep learning framework capable of finding behavioral motifs in pose estimation data. Capable of augmenting quantitative behavioral analyses of data derived from standard pose-estimation software packages. Written based on core functions from DeepLabCut, and readily works with pose data from that package. Can also work with data from other pose estimation packages such as SLEAP.

Proper citation: Variational Embedding of Animal Motion (RRID:SCR_022477) Copy   

•   Source: SciCrunch Registry

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

Open source software package to support rt-fMRI via data in formats generated by Siemens, Philips, and GE. Used to support real time functional magnetic resonance imaging.

Proper citation: Pyneal (RRID:SCR_022333) Copy   

•   Source: SciCrunch Registry

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

Software Pyton scripts to run computerised task of Reaction Time. Scripts, together with their instructions and scoresheets.Used for assessment of RTs that is freely available, compatible with all operating systems, without license and activation costs, and based on open source software platform.

Proper citation: OORTT (RRID:SCR_022331) Copy   

•   Source: SciCrunch Registry

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

Automated surgical instrument for brain tissue aspiration.Instrument for microendoscope implantation. Utilizes robotic control of needle connected to vacuum pump to aspirate brain tissue. System consists of robotic surgical instrument built around commercially available stereotaxic instrument and open source MATLAB-based GUI for control.

Proper citation: AutoStereota (RRID:SCR_022330) Copy   

•   Source: SciCrunch Registry

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

Open source video recording system for acquiring video data that is scalable, flexible, and affordable.Utilizes Raspberry Pi (RPi) miniature computer and 8-megapixel Camera Board that allows for greater manipulation of recording parameters. System may be accessed on GitHub.

Proper citation: Pi-based Remote Acquisition Technology for Motion Capture project (RRID:SCR_022325) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/raspi-aud-generator/

Stimulation system for auditory EEG experiments using Raspberry Pi3 B+ board, HiFiBerry audio card to enhance sound quality and trigger tone latency, and custom Python library to generate auditory stimuli.

Proper citation: Raspberry Pi based auditory stimulus generator (RRID:SCR_022343) Copy   

•   Source: SciCrunch Registry

https://github.com/earnestt1234/SipperViz

Software Python GUI for graphing measures of liquid ingestion in rodents from Sippers. Python GUI for visualizing Sipper data.

Proper citation: SipperViz (RRID:SCR_022463) Copy   

•   Source: SciCrunch Registry

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

Software semi automated brain atlas based analysis pipeline for c-Fos immunohistochemical data. Used to analyze c-Fos in multiple brain regions simultaneously.

Proper citation: Atlas Based Analysis (RRID:SCR_022339) Copy   

•   Source: SciCrunch Registry

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

Interactive software for visualizing and uncovering function of circuits created from large scale fruit fly brain data. Interactive computing platform for studying function of executable circuits constructed from fruit fly brain data.

Proper citation: FlyBrainLab (RRID:SCR_022337) Copy   

•   Source: SciCrunch Registry

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

Open source, MATLAB based software for forced swim test and tail suspension test video analysis.

Proper citation: DBscorer (RRID:SCR_022334) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/modular-led-displays/

Provides customized display systems used in neuroscientific studies in insects and other small animals. System includes custom built modular LED panels and software. LED panels of various sizes can be arranged/grouped in different shapes for diverse setups. System provides millisecond refresh, precise synchronization, customizable color combinations, and varied display configurations and addresses most technical challenges of small animal vision experiments and is thoroughly documented for replicability.

Proper citation: Modular LED Displays project (RRID:SCR_022704) Copy   

•   Source: SciCrunch Registry

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

Project related to tracking behavior. Used to identify subgroups of individuals that differentially attribute incentive value to food cue. Includes apparatus for studying Pavlovian conditioned approach behavior. Customized rat PavCA chambers are constructed based on modular devices purchased from Med-Associates. Code used to operate equipment and collect data was written using Med-Associates’ MEDSTATE programming language. This program is then loaded into Med-PC V operating program, also created by Med-Associates.

Proper citation: PavCA project (RRID:SCR_022508) Copy   

•   Source: SciCrunch Registry

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://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