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https://github.com/DeNardoLab/BehaviorDEPOT
Software tool for automated behavioral detection based on markerless pose tracking. Behavioral analysis tool to first compile and clean point-tracking output from DeepLabCut, and then classify behavioral epochs using custom behavior classifiers. Used to detect frame by frame behavior from video time series and can analyze results of common experimental assays, including fear conditioning, decision-making in T-maze, open field, elevated plus maze, and novel object exploration. Calculates kinematic and postural statistics from keypoint tracking data from pose estimation software outputs.
Proper citation: BehaviorDEPOT (RRID:SCR_023602) Copy
https://edspace.american.edu/openbehavior/project/photometrybox/
Portal provides open source control system for in vivo fluorescence measurements from deep brain structures developed by University of California, San Francisco scientists. Microcontroller based solution for controlling optical components in intracranial photometry system and processing resulting signal.
Proper citation: PhotometryBox (RRID:SCR_021571) Copy
Community-based initiative to promote and co-ordinate open-source software development in neuroscience hosting a number of software projects for computational and systems neuroscience, including PyNN, NeuroTools, Brian, Neo, OpenElectrophy, libNeuroML and Sumatra. Some of the projects use their Trac installation, others are on GitHub. By grouping these projects together under the NeuralEnsemble umbrella, the aim is to maximize interoperability and build components that can easily be combined into powerful systems for brain simulations and advanced data analysis. An annual CodeJam workshop is organized, bringing together scientists, graduate students, and scientific programmers to share ideas, present their work, and write code together. These workshops have been hugely effective in catalyzing open-source neuroscience software development. There is a NeuralEnsemble Google group for discussion of collaborative neuroscience software development (mainly in Python, but users of other languages are welcome!) and to provide software support.
Proper citation: NeuralEnsemble (RRID:SCR_001382) Copy
Software tool for image processing to perform automated, semi-automated, and manual cell migration detection. Open source software tool for tracking cells imaged with various imaging modalities, including fluorescent, phase contrast and differential interference contrast (DIC) techniques. Written in MATLAB. Works with Windows, Macintosh and UNIX based systems.
Proper citation: CellTracker (RRID:SCR_021718) Copy
https://github.com/Aharoni-Lab/Ephys-Miniscope
Miniaturized calcium imaging microscope with integrated dense electrode technology for synchronous acquisition of neural activity across distant regions of the brain. Device based off open-sourced UCLA Miniscope to synchronously measure single cell activity at or near spike-time resolution across distant brain regions in freely behaving mice. Used to perform calcium imaging, with dense electrode electrophysiological recording, allowing simultaneous recordings from two remote brain regions in freely behaving mouse.
Proper citation: E-Scope (RRID:SCR_025396) Copy
Core offers imaging services including design, build, upgrade, and repair optical systems. Provides high-throughput, automated, and custom-built imaging infrastructure and open-source optical tools for neuroscience and biological research. Services include Automated Whole-Brain Imaging, Histology and Spatial Transcriptomics, In-Vivo Microscopy Technical Services.
Proper citation: University College London Sainsbury Wellcome Centre Advanced Microscopy Core Facility (RRID:SCR_029090) Copy
https://code.google.com/archive/p/edlut/
Simulation software which creates spiking cell models using either a time-driven strategy or an event-driven strategy based on look-up tables. EDLUT serves as a tool for studying the computational principles of neural systems to reveal how different functionalities of the brain and central nervous system are based on cell and topology properties.
Proper citation: EDLUT (RRID:SCR_014261) Copy
http://www.nitrc.org/projects/spicodyn/
Software for the analysis of multi-site neuronal spike signals. SPICODYN processes electrophysiological signals, focusing on spiking and bursting dynamics and functional-effective connectivity analysis.
Proper citation: SpiCoDyn (RRID:SCR_015744) Copy
https://github.com/automaticanalysis/automaticanalysis
Integration framework for major open source packages in neuroimaging including SPM, FSL, FreeSurfer, EEGLAB, and Fieldtrip. Efficient neuroimaging workflows and parallel processing using Matlab and XML. Addresses challenges of processing multimodal datasets, like combining anatomy, functional MRI, diffusion, and EEG, to yield integrated views of brain. Allows to design, execute, and share pipelines utilizing multiple open source packages. Supports parallelized execution to address challenges of large cohort studies and provides quality control offering group statistics and reporting facilities to help identify outlier subjects and erroneous processing steps.
Proper citation: Automatic Analysis (RRID:SCR_003560) Copy
https://github.com/epurdom/clusterExperiment
Software open source R package for executing, evaluating and visualizing different clusterings of experimental data, including data from single cell RNA-Seq studies. Software for running and comparing different clusterings of single cell sequencing data.
Proper citation: clusterExperiment (RRID:SCR_017439) Copy
A universal tracking application specifically designed to support animal behavioral analysis. AnimalTracker consists of three main modules which can be used independently: Tracker is responsible for image processing and providing the coordinates of the identified object; Zone Designer provides tools to create custom-made investigation areas in order to design a maze-setup; and Tracking Analyzer module serves to define and obtain the parameters needed for the evaluation.
Proper citation: AnimalTracker (RRID:SCR_014397) Copy
A startup research, development and innovation company based in The Grand Duchy of Luxembourg working on four major areas: Open Research, as Information Hub; Information Technology, as The Common Brain; Collective Awareness, as Manifesto; and Biophysics, as Human Extensibility. The Information Hub researches a methodology to conduct open research using a collaborative approach designed for multi-disciplinary interventions, multi-scope goal alignment, advanced analytics and a unified research experience for international cooperation. The Common Brain researches an open source intelligent architecture for future internet, one that is deeply sustainable over a highly distributed hybrid network, self-governed, heterogenous, and logical. Manifesto researches a methodology for a collaborative approach for policy making, open standardization, accreditation, verification and compliance. Human Extensibility researches the establishment of the scientific ground for a field of science concerned with the study of the physics and physiology of the human being, to provide techniques and genetic algorithms for human extensibility.
Proper citation: Brain.io (RRID:SCR_014527) Copy
https://broadinstitute.github.io/warp/docs/Pipelines/Multiome_Pipeline/README
Software open-source, cloud-optimized pipeline developed in collaboration with members of the BRAIN Initiative (BICCN and BICAN Sequencing Working Group) and SCORCH. It supports the processing of 10x 3' single-cell and single-nucleus gene expression (GEX) and chromatin accessibility (ATAC) data generated with the 10x Genomics Multiome assay.
Proper citation: Multiome Pipeline (RRID:SCR_024217) Copy
Mindboggle (http://mindboggle.info) is open source software for analyzing the shapes of brain structures from human MRI data. The following publication in PLoS Computational Biology documents and evaluates the software: Klein A, Ghosh SS, Bao FS, Giard J, Hame Y, Stavsky E, Lee N, Rossa B, Reuter M, Neto EC, Keshavan A. (2017) Mindboggling morphometry of human brains. PLoS Computational Biology 13(3): e1005350. doi:10.1371/journal.pcbi.1005350
Proper citation: Mindboggle (RRID:SCR_002438) Copy
Computable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases.
Proper citation: Gene Ontology (RRID:SCR_002811) Copy
Web based service that offers software developers centralized online location to control and manage free and open source software projects. Open source software tool and business public software platform.
Proper citation: SourceForge (RRID:SCR_004365) Copy
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
Open source designs for customizable, MRI compatible microdrive capable of positioning probes including stimulating electrodes, recording electrodes, drug cannulae, or optogenetic fibers within brain. Design integrates cranial implant, penetration grid for guiding probes, and microdrive body assembly with actuators. Used by neuroscience community related to electrical microstimulation, neuronal recording, and local drug delivery.
Proper citation: MRI Compatible and Customizable Microdrive Design for Neuroscience Research (RRID:SCR_019247) Copy
https://broadinstitute.github.io/warp/docs/Pipelines/ATAC/README
Software open-source, cloud-optimized pipeline developed in collaboration with members of the BRAIN Initiative (BICCN and BICAN Sequencing Working Group) and SCORCH. It supports the processing of 10x single-nucleus data generated with 10x Multiome ATAC-seq (Assay for Transposase-Accessible Chromatin), a technique used in molecular biology to assess genome-wide chromatin accessibility.
Proper citation: ATAC Pipeline (RRID:SCR_024656) Copy
https://github.com/mcmelo22/Licktech/tree/main
Lickometer system based on open-source hardware platform with user-friendly interface software, capable of simultaneously receiving data from eight automated cages with two drinking bottles each. Device to acquire high-quality and detailed data. Adaptable to new types of sensors or other neuroscience tools capable of measuring brain activity simultaneously to the behavior.
Proper citation: Lickometer Box (RRID:SCR_025248) Copy
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