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https://github.com/BlueBrain/BluePyOpt

An extensible framework for data-driven model parameter optimization that wraps and standardizes several existing open-source tools. BluePyOpt abstracts the optimization and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. It also provides methods for setting up both small- and large-scale optimizations on a variety of platforms.

Proper citation: BluePyOpt (RRID:SCR_014753) Copy   

•   Source: SciCrunch Registry
  

https://github.com/openMetadataInitiative/openMINDS_controlledTerms

Software repository is part of open Metadata Initiative for Neuroscience Data Structures (openMINDS). It contains the schema-templates as well as corresponding terminologies (as JSON-LDs) for all terms that are defined and maintained centrally in this repository. Where applicable, the defined terms are connected to a matching ontological term. Schemas of openMINDS_core as well as openMINDS_SANDS reference to these controlled terms.

Proper citation: openMINDS controlledTerms metadata model (RRID:SCR_026247) Copy   

•   Source: SciCrunch Registry
  

https://github.com/markmikkelsen/Gannet

Free, open-source MATLAB-based software toolkit for analyzing edited 1H magnetic resonance spectroscopy (MRS) data.

Proper citation: Gannet (RRID:SCR_016049) Copy   

•   Source: SciCrunch Registry
  

https://github.com/BRAINSia/BRAINSTools/tree/master/BRAINSMush

Tool to generate brain volume mask from input of T1 and T2-weighted images alongside a region of interest brain mask. This volume mask omits dura, skull, eyes, etc. The program is built upon ITK and uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3.

Proper citation: BRAINSMush (RRID:SCR_009485) Copy   

•   Source: SciCrunch Registry
  

https://github.com/NOCIONS/letswave6/wiki/Download-and-setup

Open source electroencephalogram (EEG) signal processing toolbox to process and visualise EEG/MEG data and other neurophysiological signals.

Proper citation: Letswave (RRID:SCR_016414) Copy   

•   Source: SciCrunch Registry
  

https://github.com/missy139/PreSurgMapp

A MATLAB toolbox for processing the functional areas of the brain using multi-modal fMRI data for pre-surgical mapping. It is composed of three types of individual-level ICA analyses for user use. Traditional ICA (task) can be used for task fMRI. Either Traditional ICA (rest) or ICA with DICI (rest) can be used for rs-fMRI. Traditional ICA (rest) is designed for users who already have a hypothesis of the pattern of the target component and want to have manually set components by themselves. ICA with DICI (rest) is completely automatic, given that the user provides a template (provided). The software utilizes an automatic component identification method that is based on the discriminatory-index. All the components from multiple ICA runs with multiple component settings are ranked and compiled.

Proper citation: PreSurgMapp (RRID:SCR_014427) Copy   

•   Source: SciCrunch Registry
  

http://neuroimage.usc.edu/brainstorm/

Software as collaborative, open source application dedicated to analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and animal invasive neurophysiology. User-Friendly Application for MEG/EEG Analysis.

Proper citation: Brainstorm (RRID:SCR_001761) 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://cellarium.ai

Software platform to annotate cell types.

Proper citation: Cellarium (RRID:SCR_025438) Copy   

•   Source: SciCrunch Registry
  

https://pythonhosted.org/eelbrain/

Statistical analysis toolbox for MEG and EEG. There are three primary data-objects: Factor for categorical variables, Var for scalar variables, and NDVar for multidimensional data. Factor is a container for one-dimensional, categorial data – each case is described by a string label. Var is a container to associate one-dimensional numpy.ndarray objects with a name. NDVars offer numpy functionality that takes into account the dimensions. There is also a Dataset class which acts as a vessel for variable objects (Factor, Var and NDVar) describing the same cases.

Proper citation: Eelbrain (RRID:SCR_014661) Copy   

•   Source: SciCrunch Registry
  

https://github.com/nelpy

Software toolkit for neuroelectrophysiology object modeling and data analysis in Python. Open source Python package for analysis of neuroelectrophysiology data.

Proper citation: nelpy (RRID:SCR_016209) Copy   

•   Source: SciCrunch Registry
  

http://slicer.org/

A free, open source software package for visualization and image analysis including registration, segmentation, and quantification of medical image data. Slicer provides a graphical user interface to a powerful set of tools so they can be used by end-user clinicians and researchers alike. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X. Slicer is based on VTK (http://public.kitware.com/vtk) and has a modular architecture for easy addition of new functionality. It uses an XML-based file format called MRML - Medical Reality Markup Language which can be used as an interchange format among medical imaging applications. Slicer is primarily written in C++ and Tcl.

Proper citation: 3D Slicer (RRID:SCR_005619) Copy   

•   Source: SciCrunch Registry
  

https://github.com/lrq3000/spm_auto_reorient_coregister

Open source cross platform for automatic AC-PC realignment, reorientation and coregistration robust to brain damage in Statistical Parametric Mapping. Set of routines to perform auto reorient and auto coregistration in toolbox SPM12.

Proper citation: spm_auto_reorient_coregister (RRID:SCR_017281) Copy   

•   Source: SciCrunch Registry
  

https://github.com/3Dneuro/TD_Drive

Parametric, open-source implant for multi-area electrophysiological recordings in behaving and sleeping rats. 3D-printable implant for rats, capable of symmetric, bilateral wire electrode recordings, currently in up to six distributed brain areas simultaneously.

Proper citation: TD_Drive (RRID:SCR_025672) Copy   

•   Source: SciCrunch Registry
  

https://github.com/eegsynth/eegsynth

Open source Python codebase that provides real-time interface between open-hardware devices for electrophysiological recordings like EEG, EMG, and ECG, and analog and digital devices like MIDI, OSC, and analog synthesizers. This allows one to use electrical brain/body activity to flexibly control devices in real-time.

Proper citation: EEGsynth (RRID:SCR_018732) Copy   

•   Source: SciCrunch Registry
  

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

Portal related to biomedical signals.Provides wearable data acquisition device with special focus on biomedical signals such as heart activity (ECG), muscle activity (EMG) and brain activity (EEG).Open source high precision bluetooth data acquisition device.

Proper citation: Attys project (RRID:SCR_021461) Copy   

•   Source: SciCrunch Registry
  

http://ielvis.pbworks.com/w/page/116347253/FrontPage

Software toolkit consisting of MATLAB and Bash scripts for intracranial electrode localization/visualization. It maps electrodes to various anatomical and functional atlases, and overlays electrode data over functional neuroimaging data. Software for intracranial electrode localization and visualization.

Proper citation: iELVis (RRID:SCR_016109) Copy   

•   Source: SciCrunch Registry
  

https://github.com/PetaVision/OpenPV

Open source software neural simulation toolbox. C++ library for designing and deploying large scale neurally inspired computational models. Object oriented neural simulation toolbox optimized for high performance multi core, multi node computer architectures.

Proper citation: PetaVision (RRID:SCR_017451) Copy   

•   Source: SciCrunch Registry
  

https://github.com/BICCN/cell-locator/

Open source and multi-platform pinning software tool to facilitate mapping samples into common 3D spaces. Desktop application based on 3D Slicer that displays Allen Institute for Brain Science CCF or MNI atlas, color segmented by structure of brain, and allows user to create planar polyline annotation to facilitate mapping samples into corresponding atlas.

Proper citation: CellLocator (RRID:SCR_019264) Copy   

•   Source: SciCrunch Registry
  

https://broadinstitute.github.io/warp/docs/Pipelines/PairedTag_Pipeline/README

Software open-source, cloud-optimized pipeline developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) and the BRAIN Initiative Cell Atlas Network (BICAN). It supports the processing of 3' single-nucleus histone modification data (generated with the paired-tag protocol]) and 10x gene expression (GEX) data generated with the 10x Chromium Multiome assay.

Proper citation: Paired-Tag Pipeline (RRID:SCR_025042) Copy   

•   Source: SciCrunch Registry