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Suggested software
NIH BRAIN Initiative-recommended software tools
| Software Name | RRID | Description | Recommended By |
|---|---|---|---|
| NUTMEG | RRID:SCR_002748 | Software MEG/EEG analysis toolbox for reconstructing neural activation and overlaying it onto structural MR images. Toolbox runs under MATLAB in conjunction with SPM2 and can be used with Linux/UNIX, Mac OS X, and Windows platforms. | NIH BRAIN Initiative |
| BioImage Suite | RRID:SCR_002986 | Web applications for analysis of multimodal/multispecies neuroimaging data. Image analysis software package. Has facilities for DTI and fMRI processing. Capabilities for both neuro/cardiac and abdominal image analysis and visualization. Many packages are extensible, and provide functionality for image visualization and registration, surface editing, cardiac 4D multi-slice editing, diffusion tensor image processing, mouse segmentation and registration, and much more. Can be intergrated with other biomedical image processing software, such as FSL, AFNI, and SPM. | NIH BRAIN Initiative |
| MCell | RRID:SCR_007307 | Software modeling tool for realistic simulation of cellular signaling in complex 3-D subcellular microenvironment in and around living cells. Program that uses spatially realistic 3D cellular models and specialized Monte Carlo algorithms to simulate movements and reactions of molecules within and between cells. | NIH BRAIN Initiative |
| EyeWire | RRID:SCR_008816 | An online game for mapping neuronal connections in the retina. The site provides microscopic retinal images and uses crowdsourcing to make sense of the images. EyeWire is where the general public can help make discoveries about the neural structure of the retina. The challenge is to map the neural connections of the retina by analyzing images that were acquired using serial electron microscopy at the Max Planck Institute for Medical Research in Heidelberg, Germany. A retinal volume of size 350��300��60 micrometer cubed was imaged, amounting to about one terabyte of data. Retinal Connectome * Game 1: Reconstructing Neurons * Game 2: Identifying Synapses Eyewire incorporates computational technologies developed by the laboratory of Prof. Sebastian Seung at MIT. | NIH BRAIN Initiative |
| Neuroscience Gateway | RRID:SCR_008915 | Web portal that allows free access to supercomputing resources for large scale modeling and data processing. Portal facilitates access and use of National Science Foundation (NSF) High Performance Computing (HPC) resources by neuroscientists. | NIH BRAIN Initiative |
| GMA | RRID:SCR_009212 | Software package to perform Granger mediation analysis for time series. Includes single level GMA model and two-level GMA model, for time series with hierarchically nested structure. | NIH BRAIN Initiative |
| Homer2 | RRID:SCR_009586 | Software matlab scripts used for analyzing fNIRS data to obtain estimates and maps of brain activation. Graphical user interface (GUI) for visualization and analysis of functional near-infrared spectroscopy (fNIRS) data. | NIH BRAIN Initiative |
| GIMME | RRID:SCR_014115 | Software Matlab toolbox for directed functional connectivity analysis of fMRI BOLD signal from predefined regions of interest. It recovers true structure of connections and estimates weights attributed to each connection. Obtains patterns at group and individual levels. | NIH BRAIN Initiative |
| ScanImage | RRID:SCR_014307 | Open source software application for laser scanning microscopy, electrophysiology, laser scanning photostimulation, and other physiological methods focused on neurobiology. Used to control laser scanning microscopes without need for custom data acquisition hardware. Standard data acquisition boards are used to acquire data and control laser scanning. The tasks of signal integration and image processing are placed on the computer CPU. Multiple versions of ScanImage are available, each with their own features. | NIH BRAIN Initiative |
| NetPyNE | RRID:SCR_014758 | Software Python package for simulation and analysis of neuronal networks using the NEURON simulator.Used to facilitate development, parallel simulation, analysis, and optimization of biological neuronal networks. | NIH BRAIN Initiative |
| iELVis | RRID:SCR_016109 | 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. | NIH BRAIN Initiative |
| nelpy | RRID:SCR_016209 | Software toolkit for neuroelectrophysiology object modeling and data analysis in Python. Open source Python package for analysis of neuroelectrophysiology data. | NIH BRAIN Initiative |
| Human Neocortical Neurosolver | RRID:SCR_017437 | Open source software package for circuit level interpretation of human EEG/MEG data. Software tool for interpreting cellular and network origin of human MEG/EEG data. Simulates electrical activity of neocortical cells and circuits that generate primary electrical currents underlying EEG/MEG recordings. Designed for researchers and clinicians, without computational neural modeling experience, to develop and test hypothesis on circuit origin of their data. | NIH BRAIN Initiative |
| Brain Gene Expression Analysis toolbox | RRID:SCR_017438 | Software Matlab toolbox for quantitative analysis of digitized brain wide gene expression data from Allen Atlas of adult mouse brain. | NIH BRAIN Initiative |
| clusterExperiment | RRID:SCR_017439 | 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. | NIH BRAIN Initiative |
| BioWheel | RRID:SCR_017441 | Software tool for interactive graphs of high dimensional data. Interactive cloud based software tool by DIBSVIS. | NIH BRAIN Initiative |
| Mediation Analysis of Causality under Confounding | RRID:SCR_017442 | Software package to perform causal mediation analysis under confounding or correlated errors. Includes single level mediation model, two level and three level mediation model for data with hierarchical structures. Under two or three level mediation model, correlation parameter is identifiable and is estimated based on hierarchical likelihood, marginal likelihood or two stage method. | NIH BRAIN Initiative |
| microMS | RRID:SCR_017443 | Software Python platform for image guided Mass Spectrometry profiling. Provides graphical user interface for automatic cell finding and point based registration from whole slide images. Simplifies single cell analysis with feature rich image processing. | NIH BRAIN Initiative |
| MIIVsem | RRID:SCR_017444 | Software R package for estimating structural equation models using instrumental variables. | NIH BRAIN Initiative |
| MountainSort | RRID:SCR_017446 | Neurophysiological spike sorting software. | NIH BRAIN Initiative |
| Myriads | RRID:SCR_017447 | Software package for p value based multiple testing that also implements dependence test and p-value simulation. | NIH BRAIN Initiative |
| Neural Ideal | RRID:SCR_017448 | Software package for extracting neural activity codes. | NIH BRAIN Initiative |
| NEURON | RRID:SCR_017449 | Software for computational neurophysiology. Simulation environment is used for building and using computational models of neurons and networks of neurons. NEURON Users Group can participate in collaborative development of documentation, tutorials, and software. | NIH BRAIN Initiative |
| Neuron Tools | RRID:SCR_017450 | Software tools for converting data files into persistence diagrams and distance matrices. | NIH BRAIN Initiative |
| PetaVision | RRID:SCR_017451 | 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. | NIH BRAIN Initiative |
| PyNWB | RRID:SCR_017452 | Software Python package for working with Neurodata stored in Neurodata Without Borders files. Software providing API allowing users to read and create NWB formatted HDF5 files. Developed in support to NWB project with aim of spreading standardized data format for cellular based neurophysiology information. | NIH BRAIN Initiative |
| pyRayleighCuda | RRID:SCR_017453 | Python Rayleigh-Sommerfeld integral for acoustics with optional CUDA graphics processing unit (GPU) implementation. | NIH BRAIN Initiative |
| Scope | RRID:SCR_017454 | Two photon microscope control software with multi area capabilities. | NIH BRAIN Initiative |
| Seizure-Waves | RRID:SCR_017455 | Analysis and modeling code for waves of seizure activity. | NIH BRAIN Initiative |
| Silver Lab Microscopy Software | RRID:SCR_017456 | Software for use with compact Acousto-Optic Lens Microscope (AOLM) developed in the Silver Lab at UCL. Written in LabVIEW. Performs multiple imaging modes and protocols including Z-stacks, multi-plane, single-plane, sub-volume, patches and points. It comes with tools for visualising data acquired with system. | NIH BRAIN Initiative |
| StimVision | RRID:SCR_017457 | Software tool to facilitate tractography based deep brain stimulation (DBS) electrode targeting within patient specific stereotactic coordinate system used in operating room. | NIH BRAIN Initiative |
| TReNA | RRID:SCR_017458 | Methods for reconstructing transcriptional regulatory networks. | NIH BRAIN Initiative |
| FastProject | RRID:SCR_017462 | Software Python tool for low dimensional analysis of single-cell RNA-Seq data. Software package for two dimensional visualization of single cell data. Analyzes gene expression matrix and produces output report in which two-dimensional of data can be explored. | NIH BRAIN Initiative |
| ALICE | RRID:SCR_017463 | Software tool for automatic localization of intra-cranial electrodes for clinical and high density grids. Software for coregistering high density ECoG grids to MRI anatomy. | NIH BRAIN Initiative |
| Autopatcher | RRID:SCR_017464 | Software tool for neuronal recording in intact brain. | NIH BRAIN Initiative |
| cytoNet | RRID:SCR_017465 | Cloud based analysis software for cell population microscopy images. Network Analysis of Cell Communities cytoNet image analysis software designed to quantify structure of cell communities from microscope images, using principles of graph theory. | NIH BRAIN Initiative |
| DiffuserCam | RRID:SCR_017466 | Software tool as processing code. Alternating direction method of multipliers (ADMM) algorithm for recovering 3D volumes from 2D raw data captured with DiffuserCam. | NIH BRAIN Initiative |
| gene Expression Analysis Resource | RRID:SCR_017467 | Portal for visualization and analysis of multi omic data in public and private domains. Enables upload, visualization and analysis of scRNA-seq data. | NIH BRAIN Initiative |
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
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