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http://synapses.clm.utexas.edu/tools/reconstruct/reconstruct.stm

A Windows (Win32) software application for montaging, aligning, tracing, measuring, and reconstructing objects from serial microscopic section images. The software is designed for microscopy in which section resolution is much less than section thickness, such as transmitted electron microscopy (EM) where the resolution is a few nanometers while the section thickness is many tens of nanometers. Reconstruct can easily handle series with hundreds of very large, high-resolution section images. It facilitates image cropping, scaling and alignment. Multiple images can be placed side-by-side to make a montage of a section from a mosaic of images. The alignment of adjacent sections can be rapidly compared by either blending the two sections or by flickering between them. Sections can be moved while blended. Reconstruct aids in the calibration of image size. Images taken at different magnifications can be combined, calibrated and aligned. Tools for tracing and editing of objects on sections are provided. Objects can be surfaced from the traces and previewed in an OpenGL-based 3D scene window. The 3D scene can be saved as a bitmap or as a VRML file.

Proper citation: Synapse Web Reconstruct (RRID:SCR_002716) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/LONI-Inspector

A Java application for reading, displaying, searching, comparing, and exporting metadata from medical image files: AFNI, ANALYZE, DICOM, ECAT, GE, Interfile, MINC, and NIFTI.

Proper citation: LONI Inspector (RRID:SCR_004923) Copy   

•   Source: SciCrunch Registry

http://www.nsgportal.org/

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.

Proper citation: Neuroscience Gateway (RRID:SCR_008915) Copy   

•   Source: SciCrunch Registry

https://www.bci2000.org/

BCI2000 is a general-purpose system for brain-computer interface (BCI) and adaptive neurotechnology research. It can also be used for data acquisition, stimulus presentation, and brain monitoring applications. The mission of the BCI2000 project is to facilitate research and applications in the areas described. Their vision is that BCI2000 will become a widely used software tool for diverse areas of real-time biosignal processing. In order to achieve this vision, BCI2000 system is available for free for non-profit research and educational purposes. BCI2000 supports a variety of data acquisition systems, brain signals, and study/feedback paradigms. During operation, BCI2000 stores data in a common format (BCI2000 native or GDF), along with all relevant event markers and information about system configuration. BCI2000 also includes several tools for data import/conversion (e.g., a routine to load BCI2000 data files directly into Matlab) and export facilities into ASCII. BCI2000 also facilitates interactions with other software. For example, Matlab scripts can be executed in real-time from within BCI2000, or BCI2000 filters can be compiled to execute as stand-alone programs. Furthermore, a simple network-based interface allows for interactions with external programs written in any programming language. For example, a robotic arm application that is external to BCI2000 may be controlled in real time based on brain signals processed by BCI2000, or BCI2000 may use and store along with brain signals behavioral-based inputs such as eye-tracker coordinates. Because it is based on a framework whose services can support any BCI implementation, the use of BCI2000 provides maximum benefit to comprehensive research programs that operate multiple BCI2000 installations to collect data for a variety of studies. The most important benefits of the system in such situations are: - A Proven Solution - Facilitates Operation of Research Programs - Facilitates Deployment in Multiple Sites - Cross-Platform and Cross-Compiler Compatibility - Open Resource Sponsors: BCI2000 development is sponsored by NIH/NIBIB R01 and NIH/NINDS U24 grants. Keywords: General, Purpose, Systems, Brain, Computer, Interface, Research, Application, Brain, Diverse, Educational, Laboratory, Software, Network, Signals, Behavioral, Eye, Tracker,

Proper citation: Brain Computer Interface 2000 Software Package (RRID:SCR_007346) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/IO_Plugins

Decoders and encoders written in Java for the AFNI, ANALYZE, DICOM, ECAT, GE, MINC, NIFTI and other neuroimaging file formats.The plugins use Java Image I/O interfaces to read and write metadata and image data and can read and write AFNI, ANALYZE 7.5, DICOM, ECAT 7.2, GE 5.0, INTERFILE (including hrrt), MINC, NIFTI, and UCLA PACS file formats. All source code is provided and usage examples are included.

Proper citation: LONI Java Image I/O Plugins (RRID:SCR_008277) Copy   

•   Source: SciCrunch Registry

http://www.nmr.mgh.harvard.edu/DOT/resources/homer2/home.htm

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.

Proper citation: Homer2 (RRID:SCR_009586) Copy   

•   Source: SciCrunch Registry

http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula

Software tool developed for automatically reconstructing a set of major white matter pathways in the brain from diffusion weighted images using probabilistic tractography. This method utilizes prior information on the anatomy of the pathways from a set of training subjects. By incorporating this prior knowledge in the reconstruction procedure, our method obviates the need for manual intervention with the tract solutions at a later stage and thus facilitates the application of tractography to large studies. The trac-all script is used to preprocess raw diffusion data (correcting for eddy current distortion and B0 field inhomogenities), register them to common spaces, model and reconstruct major white matter pathways (included in the atlas) without any manual intervention. trac-all may be used to execute all the above steps or parts of it depending on the dataset and user''''s preference for analyzing diffusion data. Alternatively, scripts exist to execute chunks of each processing pipeline, and individual commands may be run to execute a single processing step. To explore all the options in running trac-all please refer to the trac-all wiki. In order to use this script to reconstruct tracts in Diffusion images, all the subjects in the dataset must have Freesurfer Recons.

Proper citation: TRACULA (RRID:SCR_013152) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/caworks

A software application developed to support computational anatomy and shape analysis. The capabilities of CAWorks include: interactive landmark placement to create segmentation (mask) of desired region of interest; specialized landmark placement plugins for subcortical structures such as hippocampus and amygdala; support for multiple Medical Imaging data formats, such as Nifti, Analyze, Freesurfer, DICOM and landmark data; Quadra Planar view visualization; and shape analysis plugin modules, such as Large Deformation Diffeomorphic Metric Mapping (LDDMM). Specific plugins are available for landmark placement of the hippocampus, amygdala and entorhinal cortex regions, as well as a browser plugin module for the Extensible Neuroimaging Archive Toolkit.

Proper citation: CAWorks (RRID:SCR_014185) Copy   

•   Source: SciCrunch Registry

http://becs.aalto.fi/en/research/bayes/drifter/

Model based Bayesian method for eliminating physiological noise from fMRI data. This algorithm uses image voxel analysis to isolate the cardiac and respiratory noise from the relevant data.

Proper citation: DRIFTER (RRID:SCR_014937) Copy   

•   Source: SciCrunch Registry

https://github.com/nebneuron/neural-ideal

Software package for extracting neural activity codes.

Proper citation: Neural Ideal (RRID:SCR_017448) Copy   

•   Source: SciCrunch Registry

https://github.com/Nevermore520/NeuronTools

Software tools for converting data files into persistence diagrams and distance matrices.

Proper citation: Neuron Tools (RRID:SCR_017450) Copy   

•   Source: SciCrunch Registry

https://www.icpsr.umich.edu/icpsrweb/content/addep/index.html

Provides access to data including wide range of topics related to disability. ADDEP data can be used to better understand and inform the implementation of Americans with Disabilities Act and other disability policies.

Proper citation: Archive of Data on Disability to Enable Policy (ADDEP) (RRID:SCR_016315) Copy   

•   Source: SciCrunch Registry

https://www.bpforms.org

Software toolkit for unambiguously describing molecular structure of DNA, RNA, and proteins, including non-canonical monomeric forms, crosslinks, nicks, and circular topologies. Aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts.

Proper citation: BpForms (RRID:SCR_018653) Copy   

•   Source: SciCrunch Registry

https://www.objtables.org

Software toolkit for creating reusable datasets that are both human and machine readable, combining spreadsheets with schemas including classes, their attributes, type of each attribute, and possible relationships between instances of classes.Consists of format for describing schemas for spreadsheets, numerous data types for science, syntax for indicating class and attribute represented by each table and column in workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. Used for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort.

Proper citation: ObjTables (RRID:SCR_018652) Copy   

•   Source: SciCrunch Registry

http://datasets.datalad.org/

DataLad data distribution. Super dataset collating DataLad datasets from various sources including OpenNeuro, CRCNS, etc., to provide unified access to over 200TB of neural data.

Proper citation: datasets.datalad.org (RRID:SCR_019089) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=macc

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.

Proper citation: Mediation Analysis of Causality under Confounding (RRID:SCR_017442) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/reprocontainers/

Software containerized environments for reproducible neuroimaging. Part of ReproNim - Center for Reproducible Neuroimaging Computation. DataLad dataset with collection of popular computational tools provided within ready to use containerized environments.

Proper citation: ReproNim/containers (RRID:SCR_018467) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=gma

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.

Proper citation: GMA (RRID:SCR_009212) Copy   

•   Source: SciCrunch Registry

http://ric.uthscsa.edu/mango/

A viewer for medical research images that provides analysis tools and a user interface to navigate image volumes. There are three versions of Mango, each geared for a different platform: * Mango ? Desktop ? Mac OS X, Windows, and Linux * webMango ? Browser ? Safari, Firefox, Chrome, and Internet Explorer * iMango ? Mobile ? Apple iPad Key Features: * Built-in support for DICOM, NIFTI, Analyze, and NEMA-DES formats * Customizable: Create plugins, custom filters, color tables, file formats, and atlases * ROI Editing: Threshold and component-based tools for painting and tracing ROIs * Surface Rendering: Interactive surface models supporting cut planes and overlays * Image Registration: Semi-automatic image coregistration and manual transform editing * Image Stacking: Threshold and transparency-based image overlay stacking * Analysis: Histogram, cross-section, time-series analysis, image and ROI statistics * Processing: Kernel and rank filtering, arithmetic/logic image and ROI calculators

Proper citation: Mango (RRID:SCR_009603) Copy   

•   Source: SciCrunch Registry

http://itools.loni.usc.edu/

An infrastructure for managing of diverse computational biology resources - data, software tools and web-services. The iTools design, implementation and meta-data content reflect the broad NCBC needs and expertise (www.NCBCs.org).

Proper citation: iTools (RRID:SCR_009626) Copy   

•   Source: SciCrunch Registry