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http://www.pstnet.com/hardware.cfm?ID=90
MRI Digital Projection System that uses Digital Light Processing (DLP) technology providing microsecond pixel rise times, outstanding contrast with all-digital fiber optic control that allows you to project crystal clear, sharp images. Includes: * High resolution (1024x768) DLP Projector with RF filtered enclosure, custom lens assembly, digital video (DVI) over fiber, high flow fans, internal thermal sensor * Control room device to perform DVI to Fiber conversion, remotely power down the projector, and allow use of projector remote control from control room * 30 meter fiber optic cable that runs between the projector and projector control station * Heavy duty, magnet compatible, projector stand (assembly required) * Heavy duty, magnet compatible mirror stand with mirror (assembly required) * High resolution, lenticular pitch rear projection screen for high quality image reproduction * Optional VGA to DVI converter (native DVI video cards on Windows or Macintosh recommended)
Proper citation: MRI Digital Projection System (RRID:SCR_002486) Copy
http://www.nitrc.org/projects/parser_4d/
A tool for analyzing 4D images with pathology. Originally developed for processing longitudinal images of patients with traumatic brain injury, the tool contains new image analysis algorithms that combine registration and segmentation in a coherent framework, accounting for extreme changes due to extensive tissue damage.
Proper citation: 4D-PARSeR Pathological Anatomy Regression via Segmentation and Registration (RRID:SCR_002480) Copy
https://www.genevestigator.com/gv/
A high performance search engine for gene expression that integrates thousands of manually curated public microarray and RNAseq experiments and nicely visualizes gene expression across different biological contexts (diseases, drugs, tissues, cancers, genotypes, etc.). There are two basic analysis approaches: # for a gene of interest, identify which conditions affect its expression. # for condition(s) of interest, identify which genes are specifically expressed in this/these conditions. Genevestigator builds on the deep integration of data, both at the level of data normalization and on the level of sample annotations. This deep integration allows scientists to ask new types of questions that cannot be addressed using conventional tools.
Proper citation: Genevestigator (RRID:SCR_002358) Copy
https://github.com/armintoepfer/haploclique
Software providing a computational approach to reconstruct the structure of a viral quasispecies from next-generation sequencing data as obtained from bulk sequencing of mixed virus samples.
Proper citation: HaploClique (RRID:SCR_002353) Copy
http://www.theneurohub.com.au/
Online aggregation portal of neuroscience research services that clients can use as a tool to contact, refer, and utilize such as medical services, neuropsychology assessments, and speech pathology.
Proper citation: NeuroHub: the information environment for Neuroscientists (RRID:SCR_002352) Copy
http://www.nitrc.org/projects/stfilter/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14, 2026. Software tools which can perform Stochastic Tractography and related analysis on DWMRI data. Stochastic Tractography applies a Bayesian approach towards the estimation of nerve fiber tracts from DWMRI images.
Proper citation: Stochastic Tractography System (RRID:SCR_002594) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 08, 2014. Project proposing a "liquid" format for science papers that consists of a set of research objects, connected by links. The immediate targets are the scientific research communities including publishers that, in a liquid world, will need to develop novel services and business models. Results and additional reading material (case studies, surveys, and the like) will be made available. The project also is creating an open source development effort and a platform to manage liquid publications and their evaluation. Their current main effort is developing the Liquid Journal and Liquid Conference use cases.
Proper citation: Liquid Publications: Scientific Publications meet the Web (RRID:SCR_002471) Copy
http://www.nitrc.org/projects/sspm/
Software package representing Spatial Statistical Parametric Mapping that includes two tools presently: MAGEE and FADTTS. MAGEE represents the Multiscale Adaptive Generalized Estimating Equation. It was developed specifically for analyzing multivariate neuroimaging data in 3-dimensional volume (or on 2-dimensional surface) from longitudinal neuroimaging studies. FADTTS represents Functional Analysis of Diffusion Tensor Tract Statistics. The aim of this tool is to implement a functional analysis pipeline, for delineating the structure of the variability of multiple diffusion properties along major white matter fiber bundles and their association with a set of covariates of interest, in various diffusion tensor imaging studies.
Proper citation: Spatial Statistical Parametric Mapping (RRID:SCR_002592) Copy
http://mialab.mrn.org/software/eegift/index.html
Implements multiple algorithms for independent component analysis and blind source separation of group (and single subject) EEG data. This MATLAB toolbox is compatible with MATLAB 6.5 and higher.
Proper citation: Group ICA Of EEG Toolbox (RRID:SCR_002478) Copy
http://brainproducts.com/productdetails.php?id=17
Software to manage the daily work of analyzing various neurophysiological data. Features include a history tree, automated analysis, various data format readers, and more.
Proper citation: BrainVision Analyzer (RRID:SCR_002356) Copy
http://commons.esipfed.org/datamanagementshortcourse
ESIP Federation training courses to improve the understanding of scientific data management among scientists, emerging scientists, and data professionals. The ESIP Federation, in cooperation with NOAA, seeks to share the community's knowledge with scientists who increasingly need to be better data managers, as well as to support workforce development for new data management professionals.
Proper citation: ESIP Data Management Short Course for Scientists (RRID:SCR_002597) Copy
http://www.nitrc.org/projects/pare/
A brain imaging classification tool, which can help researchers to discriminate patients from normal controls. The M3 includes three steps: feature selection, maximum uncertainty linear discriminant analysis (MLDA)-based classification and multi-classifier. A leave-one-out cross-validation (LOOCV) is further used to estimate the performance of the M3. Finally, the most discriminative features are identified.
Proper citation: M3 (RRID:SCR_002475) Copy
http://fged.org/projects/miame/
Standard specification for the Minimum Information About a Microarray Experiment that is needed to enable the interpretation of the results of the experiment unambiguously and potentially to reproduce the experiment.
Proper citation: MIAME (RRID:SCR_002349) Copy
http://toliaslab.org/code-and-algorithms/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Code and algorithms produced by the Andreas Tolias lab (Baylor College of Medicine, Department of Neuroscience) where the goal is to understand the rules by which networks of nerves cells in the neocortex orchestrate their activity to process information; to decipher the neural code.
Proper citation: BCM Department of Neuroscience Andreas Tolias Lab (RRID:SCR_003594) Copy
Organization to lead the integration of ocean, coastal, and Great Lakes observing capabilities, in collaboration with Federal and non-Federal partners, to maximize access to data and generation of information products, inform decision making, and promote economic, environmental, and social benefits to the nation and the world. This national-regional partnership is working to provide new tools and forecasts to improve safety, enhance the economy, and protect the environment. Integrated ocean information is available in near real time, as well as retrospectively. Easier and better access to this information is improving their ability to understand and predict coastal events - such as storms, wave heights, and sea level change. Such knowledge is needed for everything from retail to development planning. The Integrated Ocean Observing System (IOOS) program achieves its objectives by funding organizations through a competitive process.
Proper citation: Integrated Ocean Observing System (RRID:SCR_003598) Copy
A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context.
Proper citation: GEPAT (RRID:SCR_003597) Copy
http://www.enzolifesciences.com/
An Antibody supplier
Proper citation: Enzo Life Sciences (RRID:SCR_003900) Copy
A set of Python software packages that takes large sets of overlapping images in 2D and 3D and produces registered (aligned) 3D volumes at any size and scale. These tools were originally designed to construct 3D connectomics volumes from terabytes of image data for the Marc lab at the University of Utah Moran Eye Center.
Proper citation: Nornir (RRID:SCR_003585) Copy
https://github.com/jamesra/nornir-buildmanager/wiki
Software package that constructs 2D and 3D datasets from 2D image mosaics using the nornir tools. This produces a set of images and transforms on disk which can be accessed via Viking, HTTP, or written as a stack of images.
Proper citation: nornir-buildmanager (RRID:SCR_003584) Copy
Software tool for the visualization and annotation of 3D image data and was developed for the rapid reconstruction of neural morphology and connectivity. By dynamically loading only data from the surround of the current view point, seamless navigation is not limited to datasets that fit into the available RAM but works with much larger dataset stored in a special format on disk. Currently, KNOSSOS is limited to 8-bit data. In addition to viewing and navigating, KNOSSOS allows efficient manual neurite annotation (''skeletonization''). KNOSSOS is being used mostly for reconstructing cell morphologies from 3D electron microscopic data generated by Serial Block-Face Electron Microscopy (SBEM), with an occasional application to 2-photon and confocal optical microscopy data.
Proper citation: KNOSSOS (RRID:SCR_003582) Copy
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