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An image processing program running under Windows suitable for such tasks as tensor calculation, color mapping, fiber tracking, and 3D visualization. Most of operations can be done with only a few clicks. This tool evolved from DTI Studio. Tools in the program can be grouped in the following way: * Image Viewer * Diffusion Tensor Calculations * Fiber Tracking and Editing * 3D Visualization * Image File Management * Region of Interesting (ROI) Drawing and Statistics * Image Registration
Proper citation: MRI Studio (RRID:SCR_001398) Copy
http://www.farsight-toolkit.org/wiki/FARSIGHT_Toolkit
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A collection of software modules for image data handling, pre-processing, segmentation, inspection, editing, post-processing, and secondary analysis. These modules can be scripted to accomplish a variety of automated image analysis tasks. All of the modules are written in accordance with software practices of the Insight Toolkit Community. Importantly, all modules are accessible through the Python scripting language which allows users to create scripts to accomplish sophisticated associative image analysis tasks over multi-dimensional microscopy image data. This language works on most computing platforms, providing a high degree of platform independence. Another important design principle is the use of standardized XML file formats for data interchange between modules.
Proper citation: Farsight Toolkit (RRID:SCR_001728) Copy
http://bmia.bmt.tue.nl/software/viste/
A powerful, open source, platform-independent application for the visualization and analysis of complex, high-dimensional imaging data such as Diffusion Tensor Imaging (DTI) and High Angular Resolution Diffusion Imaging (HARDI). It has a plugin-based architecture which allows third parties to develop new plugins to extend the tool. Overview of the many features: * vIST/e is programmed in C++. It uses the Visualization Toolkit for visualization and pipelined data processing, as well as the cross-platform toolkit Qt Framework for an easy-to-use Graphical User Interface. * vIST/e introduces a powerful new plugin system, which allows for modular development with increased extensibility and stability. * Powerful GPU-based visualization techniques allow for smooth, real-time visualization of large data sets. Using custom ray tracing algorithms created with OpenGL, vIST/e can render DTI ellipsoids and HARDI spherical harmonics glyphs up to 4th order. The high frame rates offered by modern GPU technology allows for interactive exploration of this complex data. * Diffusion Tensor Imaging data can be visualized and interactively explored in a number of ways, including multiple cross-sections, volume rendering, and tensor glyphs. Derived scalar volumes, including various different anisotropy measures, can be computed and visualized. Data from other modalities, such as structural MRI, can be shown alongside the DTI data. * Various fiber tracking methods allow for fast and accurate reconstruction of fiber pathways. Interactively defined Regions of Interest (ROIs) can be used for seeding and filtering of fibers. Fibers are visualized either as lines, optionally using a powerful, GPU-based lighting engine, or as 3D structures such as tubes. * Scalar volumes, glyphs, and fibers can be colored using a wide array of coloring option. Customizable color loop-up tables allow for highly flexible visualization of scalar data. * Visualization and processing of various different HARDI formats is supported. HARDI data is interactively visualized using highly detailed glyphs rendered on the GPU. HARDI glyphs can be visualized in combination with DTI glyphs, for a better overview of complex diffusion data. * vIST/e includes support for NVIDIA's Compute Unified Device Architecture (CUDA), which enables highly parallel, GPU-based data processing, allowing for significant speed-up of computationally expensive algorithms.
Proper citation: vIST/e (RRID:SCR_001627) Copy
An integrated and flexible software package for processing of DTI data, and in general for the correction of diffusion weighted images to be used for DTI and potentially for high angular resolution diffusion imaging (HARDI) analysis. It can be run on both Linux and Mac platforms. It is composed of two modules named DIFF PREP and DIFF CALC. * DIFF_PREP - software for image resampling, motion, eddy current distortion and susceptibility induced EPI distortion corrections, and for re-orientation of data to a common space * DIFF_CALC - software for tensor fitting, error analysis, color map visualization and ROI analysis In addition, TORTOISE contains additional Utilities, such as a tool for the analysis of multi-center phantom data.
Proper citation: TORTOISE (RRID:SCR_001645) Copy
http://www.stat.cmu.edu/~fiasco/
Collection of software designed to analyze fMRI data using a series of processing steps. The input is the raw data, and the outputs are statistical brain maps showing regions of neural activation. Corrections for different systematic variations in the k-space (raw) data obtained from an fMRI session (head motion, ghosting, etc) are performed first. The image is then reconstructed (using the Fast Fourier Transform) and statistical analyses run. The user has a great deal of flexibility in choosing which corrections and statistics are executed. FIASCO emphasizes correct statistical models, for example for group comparisons.
Proper citation: Functional Image Processing software Computational Olio (RRID:SCR_001689) Copy
http://www.cabiatl.com/mricro/ezdicom/index.html
Software designed to display most medical images, including MRI, CT, X-ray, and ultrasound. All versions of ezDICOM can automatically detect the format of a medical image and display it on the screen. The software is easy to use, mature, and can view a wide range of medical images including proprietary formats as well as images in the DICOM standard. The software will also automatically recognize and display Analyze, GE (LX, Genesis), Interfile, Siemens (Magnetom, Somatom) and NEMA images.
Proper citation: ezDICOM (RRID:SCR_001686) Copy
A freely available software tool available for the Windows and Linux platform, as well as the Online version Applet, for the analysis, comparison and search of digital reconstructions of neuronal morphologies. For the quantitative characterization of neuronal morphology, LM computes a large number of neuroanatomical parameters from 3D digital reconstruction files starting from and combining a set of core metrics. After more than six years of development and use in the neuroscience community, LM enables the execution of commonly adopted analyses as well as of more advanced functions, including: (i) extraction of basic morphological parameters, (ii) computation of frequency distributions, (iii) measurements from user-specified subregions of the neuronal arbors, (iv) statistical comparison between two groups of cells and (v) filtered selections and searches from collections of neurons based on any Boolean combination of the available morphometric measures. These functionalities are easily accessed and deployed through a user-friendly graphical interface and typically execute within few minutes on a set of 20 neurons. The tool is available for either online use on any Java-enabled browser and platform or may be downloaded for local execution under Windows and Linux.
Proper citation: L-Measure (RRID:SCR_003487) Copy
http://www.idoimaging.com/program/280
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023.Comprised of a large array of sophisticated programs, this comprehensive software package with tools based around the MINC file format. Utilities are provided for conversion, viewing, editing, registering, segmentation, and a wide array of analysis. Many programs are in Perl. MINC software tools for neurological imaging are free. Input format: Analyze, DICOM, Minc
Proper citation: MINC Brain Imaging Toolbox (RRID:SCR_003519) Copy
http://wiki.na-mic.org/Wiki/index.php/2010_Winter_Project_Week_Spine_Segmentation_Module_in_Slicer3
3D Slicer module for automated segmentation of the spine. This is an implementation of a novel model-based segmentation algorithm. This work was presented at the NA-MIC Week in Salt Lake City, Jan 2010.
Proper citation: SpineSegmentation module for 3DSlicer (RRID:SCR_002593) Copy
http://www.nitrc.org/projects/tapir/
A set of command line tools allowing 2D and 3D image registration, mainly for medical imaging (although also relevant to other image registration problems).
Proper citation: TAPIR (RRID:SCR_002596) Copy
A toolbox with graphical user interfaces for processing infant brain MR images. Longitudinal (or single-time-point) multimodality (including T1, T2, and FA) (or single-modality) data can be processed using the toolbox. Main functions of the software (step by step) include image preprocessing, brain extraction, tissue segmentation and brain labeling. Linux operating system (64 bit) is required. A workstation or server with memory >8G is recommended for processing many images simutaneously. The graphical user interfaces and overall framework of the software are implemented in MATLAB. The image processing functions are implemented with the combination of C/C++, MATLAB, Perl and Shell languages. Parallelization technologies are used in the software to speed up image processing.
Proper citation: iBEAT (RRID:SCR_002470) Copy
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
http://www.vigenetech.com/microvigeneV3.0.htm
Automated software program for image analysis based on microarray based image application. Various output styles are available, including image overlay with warping and registration and scattered correlation plot with 2D or 3D spot profile. Outputs can be formatted in text, xml, excel, or custom format.
Proper citation: MicroVigene (RRID:SCR_002820) Copy
http://www.nikoninstruments.com/Products/Software/NIS-Elements-Basic-Research
Software tool for acquisition and device control for standard research applications, requiring four dimensional imaging. Provides access to advanced image capture, archiving, and analysis solutions that are easy-to-use and provide maximum workflow. Handles multi dimensional imaging with support for capture, display, data management, analysis and additional options for peripheral device control, and multi-dimensional acquisition. Provides advanced image processing options such as database capabilities and report generation, intensity over time measurement, and Extended Depth of Focus functionality.
Proper citation: NIS-Elements Basic Research (RRID:SCR_002776) Copy
http://www.perkinelmer.com/pages/020/cellularimaging/products/volocity.xhtml
3D image analysis software to visualize, analyze and validate 3D fluorescence images from a wide range of confocal microscopy, widefield and high content screening systems. It is fully integrated for a seamless user experience.
Proper citation: Volocity 3D Image Analysis Software (RRID:SCR_002668) Copy
http://www.loni.usc.edu/Software/SHIVA
A Java-based visualization and analysis application that can process 2D and 3D image files and provides convenient methods for users to overlay multiple datasets. * Simultaneous visualization of multiple image volumes. * Tools for labeling and masking of structures. * Framework for the Mouse Atlas Project.
Proper citation: Synchronized Histological Image Viewing Architecture (RRID:SCR_002690) Copy
http://www.math.uh.edu/~mpapadak/centerline/
An application for the automatic segmentation and tracing of three-dimensional neuronal images.
Proper citation: centerline (RRID:SCR_002961) Copy
http://www.jainlab.org/downloads.html
Automatic software program for microarray image quantification.
Proper citation: UCSF Spot (RRID:SCR_002985) Copy
http://code.google.com/p/rna-star/
Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays.
Proper citation: STAR (RRID:SCR_004463) Copy
http://www.picsl.upenn.edu/ANTS/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Software package designed to enable researchers with advanced tools for brain and image mapping. Many of the ANTS registration tools are diffeomorphic*, but deformation (elastic and BSpline) transformations are available. Unique components of ANTS include multivariate similarity metrics, landmark guidance, the ability to use label images to guide the mapping and both greedy and space-time optimal implementations of diffeomorphisms. The symmetric normalization (SyN) strategy is a part of the ANTS toolkit as is directly manipulated free form deformation (DMFFD). *Diffeomorphism: a differentiable map with differentiable inverse. In general, these maps are generated by integrating a time-dependent velocity field. ANTS Applications: * Gray matter morphometry based on the jacobian and/or cortical thickness. * Group and single-subject optimal templates. * Multivariate DT + T1 brain templates and group studies. * Longitudinal brain mapping -- special similarity metric options. * Neonatal and pediatric brain segmentation. * Pediatric brain mapping. * T1 brain mapping guided by tractography and connectivity. * Diffusion tensor registration based on scalar or connectivity data. * Brain mapping in the presence of lesions. * Lung and pulmonary tree registration. * User-guided hippocampus labeling, also of sub-fields. * Group studies and statistical analysis of cortical thickness, white matter volume, diffusion tensor-derived metrics such as fractional anisotropy and mean diffusion.
Proper citation: ANTS - Advanced Normalization ToolS (RRID:SCR_004757) Copy
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