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A software application that automatically detects neurons (dendritic trees, axons and spines), microtubules, and other filament-like structures in 2D, 3D and 4D. Imaris FilamentTracer uses strategies that involve an optimal combination of automated analysis and operator decision. The choice of the best method is an essential element in optimizing efficiency. FilamentTracer allows the choice between four complementary tracing strategies ranging from manual to automatic and utilizes a creation wizard to easily guide the user through the creations steps. It has been specifically designed to deal with the complex problem of spine analysis over time.

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• SciCrunch
• 17 years ago - by Anonymous

An interactive, graphic, fiducial marking software for placing, editing and tracking fiducial marks on images in a tomography tilt series. You can also use this tool to view the tilt series as well as crop it.

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• SciCrunch
• 17 years ago - by Anonymous

A cross-platform system for exploring diffusion tensor images and to reconstruct fiber tracts between two regions of interest, intended for tdoctors, medical technicians or medical researchers. The Fiber-Tracking tool allows the user to load data from MRIs or similar images (like a basic 3D image viewer), load DTI datasets (7 diffusion- weighted images), calculate the fractional anisotropy (FA) and the mean diffusivity (MD) images, and also load ROIs to reconstruct fibers.

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• SciCrunch
• 17 years ago - by Anonymous

FACT (Functional MRI Analysis and Clustering Tools) is free software for analyzing time series data like fMRI and perfusion MRI. It provides correlation analysis, t-test and temporal clustering analysis -- Kohonen Clustering Network and Fuzzy Clustering. A set of analysis tools applicable to fMRI time-series data.

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• SciCrunch
• 17 years ago - by Anonymous

EM3D is a software application designed to facilitate the analysis and visualization of electron microscope (EM) tomography data by cellular and molecular biologists. Such data are collected as a tilt series, a sequence of 2D electron micrographs taken at many tilt angles with respect to the electron beam. EM3D features an integrated graphical user interface that automates most of the initial alignment and reconstruction of the tilt-series data to form a 3D volume. These functions seamlessly connect with segmentation and model-generation tools that permit the user to easily and reliably extract specific structural components from the reconstructed volume. The 3D models can then be visualized and manipulated using an extensive package of surface- and volume-rendering techniques. EM3D also provides a set of analysis tools to quantify structural information from the models, including their moments, proximity relationships, and spatial reliability. Altogether, EM3D facilitates the analysis of 3D cell structure at the full resolution of a reconstructed volume (2-3 nm)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

Software tool as biological sequence alignment editor written for Windows 95/98/NT/2000/XP/7 and sequence analysis program. Provides sequence manipulation and analysis options and links to external analysis programs to view and manipulate sequences with simple point and click operations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

Software collection of libraries and applications implementing large parts of DICOM standard for medical image communication.Includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over network connection, as well as demonstrative image storage and worklist servers.

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• SciCrunch
• 17 years ago - by Anonymous

COMKAT is a software package for compartmental modeling oriented for biomedical image quantification. Free for academic research use, COMKAT has various functions for modeling and imaging analysis in both command-line function and GUIs. COMKAT is MATLAB software for compartmental modeling oriented to nuclear medicine applications (PET & SPECT). It supports models of a wide range complexity including multiple injection, receptor model with saturation. It supports many image formats, including DICOM images. Using either the command line interface or GUI, models are easily specified, solved or used to fit experimental data. Sensitivity equations are supported. No mathematical derivations are required on the part of the user.

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• SciCrunch
• 17 years ago - by Anonymous

Software tool to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. It counts cells and also measures the size, shape, intensity and texture of every cell (and every labeled subcellular compartment) in every image. It was designed for high throughput screening but can perform automated image analysis for images from time-lapse movies and low-throughput experiments. CellProfiler has an increasing number of algorithms to identify and measure properties of neuronal cell types.

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• SciCrunch
• 17 years ago - by Anonymous

A group of software packages for image analysis, mainly used in MRI image processing. BRAINS (Brain Research: Analysis of Images, Networks, and Systems) contains manual and automated tools for structural identification and methods for tissue classification and cortical surface generation. BRAINS2 is most commonly used to analyze magnetic resonance (MR) scans, but the package can also be used to analyze images acquired with positron emission tomography (PET), single photon emission computed tomography (SPECT), and functional magnetic resonance (fMR). It is implemented in an object-oriented, cross-platform compatible manner and includes a toolbar and command line interface, a graphical interface, and a computational kernel.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 19, 2015. Commercial brain atlases distributed by Theime Medical Publishers. It supports a complete electronic version of the Talairach Atlas, as well as gyral-level description of the human brain and atlases for cerebral vasculature, cranial nerves and a probabilistic functional atlas. In addition, this tool permits the incorporation of user image data, both structural and functional, into the viewer for direct co-visualization with the atlas. This CD-ROM provides numerous tools for the analysis of functional images: It contains the fully color-coded and labeled Talairach-Tournoux brain atlas in the axial, coronal and sagittal orientations, along with Brodmann''s areas and gyri in the axial orientation. -Allows anatomical and functional images to be loaded and registered. -Enables interactive placement of the Talairach landmarks in 3D Space. -Provides automatic data-to-atlas warping based on the Talairaich proportional grid system transformation. In addition, real-time interactive warping for fine tuning is available. -Allows the user to place marks on the activation loci in the warped functional images, display these marks with the atlas, and edit them simultaneously on the axial, cornal and sagittal orientations. Mark placement is assisted by a grey-value thresholding feature. -Provides simultaneous display of the atlas, anatomical image and functional image withing one interactively blended image. Atlas-data blending and anatomical-functional image blending are controlled independently. -Labels the data by means of the atlas. The atlas can be flipped left/right so that Brodmann''s areas areas and gyri can be labeled on both hemispheres. -Provides additional functions such as friendly navigation, simultaneous display of axial, coronal and sagittal atlas plates, cross-referenced display, image and atlas sequencing, readout of the Talairach coordinates and intensities, save, print, help.

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• SciCrunch
• 17 years ago - by Anonymous

Microtomy is a standard technique used for 2D microscopy, but it can also provide the foundation for 3D analysis using AutoAligner. AutoAligner reads a stack of serial sections and automatically aligns the single images, building up a 3D space that can be explored using Imaris. Each image is aligned in translation and rotation relative to its precursor image in the sequence. In addition to a fully automated mode, AutoAligner also provides manual control for neighboring images that are too different from each other for automatic alignment. The visual alignment tool uses fast display techniques for aligning images in real time.

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• SciCrunch
• 17 years ago - by Anonymous

BrainVISA is a modular an customizable software platform built to host heterogeneous tools dedicated to neuroimaging research. Many toolboxes have already been developed for BrainVISA (T1 MRI, sulcal identification and morphometry, cortical surface analysis, diffusion imaging and tractography, fMRI, nuclear imaging, EEG and MEG, TMS, histology and autoradiography, etc.). Anatomist is a software for interactive visualization of multimodal data and for manipulation of structured 3D objects. It allows to build scenes that merge or combine images, meshes, regions of interest, fibers, textures, color palettes, referential changes, etc. A user can interact in 3D and in real time with the objects of an Anatomist scene: change point of view, select objects, add/suppress objects, change colors, draw regions of interests, do manual registration, etc. BrainVISA main features are: * Harmonization of communications between different software. For instance, BrainVISA toolboxes are using home-made software but also third-party software such as FreeSurfer, FSL, SPM, nipy, R-project, Matlab, etc. * Ontology-based data organization allowing database sharing and automation of mass of data analysis. * Fusion and interactive visualization of multimodal data (using Anatomist software). * Automatic generation of graphical user interfaces. * Workflow monitoring and data quality checking. * Full customization possible. * Runs on Linux, Mac and Windows. * Programming Language: C++, Python * Supported Data Format: ANALYZE, DICOM, GIfTI, MINC, NIfTI-1, Other Format

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• SciCrunch
• 17 years ago - by Anonymous

Software tool for visualizing, manipulating, and understanding data from tomography, microscopy, MRI and other imaging processes.Used to import and export options, to processes 3D image filtering and DTI based fiber tracking to visualization, volume and surface rendering, author tools for virtual reality navigation, video generation, and more.

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• SciCrunch
• 17 years ago - by Anonymous

Data analysis software with the following main features: fMRI spatial and temporal pre-processing (gaussian filtering) with motion correction, time slicing and template co-registration ; fMRI multithreaded bloc processing with one or more conditions (up to 999), lateralization index, paradigm design (box-car style with HRF convolution), anatomic coregistration, multiplanar reconstructions, opengl 3D surfacic rendering. DPTools and Activ 2000 are now one single software: DPTools v 3.0 and above. All the features already included in DPTools are available for the fMRI processings (statistics, motion correction, time slicing, aso). DPTools 3.0 can read Siemens Mosaic and Philips REC/PAR files for diffusion / dynamic series, and can export files to SPM99 format. Features: * Images Conversion * Paradigm Creation * Images Pre-Processing * Images Processing * Statistics * Co-registration * 3D * Filming * Loading / Saving * Batch Script * PACS Integration * and more... Activ 2000 is freely downloadable (46 MB)

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• SciCrunch
• 17 years ago - by Anonymous

Data-, machine-, and application- independent software system for the visualization and analysis of multidimensional images. This transportable, very inexpensive software system, has capabilities for visualizing, manipulating, and analyzing multidimensional, multimodality image information. It is designed to run on Unix machines under X-windows. It uses a data protocol that is a multidimensional generalization of the ACR-NEMA standards. We have tested it extensively on SGI and Sun workstations and PCs. Other recipients of 3DVIEWNIX have installed it on a variety of platforms including IBM RS6000s, HP700s, and Stardent, all from a single source code version. UNIQUE FEATURES OF 3DVIEWNIX * Transportable - based on UNIX, X-window, and C * Based on multidimensional generalization of ACR-NEMA standards of data representation * Application-independent * Image dimensionality independent * Can handle rigid, non-rigid, static, and dynamic objects and object assemblies * Can handle object information from multiple modalities and longitudinal acquisitions * Multitudes of visualization, manipulation, and analysis methods incorporated * Open software system distributed with source code

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software tool to correct gradient non-linearity distortions in MR structural images. This correction improves test-retest reproducibility crucial for multi-site studies.

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• SciCrunch
• 17 years ago - by Anonymous

A plated array of approximately 450 small molecules that have a history of use in human clinical trials. The collection was assembled by the National Institutes of Health (NIH) through the Molecular Libraries Roadmap Initiative as part of its mission to enable the use of compound screens in biomedical research. Similar collections of FDA approved drugs have proven to be rich sources of undiscovered bioactivity and therapeutic potential. The clinically tested compounds in the NCC are highly drug-like with known safety profiles. These compounds can provide excellent starting points for medicinal chemistry optimization and, for high-affinity targets, may even be appropriate for direct human use in new disease areas.

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• SciCrunch
• 17 years ago - by Anonymous

Diffusion tensor imaging (DTI) tractography: An automated system for etiologic classification of ischemic stroke -- Causative Classification System for Ischemic Stroke DTI Task Card for Siemens systems, DTI Visualization platform independent tool kit, PWI analysis tools for bolus-tracking data

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• SciCrunch
• 17 years ago - by Anonymous

Database and associated software tools providing access to clinical and research data on stroke, including deidentified patient data. Data types include imaging (e.g. CT, MRI, PET), clinical demographic data, genetic data, simulation perfusion data for verifying deconvolution algorithms used in bolus-tracking perfusion-weighted imaging (PWI). Also available are programs for performing deconvolution of bolus-tracking PWI, DTI tractography and an automated program for etiologic classification of ischemic stroke -- Causative Classification System for Ischemic Stroke (CCS)

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• SciCrunch
• 17 years ago - by Anonymous