Analyzes, processes and visualizes multi-dimensional microscopy images. BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes.
Designed for easy visualization and analysis of multidimensional image data. VisBio software is an end-user application built from the ground up to handle visualization and analysis of multidimensional image data, regardless of size or dimensionality. By creating low-resolution thumbnail images during data import, the program conserves memory while providing fluid image browsing and animation capabilities. Other tools include flexible color mapping, semitransparent volume rendering, 3D slicing at arbitrary orientations, 3D measurements, movie capturing, and powerful data export tools.
Serves for effective segmentation of multidimensional datasets. MIB can recognize several number of imaging formats and offers a variety of image processing tools. It also simplifies utilization and quantification of acquired data. It permits users to segment large datasets, to realize 3D visualization, and to quantify images and models. Its parameters enable users to insert plugin s to customize the program for specific needs.
An application for semi-automated tracing of neurons to quickly annotate noisy datasets and construct complex neuronal topologies. Simple Neurite Tracer is designed to allow easy semi-automatic tracing of neurons or other tube-like structures (e.g. blood vessels) through 3D image stacks. The plugin has built-in tools for analysis and hardware accelerated 3D visualization of the results. Data can be imported and exported in SWC files for interaction with other software, or details of the traces can be exported as CSV files for analysis in spreadsheets or statistical software. The native file format is open and XML-based.
Allows to navigate, share and collaboratively annotate massive image data sets of biological specimens. CATMAID combines three main components: a centralized data server, decentralized image servers and the client-side user interface. The interface is applicable to any 2D or 3D multimodal biological image datasets, as shown in examples of stitched confocal 3D volumes. Additionally, the interface can be used to navigate, annotate and bookmark locations in any large image canvas.
An interactive 3D axon tracking and labeling tool to obtain quantitative information by reconstruction of the axonal structures in the entire innervation field. AxonTracker-3D has been developed to facilitate the connectome function analysis in large-scale quantitative neurobiology studies. It can display the three orthogonal views of the current location of the centerline along with a visualization of the tracking results. The workflow consists of three steps: (i) re-slice the axon tubes along its orientation; (ii) extract 2D and 3D features from the slices and spheres rounding the center points; (iii) select samples to train AdaBoost classifier. Questions such as whether the spatial distribution of the axons are random in nature or follow a certain pattern can be answered with this tool.
An interactive Qt4 analysis tool for attaching the intrinsic root coordinate system to 3-D confocal recordings of the Arabidopsis root apical meristem. This allows quantitative comparative studies of root populations in a sound and intuitive context. iRoCS Toolbox consists of the data browser labelling and a set of command line tools for batch processing. Main features are: (i) 3-D Visualization of the volume in an orthographic view; (ii) manual annotation of anatomical reference structures (QC, nuclei); (iii) automatic detection and annotation of cells and/or nuclei with several meaningful properties, like position, radius, tissue, cell file, cell cycle state, volume; (iv) full control. Any step can be manually corrected and re-fed into the modeling; (v) retrieval and localization of key events like cell divisions.
Enables rapid identification of phenotypically abnormal structures. Data are easily loaded by drag and drop, with support for most commonly used file formats. On loading the registration results, embryos may be overlaid with the t-statistic heatmaps to reveal regions of dysmorphology. We have adopted a hot red/blue colour scheme to be consistent with previously reported results. The heatmap data can be filtered by t statistic value to emphasize regions of different statistical significances. Vector field data can also be loaded into VPV and filtered by magnitude to identify where the most significant deformations have taken place during registration.
Offers a platform for handling dendritic structures. TREES Toolbox is a standalone software that allows users to create realistic synthetic branched structures and to automatically rebuild neuronal branching. The application provides methods to investigate and visualize both dendritic and axonal trees as well as their branching. The application is also able to compare multiple branching structures.
Provides solutions to users for viewing, modeling, and analyzing 3-D image data for structural biology. IMOD is designed for observing data from tomographic, serial section, and optical section reconstructions. Moreover, this program is also able to measure areas, volumes, and contour lengths, and to count objects of any model class.
Exploits volumetric data and eases research in volume rendering. Drishti implements mesh generation and coloring options. It can resample, filter, enhance contrast and trim the volumes inputted. It serves to visualize volume rendered images. This tool permits researchers to make certain regions transparent based on the surface normal. It can be applied to tomography data or electron-microscopy data.
Allows users to visualize and compare multiple 3D image datasets. JIV provides a method to display 3D medical imaging datasets by three orthogonal 2D slices through the same location in the volume. It assists users to observe slices side-by-side, all at the same position in the volume. This software can be used in remote data processing - when data goes to a central, well-equipped, site for image processing and storage.
Restores images from microscopic data. Huygens is based on the deconvolution approach that reassigns out-of-focus light to its origin, thus improves signal-to-noise in images. It can use physically-acquired or simulated point-spread functions (PSFs) for characterization of optical system being deconvolved. The tool shows high-performance in in-house tests on deconvolution compared to other software packages. It provides intuitive wizards for parameter selection and processing.
Allows to realize analysis and visualisation of 3D biological image data, and more particularly traced neurons. NAT accepts 3D images in NRRD and 'Amira' AmiraMesh formats. The data can be manipulated and visualized in 3D. The manipulation includes applying calculated registrations, e.g. using the 'CMTK' registration suite. This tool permits morphological comparison between neurons including clustering and searching.
Assists in updating image calibration after the first reslicing. Dynamic Reslice is a plugin for ImageJ and enables orthogonal slice through the volume represented by the stack. This software is compatible with the Fiji script. Users can use this plugin to drawn resliced window and change the region of interest (ROI) shape with some options like a 90° rotation or a vertical flip.
Allows browsing of time series of multi-channel image-stacks. Image5D is a new image type for ImageJ that holds time series of z-stacks. This package is a collection of plugins that can open, save and process Image5Ds. It aims to show Image5Ds in a window that displays x/y sections of the image at the selected slice, frame and channels.
Assists in the creation and visualization of 3D fluorescence volume rendering. MicroSCoBioJ contains three plugins: (1) Mesh Maker MicroSCoBioJ that computes the triangles or tetrahedra mesh corresponding to an user-defined treshold; (2) Mesh Viewer MicroSCoBioJ that shows up to four different meshes and displays the mesh as points, lines, or fill surface; and (3) WAT MicroSCoBioJ Weight Adaptive Threshold.
Combines state-of-the-art automated neuron tracing and machine learning-enabled neuron classification tools. Aivia provides methods for analyzing time-lapse images. It covers a wide range of applications such as cell/nuclei counting, cell/nuclei tracking, 3D neuron detection and analysis, machine learning cell classification, particle tracking, wound healing and calcium oscillation tracking. Aivia also comes with editing tools to help get even better results.
Enables users to view the sample. Pannoramic Viewer is a digital microscope application that permits to make annotations and measurements. These functions can be easily expanded through its various software modules. It provides several features: (i) Seamless zooming and moving of the virtual slide, (ii) bookmarking on the spot, defining the specific part of the sample by drawing, finding and reading of previously made bookmarks, or (iii) fluorescent slide handling, separate channel view & pseudo-colorization.
Allows users to visualize, manipulate, and understand data from imaging modalities such as computed tomography, microscopy or Magnetic resonance imaging (MRI). Amira 3D Software for Life Sciences provides features to import and process 2D and 3D images data, visualization techniques and tools for visual analysis. Users can also create and share presentations. The base product can be customized by adding functional extensions to fit special needs in different application areas.
Displays datasets from confocal laser scanning microscopy (CLSM). PView offers a graphical platform that allows users to interplay with pre-computed models as well as to figure large objects. It includes several features coupled to speed up techniques for picking up multiple models’ resolutions and changing scene colors or grid step.
Manages instrument control, image processing and data analysis. SlideBook can drive hundreds of devices including microscopes, stages, lasers, wheels, piezos, scanners or shutters. It acquires data in 3D format over time, color, and specimen locations in customizable experiment protocols. This tool offers a solution to investigate images and obtain statistical data via a wide variety of algorithms while maintaining original data integrity.
Contains functionalities for processing and analysis image data. GoFigure2 is a platform which allows users to visualize and navigate through 4D multichannels bio-images. Besides, it aims to provide an automatic segmentation of nuclei and cell membranes and to enable the way of extracting data from bio-images.
Allows deconvolution and visualization of image sets. AutoQuant is a package of 2D and 3D restoration algorithms that permits users to improve the resolution and contrast of images that have undergone distortions during the image acquisition process, for thus improving their analysis. Users can choose the algorithm that fits their requirements.
Assists in focusing microscopic images of 3D objects and organisms. Extended Depth of Field is based on different wavelet algorithms. This ImageJ plugin offers users two interfaces: a simplified mode and an expert mode with a complete set of parameters. It benefits from a RGB to grayscale conversion method that assures contrast and intensity in order to process color data.
Permits creation, edition, and annotation of a collection of globular objects. VANO is a cross-platform 3D annotator that can be used to build a 3D digital nuclei atlas for Caenorhabditis elegans and a 3D digital atlas of the nuclei of the ventral nerve cord of late stage Drosophila melanogaster embryos. This tool also serves for annotating images in contexts where the image objects have an irregular shape or for collecting prior information and statistics of image objects.
Offers a viewer for atlases. JAtlasView is a standalone software furnishing features to locate and display sections through the data while providing a 3D visualization. The JAtlasVIewer includes functions to manage data, 3D visualization, orientation, anatomy and sections that have to be displayed. This application is built as a modular program that can be customized or integrated within other software.
Allows to explore complex microscopy data. Voxx is a volume visualization software provides interactive inspection and manipulation of 3D images on personal computers (PCs). The software renders set of images in back-to-front order, combining them by using alpha blending or maximum intensity projection and user-defined transfer functions. It is also useful for qualitative assessment of complex intracellular structures.
Allows visualization of scientific images. viewer4d is a cross-library for inspection of 2D, 3D, as well as 4D images, i.e. a time-lapse sequence, or collection of results of image processing parametric study, of 3D images. The software can zoom in and inspect values of individual voxels and their neighborhood. It aims to assist scientist in addressing their daily images inspecting activities.
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