Advances in imaging techniques and high-throughput technologies are providing scientists with unprecedented possibilities to visualize internal structures of cells, organs and organisms and to collect systematic image data characterizing genes and proteins on a large scale. To make the best use of these increasingly complex and large image data resources, the scientific community must be provided with methods to query, analyze and crosslink these resources to give an intuitive visual representation of the data.
Allows users to visualize 3D/4D/5D image and to analyze system for bioimages and surface objects. Vaa3D consists of a container of modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics) and data management. Moreover, this platform can be used for developing 3D image analysis algorithms for high-throughput processing.
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.
Permits 2D visualization and interpretation of 3D image stacks. SME is an ImageJ/Fiji plugin that focuses on maintaining spatial consistency in the projection both within one channel and between channels. The software provides a 2D representation with minimal distortion for objects lying on or close to a 2D manifold embedded in the 3D-observed volume. It (i) improves spatial consistency, (ii) preserves image resolution, (iii) preserves consistency between multiple channels, (iv) works on wide-field and confocal image stacks, and (v) is parameter free.
An open source, platform-independent viewer making use of the latest web technologies that allows seamless access to images and associated metadata for each image. HTML5 PivotViewer provides a powerful method to allow end users to mine their data.
A plugin for bone image analysis in ImageJ. BoneJ provides free, open source tools for trabecular geometry and whole bone shape analysis. It calculates several trabecular, cross-sectional and particulate parameters in a convenient format. Java technology allows BoneJ to run on commodity computers, independent of scanner devices, fully utilising hardware resources. ImageJ’s plugin infrastructure provides a flexible working environment that can be tailored to diverse experimental setups. BoneJ is a working program and a starting point for further development, which will be directed by users’ requests and the emergence of new techniques.
Allows the extraction of junctions, centerlines and filament lengths of biopolymer networks in 2D and 3D images. SOAX provides users a solution to analyze quantitatively, reproductively, and objectively the image data. It uses the stretching open active contours (SOACs) method to initialize automatically images. This tool permits 3D visualization in order to visually check results against the image and to explore image data.
Automates analysis of neuronal morphologies in immuno-fluorescence images. SynD intends to assist users in quantifying dendrite and synapse characteristics. The application performs successively the detection of soma, neurites, and synapses. It can be used to enable the simultaneous analysis of multiple morphological features and permits the screening of genetic and pharmacological treatments.
Allows users to implement and assemble control software for custom-built microscope systems. Helio provides a framework, built around a collection of components arrangeable according user needs, which can support multiple hardware and functional combinations. The application is able to handle a wide range of laser-scanning including galvanometric scan mirrors or resonant scanners as well as camera images.
Offers a platform of pre-processing image tools. Scintillate is an open source software that allows users to evaluate time-series calcium imaging. It was developed with the aim of complementing the existing acquisition and pre-processing systems. The application includes a set of methods for detection and visualization of images. It can estimate the value of the sample being viewed, assess the viability of the preparation in seconds, spare microscope time, lamp hours and reduce distress to the subject.
Allows to visualize confocal microscopy data. FluoRender can preserve original fluorescence intensity values on graphics hardware and supports far more than three Red-Green-Blue (RGB) channels. It permits to proceed analysis of many channels of volume data from mutant-control scans and to construct anatomical atlases. The tool allows to visualize simultaneously 96 independent channels without convertion into RGB channels or pseudosurfaces.
Furnishes applications for images treatment, analysis, visualization and development of algorithms in C or C++. Image Processing Toolbox permits to segment pictures, improve the quality, reduce the noise and background, treat 3D images. It can be used for geometrical transformations and calibration of images. This tool is able to automate these tasks and to interactively manipulate region of interest (ROI).
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.
A version of the public domain image analysis software NIH Image that has been extended to handle the loading, display and analysis of scanning microscope images. Image SXM supports SAM, SCM, SEM, SFM, SLM, SNOM, SPM and STM images.
Offers read-only access to the information contained in files in CZI format. libCZI provides several functionalities such as: (1) reading subblocks and get the content as a bitmap; (2) reading subblocks which are compressed with JPEG-XR; (3) works with tiled images and pyramid images; (4) composing multi-channel images with tinting and applying a gradation curve; and (5) giving access to metadata.
Performs high-throughput cell tracking and ancestry recording. CellAnimation is useful for a number of microscopy assays such as colony and cell counting or focal adhesion tracking. It permits users to choose multiple cell sub-populations based on shape and motility parameters and to construct multiple virtual stains that highlight specific sub-populations. This tool offers solution for the exploration of patterns and clusters that may be present in the cell population.
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.
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