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.
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.
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 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.
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.
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.