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.
A re-slicing browser for terabyte-sized multi-view image sequences. BigDataViewer was developed with multi-view light-sheet microscopy data in mind and integrates well with Fiji's SPIMage processing pipeline. Conceptually, the visualized data comprises multiple data sources. Each source provides one 3D image (for each time-point in the case of a time-lapse sequence). For example, in a multi-angle selective plane illumination microscopy (SPIM) sequence, each angle is a source. In a multi-angle, multi-channel SPIM sequence, each channel of each angle is a source. BigDataViewer comes with a custom data format that is optimized for fast random access to very large data sets. This permits browsing to any location within a multi-terabyte recording in a fraction of a second. The file format is based on XML and HDF5. Images are represented as tiled multi-resolution pyramids, and stored in HDF5 chunked multi-dimensional arrays. The XML file contains metadata, for example the registration of sources to the global coordinate system.
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.
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.
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.
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.
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.