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CUBIC / Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis
Provides a cleared 3D brain image processing and analysis methods for light-sheet fluorescence microscopy (LSFM). CUBIC is a standalone software getting its name from the CUBIC protocol wich is a chemical sample clearing protocol especially designed for brain tissues. It provides multiple functionalities: (i) The image file conversion and manipulation, (ii) the detection of sample edges, (iii) the brain alignent and (iv) the atlasing of the brain sample.
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.
BDV / BigDataViewer
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.
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.
LLSpy / Lattice light-sheet post-processing utility
Simplifies lattice light sheet data processing. LLSpy automates: the detection of experimental parameters from the data folder structure and metadata, and the choice of optical transfer functions (OTFs). It can conduct image corrections and manipulations, and simplifies file handling. This tool provides functions such as drag-and drop queue or visual progress indicator. It can be used with a graphical user interface or a command line interface.
Amira 3D Software for Life Sciences
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.
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