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.
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.
Allows users to augment custom-built light-sheet microscope with real-time visualization capabilities. ClearVolume enables live streaming of 3D data in real time over the Internet, and permits the immediate 3D perception of the imaged processes. It can be used for aligning and calibrating light-sheet microscopes. Moreover, the overall 3D point spread function of the optical system and the full 3D structure of the beam can be visualized.
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 automated workflow for processing large multiview, multi-channel, multi-illumination time-lapse selective plane illumination microscopy (SPIM) data on a single workstation or in parallel on a HPC cluster. The pipeline relies on snakemake to resolve dependencies among consecutive processing steps and can be easily adapted to any cluster environment for processing SPIM data in a fraction of the time required to collect it.
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.
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.
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.
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.
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.
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.
0 - 0 of 0
1 - 3 of 3