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 open access and user friendly 3D automatic quantitative analysis tool for single plane illumination microscopy (SPIM) data. OpenSegSPIM is designed to extract quantitative relevant information from SPIM image stacks, such as the number of nuclei/cells and provide quantitative measurement (volume, sphericity, distance, intensity) on light sheet microscopy (LSM) images. Typically, it is a useful quantitative analysis tool for different biological samples such as neurospheres, zebrafish embryos, drosophila embryos, skin sample, mouse embryos and other organotypic cell culture. The OpenSegSPIM pipeline consists of a succession of step each one being enabled once the previous step has been completed. To provide a simple interface OpenSegSPIM minimizes the number of parameters without loss of segmentation quality. Furthermore, parameter input is an interactive process. For example, image smoothing is done in a few steps and the user only needs to measure the diameter of the nuclei. To facilitate the difficult step of parameter tuning the intermediate results are visualized in real time and can be evaluated.
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.
Provides a root system architecture characterization software. ARIA is based on a mathematically rigorous approach of converting root images into graphs. It automates phenotyping with the potential of adding additional features. This tool completes large phenotyping experiments required for many quantitative genetic studies. It is able to analyze 2D flat plane images and 3D images of roots.