Multidimensional microscopic image data sets are widely used in modern biology studies, especially in screening various phenotypic data. Analyzing microscopic data is highly useful and fruitful, such as observing the dynamics of microtubule spindles during mitosis, profiling gene expression of cells, and reconstructing the three-dimensional (3D) morphology of neurons. Image visualization also enables effective development of high-content high-throughput bioimage informatics techniques to extract biologically meaningful knowledge from microscopic images.
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.
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.
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.
Allows users to analyze and visualize electron microscope (EM) tomography data. EM3D is a program that contains a graphical user interface (GUI), and that can combine dual axis data sets, i.e two data sets taken orthogonal to one another. It provides a set of analysis tools to quantify structural information from the models, including their moments, proximity relationships, and spatial reliability.
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.
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.
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.