Image visualization software tools | Super resolution imaging analysis
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.
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.
Allows deconvolution and visualization of image sets. AutoQuant is a package of 2D and 3D restoration algorithms that permits users to improve the resolution and contrast of images that have undergone distortions during the image acquisition process, for thus improving their analysis. Users can choose the algorithm that fits their requirements.
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.
Provides a complete set of tools for automated processing, analysis and visualization of data acquired by single-molecule localization microscopy (SMLM) methods. ThunderSTORM is a program that offers many different processing and post-processing methods so that users can adapt the analysis to their data. It is able to process the data using any combination of the implemented feature enhancing, spot detection and fitting methods.
Allows browsing of time series of multi-channel image-stacks. Image5D is a new image type for ImageJ that holds time series of z-stacks. This package is a collection of plugins that can open, save and process Image5Ds. It aims to show Image5Ds in a window that displays x/y sections of the image at the selected slice, frame and channels.
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.
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.