Integrates current global statistic methods. JACoP is a colocalization analysis tool which combines currently used colocalization methods and an object-based tool named three-dimensional (3D) object counter as plugins to the public domain ImageJ software. In order to simplify its utilization, this tool includes a many functions allowing users to select image side-by-side.
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Serves for colocalization analysis. Coloc consists in a Fiji's plugin that implements and performs the pixel intensity correlation. This tool requires a two color image for realizing analysis, and users can specify their region of interest (ROI) for obtaining accurate results. It gathers an auto threshold calculation method and effect of noise on Pearson's and Manders' coefficients.
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.
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.
Performs the Costes test for statistical significance. Colocalization test is ImageJ plugin that executes one of a set of three statistical tests. It also compares the Persons correlation coefficient of two colour channels in the real image data against a white noise image, or the same image data with one of the colour channels spatially shifted.
An imaging and image analysis framework for virtual colocalization studies in larval zebrafish brains. ViBE-Z contains a database with precisely aligned gene expression patterns, an anatomical atlas, and a software. ViBE-Z software creates high-quality data sets through fusion of multiple confocal stacks, it aligns 3D gene or protein expression patterns of different zebrafish larvae of a given developmental stage to a common reference, and it stores the aligned patterns in the ViBE-Z database. Together with the anatomical segmentation (ViBE-Z atlas), this database allows users to explore the colocalization of all contained patterns in their anatomical context.
A live cell imaging, tracking & analysis software that rises to the challenge of monitoring temporal changes in biological systems (2D and 3D images over time). ImarisTrack is based on a choice of multiple sophisticated manual and automatic tracking algorithms and also includes an intuitive and interactive track editing tool if manual correction is necessary.