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.
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.
Assists users to analyze spatial point patterns. spatstat is a program containing the following functions: model-fitting, exploratory data analysis, and simulation. This program permits users to manage different datasets including among other inhomogeneous point patterns, spatial sampling regions of arbitrary shape. Furthermore, it embeds an algorithm allowing researchers to fit point process models to point pattern data.
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.
Performs measurement of object-based fluorescence signal colocalization in biological systems. MatCol is an object-based colocalization tool designed to produce reproducible measurements and increase the speed at which object-based colocalizations can be quantified. The software can be used to visualize protein and/or DNA colocalizations and fine tune user-defined parameters for the colocalization analysis, including the application of median or Wiener filtering to improve the signal to noise ratio.
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.