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.

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.

Identifies local interactions and global biases in a wide range of cell biology experiments. DeBias is a mathematical tool for cell biologists that assists interpreting data. It assesses global bias and local interactions between coupled cellular variables. During the analysis of interacting variables, it proceeds to an elimination of confounding factors to simplify interpretation of results.

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.

Provides assistance for distance analysis and object-based 3D co-localization. DiAna incorporates two 3D procedures for image segmentation and 3D automated object-based co-localization in-depth analysis. It measures the distribution of distances between objects in 3D. This software allows users to label images and provides features tools for the segmentation of the objects and extended functionalities for 3D distance analysis and 3D measurements.

Allows spatial point pattern and interaction analysis. MosaicIA provides standardized ways to (1) correct for the influence of the distribution of points within one set onto the distance distribution to another set; (2) infer parameters of the interaction potential, such as the strength and length scale of the interaction; (3) perform statistical hypothesis tests for the presence of an interaction. It has been tested on both synthetic and real-world data.

Provides a method for determining true and random colocalization for experimental scenarios. CDA calculates modified Manders coefficients, M1ROI and M2ROI and detects colocalization in cellular and subcellular compartments thanks to standard confocal microscopy and computational image correlation techniques. The module can be used through the ImageJ software and can be applied to various fields including fluorescent wide field or confocal microscopy.

Quantifies colocalization of proteins within specific organelles in whole-cell images. OBCOL is a plugin for ImageJ that divides two, three and four-dimensional multichannel confocal microscope images into discrete structures. It can be useful to investigate and constitute sets of proteins within recycling endosomes of living cells. This tool simplifies calculations of a variety of statistical measurements from discrete structures.

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.

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.

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.

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.

Combines state-of-the-art automated neuron tracing and machine learning-enabled neuron classification tools. Aivia provides methods for analyzing time-lapse images. It covers a wide range of applications such as cell/nuclei counting, cell/nuclei tracking, 3D neuron detection and analysis, machine learning cell classification, particle tracking, wound healing and calcium oscillation tracking. Aivia also comes with editing tools to help get even better results.

Allows users to find and analyze colocalization of bright intensity spots such as cells, particles, vesicles, comets, or dots. ComDet needs an image containing two color channels to work on colocalization. It automatically detects the number of channels. After the detection, ComDet marks detected particles with rectangles of their own channel colour and colocalized particles in color.

Allows users to set the thresholds for colocalization analysis. Colocalization can generate a 2D Histogram/Scatterplot/Fluorogram useful for visualizing the correlation of the pixel intensities, over all pixels/voxels in the image. It also makes a linear regression fit of the data in the scatter plot. It does auto threshold determination, and uses an iterative procedure to determine what pair of thresholds for the 2 channels of the scatterplot give a Pearson's correlation coefficient (r) of zero for the pixels below the thresholds.

Displays a correlation diagram for two images.

Manages instrument control, image processing and data analysis. SlideBook can drive hundreds of devices including microscopes, stages, lasers, wheels, piezos, scanners or shutters. It acquires data in 3D format over time, color, and specimen locations in customizable experiment protocols. This tool offers a solution to investigate images and obtain statistical data via a wide variety of algorithms while maintaining original data integrity.