Colocalization evaluation software tools | Laser scanning microscopy image analysis

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.