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.
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.
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.
Assists users in measuring intercellular colocalization. CIRCOAST is an application that characterizes colocalization with network structures independent of the changes in cell and vessel network density found across study groups from both in vitro and in vivo experiments. This method supports the analysis of 2D images that are maximum projections of 3D confocal z-stacks. It is limited to approximating cells as circular shapes.
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.
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.
Displays the localization of signals and measures colocalization in microscopy images. EzColocalization simplifies customization of analyses for a wide variety of experiments and researcher needs. It can choose specific types of cells or organisms, visualize and measure colocalization, and automate analyses. This tool can solve real-world problems in diverse image sets. It is useful for estimating where particular types of molecules occur in cells and organisms in relation to other types of molecules.
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.
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 users to analyze colocalized points for GFP-LC3 and mCherry on confocal images. Green and Red Puncta Colocalization starts from RGB files derived from epifluorescent micrographs and can be run through the ImageJ software. The plugin can be used to highlight, calculate and tabulate the traces of green, red and colocalized puncta. Users can also count the total of number of cells detected in the field.
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.
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. Colocalization_Finder is a graphical module that allows users, by drawing a rectangular selection on a diagram, to highlight corresponding pixels on a RGB overlap of the original images, and if selected, on a 3rd image. The analysis can be restricted to pixels having values with a minimum ratio.
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.