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 open-source segmentation software using Voronoï tessellation constructed from the coordinates of localized molecules. It allows precise, robust and automatic quantification of protein organization at different scales, from the cellular level down to clusters of a few fluorescent markers. SR-Tesseler is insensitive to cell shape, molecular organization, background and noise, allowing comparing efficiently different biological conditions in a non-biased manner, and perform quantifications on various proteins and cell types. SR-Tesseler software comes with a very simple and intuitive graphical user interface, providing direct visual feedback of the results.
Serves for effective segmentation of multidimensional datasets. MIB can recognize several number of imaging formats and offers a variety of image processing tools. It also simplifies utilization and quantification of acquired data. It permits users to segment large datasets, to realize 3D visualization, and to quantify images and models. Its parameters enable users to insert plugin s to customize the program for specific needs.
Provides a user-friendly means of visualizing, filtering and analyzing localization microscopy (LM) data. PALMsiever includes drift correction, clustering, intelligent line profiles, many rendering algorithms, and 3D data visualization. It incorporates the main analysis and data processing modalities used by experts in the field, as well as several new features we developed, and makes them broadly accessible. It can easily be extended via plugins and is provided as free of charge open-source software.
An interactive open-source software with a graphical user interface, which allows performing processing steps for localization data in an integrated manner. This includes common features and new tools such as correction of chromatic aberrations, drift correction based on iterative cross-correlation calculations, selection of localization events, reconstruction of 2D and 3D datasets in different representations, estimation of resolution by Fourier ring correlation, clustering analysis based on Voronoi diagrams and Ripley’s functions. SharpViSu is optimized to work with eventlist tables exported from most popular localization software. The functionality of SharpViSu is extendable via plugins, such as ClusterViSu for comprehensive cluster analysis of localization microscopy data. It includes tools such as calculations of Voronoi and Ripley statistics with Monte-Carlo simulations, different modes of reconstruction (e.g. based on Gaussian blur or Ripley’s functions) and segmentation of density maps, retrieval of geometrical properties of detected clusters, segmentation based on Voronoi tessellation.
Allows local density estimation, segmentation and quantification of 3D single-molecule localization microscopy (SMLM) data. voronoi3D was validated using simulated and experimental data, illustrating its applicability to different biological objects of interest. It can be used to quantify 3D information such as spatial organization, local density, volume and shape of labelled protein clusters in 3D and number of molecules within a given cluster.
Allows users to detect and count fluorescent signals in microscopy images of cells. Blob Finder is a free software that performs two types of analysis: (i) an average count, for quantifying the number of nuclei and signals in an image; (ii) and a single cell analysis, that assigns each signal to the closest cell and get a signal count for each cell in the image. It also performs on-z_stacks of the cell with a maximum projection to project the image data into a 2D image.
Provides a method for the segmentation and classification of 3D datasets in biological development. Generic 3D segmentation and classification in biological development is a software that builds his nuclei segmentation approach by learning from samples supplied by the user for the existing objects in image. This ImageJ plugin is based on the adaptive generic iterative thresholding algorithm (AGITA).
Automates cell shape extraction in C. elegans embryos. BCOMS provides a user-friendly framework that computerizes not only the segmentation process but also the evaluation process. The performance of BCOMS was validated by comparisons with the ground truth and by comparing the results in two adjacent time points. This method is also applicable to other model organisms by customizing the biological constraints.
Assists in segmentation of fluorescence microscope images of punctate patterns. Active Mask Segmentation Plugin is an extension from the algorithm termed active mask segmentation developed as a module usable through the ImageJ software. It uses four types of methods including active-contour, multiresolution, multiscale and region-growing methods with the aim of increasing the speed and the flexibility.
Captures the mass spectrometry (MS) lesion spatial distribution and identifies lesions regardless of their orientation, shape or size. RMNMS detects MS lesions using a training library containing T2-weighted (T2W) and FLAIR images along with manual T2W lesion masks. Moreover, it assists users in the detection of presence of lesions as lesion-wise measures.
Segments nearly elliptic objects via parametric active contour. E-Snake applies an active contour (named snake) segmentation method by using exponential splines as basis functions to represent the outline of the shape. This ImageJ plugin emulates elliptical and circular shapes and can produce an approximation of any closed curve in the plane. These proprieties can be useful to delineate cross sections of cylindrical-like conduits and to outline blob-like objects.
A simple, user-friendly tool for interactive image classification, segmentation and analysis. It is built as a modular software framework, which currently has workflows for automated (supervised) pixel- and object-level classification, automated and semi-automated object tracking, semi-automated segmentation and object counting without detection. Most analysis operations are performed lazily, which enables targeted interactive processing of data subvolumes, followed by complete volume analysis in offline batch mode.
Consists of a classification plugin for ImageJ. ImageSURF uses standard bitmap formats for: (1) class annotations, (2) making the training process open, repeatable and (3) incorporating large training sets created by multiple users across multiple sessions with the software of their choice. This tool utilizes primitive data structures to avoid the substantial overheads of object data structures such as the WEKA Instance. It can be used for studying the aggregation and deposition of amyloid-β peptide in brain tissue of Alzheimer’s disease rodent models.
Automates investigation related to dynamic microtubules within total internal reflection fluorescence (TIRF) images. MTrack is an ImageJ or Fiji plug-in that consists of two main components: the first one is able to generate trajectories by considering microtubules and their growing; the second one calculates population statistics and fits models of dynamic behavior by exploiting results from the first module.
Assists in exploration of possible watershed segmentation. Interactive-H-Watershed is a plugin for the image analysis software ImageJ. It provides an interactive way to explore local minima (maxima) on the fly. This module is based on Watershed, a common tool to segment objects in an 2D and 3D images. The method permits to gradually flood the valleys starting from their lowest point.
Performs image segmentation and registration. CMP-BIA is dedicated to ImageJ/Fiji and contains a plugin named jSLIC. This plugin is a segmentation method for clustering, in a given image, similar regions (as known as superpixels) which are usually used for other segmentation techniques, classification and registration. It gives reliable superpixels shapes, with no need of decreasing their size.
Allows users to visualize, manipulate, and understand data from imaging modalities such as computed tomography, microscopy or Magnetic resonance imaging (MRI). Amira 3D Software for Life Sciences provides features to import and process 2D and 3D images data, visualization techniques and tools for visual analysis. Users can also create and share presentations. The base product can be customized by adding functional extensions to fit special needs in different application areas.
Contains functionalities for processing and analysis image data. GoFigure2 is a platform which allows users to visualize and navigate through 4D multichannels bio-images. Besides, it aims to provide an automatic segmentation of nuclei and cell membranes and to enable the way of extracting data from bio-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.
Focuses on combinatorial optimization via graph cuts for digital image analysis. GC is a library aiming to finds solution to energy minimization based discrete labeling problems such as image segmentation. The software provides access to several algorithms, such as maximum flow algorithms, Metric approximation, Multi-label discrete energy optimization, and Image segmentation.
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