It is the ideal "glue" for easily integrating dissimilar fluorescent microscope hardware and peripherals into a single custom workstation, while providing all the tools needed to perform meaningful analysis of acquired images. The software offers many user-friendly application modules for biology-specific analysis such as cell signaling, cell counting, and protein expression.
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.
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.
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.
Allows users to determine Fourier descriptors and the curvature starting from a closed curve. Fourier Shape analysis is a module that can be run through the ImageJ software. The application consists of three main features allowing the computation of Fourier descriptors, the generation of elliptic Fourier descriptors including a normalized set of coefficients such as rotation or scale invariant, as well as the calculation of curvature.
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.