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.
Generates 2D image sequences that show simulated living cell populations. TRAgen creates GT-enabled image sequences with vast amounts of cells highlithing several tracking events, such as cells moving and changing shape, cells having contact and overlapping, and cells splitting due to cell division. It is primarily designed to operate at inter-cellular scope, and works with 2D masks of all common biomedical shapes, including those of nuclei and cells themselves.
Allows users to simulate Fluorescence microscope images with cell populations. SIMCEP is a simulation platform for generating synthetic images of fluorescence-stained cell populations with realistic properties. It can be used in connection with the applications of fluorescence microscopy, and especially in the validation of analysis methods. This tool provides a view of the studied phenomenon in a risk-free environment.
Assists in digital phantoms and simulation of image formation in 3d cell imaging. CytoPacq is a toolbox that consists of three individual modules: (i) 3D-cytogen, a module generating the digital cell phantoms, (ii) 3D-optigen, a module simulating the transmission of the signal through the optical system and (iii) 3D-acquigen, a module simulating the phenomenon manifesting themselves during image capture with digital CCD cameras.
Allows users to perform simulation and analysis of forster resonance energy transfer (FRET) in nucleic acids. FRETmatrix is based on a matrix base-centred calculation scheme to build nucleic acid geometries. Moreover, this program can be used, in combination with base–base FRET, for reconstructing the 3D structure of local kinks, such as protein/ligand binding sites, bulges, junctions and DNA lesions.
A generation of a synthetic confocal microscopy images. ConfocalGN is a tool developed to simulate confocal datasets from ground truth, a measure of the point spread function (PSF), and the noise and signal distribution. From sample confocal image, this software is also able to automatically extract the characteristic of the noise to ensure that the simulated images possess the same noise properties as the real images.