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.
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Creates interactive surface plots from all image types. Interactive 3D Surface Plot assists in interpreting the luminance of an image, and in viewing the position of the plot. The plugin has several modes for displaying surface plots: (1) drawing mode; (2) display colors; (3) axes; and (4) invert. It allows users to realize 3D projection.
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.
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.
A modular software tool for efficient quantification of biological tissues based on volume data obtained by biomedical image modalities. TiQuant includes a number of versatile image and volume processing chains tailored to the analysis of different tissue types which have been experimentally verified. It implements a novel method for the reconstruction of three-dimensional surfaces of biological systems, data that often cannot be obtained experimentally but which is of utmost importance for tissue modelling in systems biology.
Serves for the processing of 3D laser scanning multiphoton microscopy images. CANDLE is a program that performs about low signal-to-noise ratio (SNR) conditions typically encountered when imaging deep in scattering biological specimens. It locally adapts the amount of smoothing to deal with the noise inhomogeneity inherent to laser scanning fluorescence microscopy images.
Computes a 3D triangular mesh of the tissue. DRACO-STEM is based on the dualization of a simplicial complex of adjacency, and the triangulation and optimization of the resulting polyhedral geometry to proceed. This tool follows three steps for the processing: delaunay complex creation, adjacency complex optimization and dual reconstruction. It was applied to triangular tissue meshes generated from a dataset of segmented tissue images.
