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BioImageXD
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.
SQUIRREL / Super-resolution QUantitative Image Rating and Reporting of Error Locations
Quantifies image quality in super-resolution microscopy. Squirrel produces a quantitative map of super-resolution artifacts and metrics and proposes to users optimizing imaging parameters. This ImageJ module offers the possibility to combine super-resolution renderings of the same structure to avoid overall error contributions. It features also Fourier Ring Correlation (FRC) for the mapping of resolution across super-resolution images.
SharpViSu
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.
FindFoci
Determines regions of peak intensity into 2D and 3D images. FindFoci is a toolkit for ImageJ/J2 software that identifies potential foci and then, expands these into peaks that are gathered to finally remove the insignificant ones. It is composed of six algorithms including FindFoci GUI that allows parameters to be interactively updated. Additionally, the software includes six other plugins that extends features of the primary algorithm by permitting to compare regions of interest (ROI) points or align the identified foci.
Amira 3D Software for Life Sciences
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.
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