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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.


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.

Anisotropic Diffusion 2D

Serves for vector-valued image regularization. Anisotropic Diffusion 2D is a program based on variational methods and partial differential equations (PDEs). This tool consists in a single generic anisotropic diffusion equation that provides a simple interpretation of the regularization process in terms of local filtering with spatially adaptive Gaussian kernels. It also offers the possibility to specialize a generic expression into different regularization PDEs depending on different applications: flow visualization, image restoration, magnification, or inpainting.


Allows automatization of complex microscopy protocols. YouScope is an open-source microscope control platform for implementing complex measurement protocols. The software enables users to perform single-cell imaging as well as microplate imaging on a motorized light-microscope. It also provides a set of tools and configurable measurement types. The platform offers a large set of plug-in interfaces, allowing existing protocols to be extended, and allowing creation of new protocols from parts of existing ones.

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.