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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.


Allows the definition of a broad range of phenotypes, encompassing highly nontrivial population-level effects such as cell-type heterogeneity or local cell-density effects. SimuCell is an open-source framework for specifying and rendering realistic microscopy images containing diverse cell phenotypes, heterogeneous populations, micro-environmental dependencies and imaging artifacts. SimuCell differs from existing cell population generators in three ways: (i) it can generate heterogeneous cellular populations composed of diverse cell types, (ii) it allows users to specify interdependencies between population, biomarker and cell phenotypes, and (iii) it was designed to be easily extensible, providing a standard framework for defining new plugins that can also be shared through the SimuCell website.

TRAgen / Track generator

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.

STSE / Spatio-Temporal Simulation Environment

Assists in constructing microscopy image-based simulations. STSE is a software platform allowing an uninterrupted workflow including digitization, representation, analysis, and mathematical modeling. The main benefit of this application is that it acts as an adhesive between different steps of the workflow, permitting the users to tailor the platform to their specific needs. This module is a part of the Systems Biology Operational Software (SBOS).