MISA++: A standardized interface for automated bioimage analysis.

Gerst R, Medyukhina A, Figge MT (2020) MISA++: A standardized interface for automated bioimage analysis. SoftwareX 11, 100405.


Modern imaging techniques, such as lightsheet fluorescence microscopy (LSFM), allow the capture of whole organs in three spatial dimensions. The analysis of these big volume image data requires a combination of user-friendly and highly efficient tools. We here present MISA++, an image analysis framework that allows easy integration of custom high-performance C++ tools into third-party applications via standardized components for parallelization, data and parameter handling, command line interface, and communication with third-party applications. We demonstrate its capabilities by implementing a plugin for ImageJ that provides a graphical user interface for any application built with our framework, and a high-performance re-implementation of our Python-based algorithm to segment glomeruli in LSFM images of whole murine kidneys.


Marc Thilo Figge
Ruman Gerst
Anna Medyukhina


doi: 10.1016/j.softx.2020.100405