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.