MISA++: A standardized interface for automated bioimage analysis | Zendy

Ruman Gerst | Zendy; Anna Medyukhina | Zendy; Marc Thilo Figge | Zendy

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MISA++: A standardized interface for automated bioimage analysis

Author(s) -

Ruman Gerst,

Anna Medyukhina,

Marc Thilo Figge

Publication year - 2020

Publication title -

softwarex

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.528

H-Index - 21

ISSN - 2352-7110

DOI - 10.1016/j.softx.2020.100405

Subject(s) - python (programming language) , computer science , interface (matter) , plug in , graphical user interface , computer graphics (images) , user interface , data mining , computer vision , computer hardware , embedded system , operating system , bubble , maximum bubble pressure method

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.

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