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The cell-shape-wizard. User guidance for active contour-based cell segmentation

: Franz, Daniela; Hüttmayer, Hanna; Stamminger, Marc; Wiesmann, Veit; Wittenberg, Thomas


Handels, H. ; Univ. Lübeck, Institut für Medizinische Informatik:
Bildverarbeitung für die Medizin 2015 : Algorithmen - Systeme - Anwendungen; Proceedings des Workshops vom 15. bis 17. März 2015 in Lübeck; BVM 2015
Berlin: Springer, 2015 (Informatik aktuell)
ISBN: 978-3-662-46223-2 (Print)
ISBN: 978-3-662-46224-9 (Online)
ISBN: 3-662-46223-0
Workshop Bildverarbeitung für die Medizin (BVM) <2015, Lübeck>
Fraunhofer IIS ()
Segmentierung; modellbasierte Segmentierung; medizinische BV; kantenbasierte Segmentierung; Filterung; Computer Assistierte Mikroskopie

Cell segmentation on fluorescent micrographs requires preprocessing, cell-background separation and cell-cell separation. The presence of touching or overlapping cells requires more sophisticated segmentation methods – such as Active Contours (AC) – for cell-cell separation, but the usage and parametrization of these methods is often infeasible for users with no image processing expertise. We present the Cell-Shape- Wizard which introduces an abstraction layer between a complex AC approach and the users. It couples tight user guidance with the benefits of interactive cell segmentation of fluorescence micrographs. We have evaluated the wizard in a small user study with four subjects. Results show, that the wizard concept is well applicable to cell segmentation. Segmentation results are compared to manual reference annotations and result in a mean Jaccard index of 0.72. With the Cell-Shape-Wizard life scientist are able to segment their fluorescence micrographs semiautomatically on their own, without being forced to acquire additional knowledge in image processing.