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

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.