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Using simulated fluorescence cell micrographs for the evaluation of cell image segmentation algorithms

: Wiesmann, Veit; Bergler, Matthias; Palmisano, Ralf; Prinzen, Martin; Franz, Daniela; Wittenberg, Thomas

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BMC bioinformatics. Online journal 18 (2017), Art. 176, 12 pp.
ISSN: 1471-2105
Deutsche Forschungsgemeinschaft DFG
CRC 796 A4
Journal Article, Electronic Publication
Fraunhofer IIS ()
Segmentierung; modellbasierte Segmentierung; Mikroskope; medizinische BV; kantenbasierte Segmentierung; Computer Assistierte Mikroskopie; computational imaging; Algorithmen

Background: Manual assessment and evaluation of fluorescent micrograph cell experiments is time-consuming and tedious. Automated segmentation pipelines can ensure efficient and reproducible evaluation and analysis with constant high quality for all images of an experiment. Such cell segmentation approaches are usually validated and rated in comparison to manually annotated micrographs. Nevertheless, manual annotations are prone to errors and display inter- and intra-observer variability which influence the validation results of automated cell segmentation pipelines.
Results: We present a new approach to simulate fluorescent cell micrographs that provides an objective ground truth for the validation of cell segmentation methods. The cell simulation was evaluated twofold: (1) An expert observer study shows that the proposed approach generates realistic fluorescent cell micrograph simulations. (2) An automated segmentation pipeline on the simulated fluorescent cell micrographs reproduces segmentation performances of that pipeline on real fluorescent cell micrographs.
Conclusion: The proposed simulation approach produces realistic fluorescent cell micrographs with corresponding ground truth. The simulated data is suited to evaluate image segmentation pipelines more efficiently and reproducibly than it is possible on manually annotated real micrographs.