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

BMC Bioinformatics

Research Article

Daniela Franz¹  Veit Wiesmann¹  Matthias Bergler¹  Martin Prinzen¹  Thomas Wittenberg²  Ralf Palmisano³ 

[1] Fraunhofer Institute for Integrated Circuits IIS, Am Wolfsmantel 33, 91058, Erlangen, Germany;Fraunhofer Institute for Integrated Circuits IIS, Am Wolfsmantel 33, 91058, Erlangen, Germany;Friedrich-Alexander University Erlangen-Nuremberg, Cauerstraße 11, 91058, Erlangen Erlangen, Germany;Optical Imaging Centre Erlangen (OICE), Hartmannstraße 14, 91052, Erlangen, Germany;

关键词: Fluorescence microscopy;    Simulation;    Evaluation;    Image analysis;    Cell segmentation;   

DOI  :  10.1186/s12859-017-1591-2

 received in 2016-08-04, accepted in 2017-03-09,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundManual 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.ResultsWe 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.ConclusionThe 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.

【 授权许可】

CC BY   
© The Author(s) 2017

【 图 表 】

12864_2017_3781_Article_IEq3.gif