title: Performance and sensitivity evaluation of 3D spot detection methods in confocal microscopy.
abstract: Reliable 3D detection of diffraction-limited spots in fluorescence microscopy images is an important task in subcellular observation. Generally, fluorescence microscopy images are heavily degraded by noise and non-specifically stained background, making reliable detection a challenging task. In this work, we have studied the performance and parameter sensitivity of eight recent methods for 3D spot detection. The study is based on both 3D synthetic image data and 3D real confocal microscopy images. The synthetic images were generated using a simulator modeling the complete imaging setup, including the optical path as well as the image acquisition process. We studied the detection performance and parameter sensitivity under different noise levels and under the influence of uneven background signal. To evaluate the parameter sensitivity, we propose a novel measure based on the gradient magnitude of the F1 score. We measured the success rate of the individual methods for different types of the image data and found that the type of image degradation is an important factor. Using the F1 score and the newly proposed sensitivity measure, we found that the parameter sensitivity is not necessarily proportional to the success rate of a method. This also provided an explanation why the best performing method for synthetic data was outperformed by other methods when applied to the real microscopy images. On the basis of the results obtained, we conclude with the recommendation of the HDome method for data with relatively low variations in quality, or the Sorokin method for image sets in which the quality varies more. We also provide alternative recommendations for high-quality images, and for situations in which detailed parameter tuning might be deemed expensive.
authors.affiliation: Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic.
authors.forename: Karel
authors.initials: K
authors.lastname: Štěpka
authors.affiliation: Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic.
authors.forename: Pavel
authors.initials: P
authors.lastname: Matula
authors.affiliation: Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic.
authors.forename: Petr
authors.initials: P
authors.lastname: Matula
authors.affiliation: IPMB and BIOQUANT, Department of Bioinformatics and Functional Genomics, and DKFZ, University of Heidelberg, Heidelberg, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Wörz
authors.affiliation: IPMB and BIOQUANT, Department of Bioinformatics and Functional Genomics, and DKFZ, University of Heidelberg, Heidelberg, Germany.
authors.forename: Karl
authors.initials: K
authors.lastname: Rohr
authors.affiliation: Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic.
authors.forename: Michal
authors.initials: M
authors.lastname: Kozubek
mesh_terms: D000465:Algorithms; D007091:Image Processing, Computer-Assisted / Q000379:methods; D021621:Imaging, Three-Dimensional / Q000379:methods*; D018613:Microscopy, Confocal / Q000379:methods*; D008856:Microscopy, Fluorescence / Q000379:methods; D012680:Sensitivity and Specificity
keywords: 3D imaging; diffraction-limited spot detection; fluorescence microscopy; parameter sensitivity