An Auxiliary Task for Learning Nuclei Segmentation in 3D Microscopy - PowerPoint PPT Presentation

May 28, 2023 •359 likes •435 views

An Auxiliary Task for Learning Nuclei Segmentation in 3D Microscopy Images Peter Hirsch, Dagmar Kainmueller MDC Berlin/BIH MIDL 2020 C. elegans L1 larva, 3d, near-isotropic 0 . 116 0 . 116 0 . 122 m 3 , average size of 140 140

An Auxiliary Task for Learning Nuclei Segmentation in 3D Microscopy Images Peter Hirsch, Dagmar Kainmueller MDC Berlin/BIH MIDL 2020
C. elegans L1 larva, 3d, near-isotropic 0 . 116 × 0 . 116 × 0 . 122 µ m 3 , average size of 140 × 140 × 1100 pixel We thank Long et. al [1] for providing the 3d nuclei data and segmentation.
one nucleus two nuclei (A) (B) (C) (D) Exemplary Boundary label Center point Prediction nuclei vectors
◮ consistently get improvement with auxiliary task: ◮ +1.5-4% in terms of AP 0 . 5 ◮ +1-2.5% in terms of avAP ◮ StarDist[2]: avAP : 0.628, AP 0 . 5 : 0.765 ◮ our best model: avAP : 0.638 , AP 0 . 5 : 0.750 conclusion : ◮ performance on par with StarDist yet simpler ◮ easy to integrate into existing systems
Peter Hirsch Kainmueller Lab Dagmar Kainmueller Preibisch Lab Stephan Preibisch example detection and segmentation: cyan: TP , yellow: FP, red: FN
References [1] F. Long, H. Peng, X. Liu, S. K. Kim, and E. Myers. A 3d digital atlas of c. elegans and its application to single-cell analyses. Nature methods , 6(9):667, 2009. [2] M. Weigert, U. Schmidt, R. Haase, K. Sugawara, and G. Myers. Star-convex polyhedra for 3d object detection and segmentation in microscopy. arXiv:1908.03636 , 2019.

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