4D segmentation algorithm with application to 3D+time image segmentation

DOI10.1007/S13160-022-00519-WMaRDI QIDQ2111549zbMATH OpenOpenAlexFDO

Authors Markjoe Olunna Uba, Karol Mikula, Seol Ah Park

Publication date 17 January 2023

Published in Japan Journal of Industrial and Applied Mathematics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/2111.11866

zbMATH Keywords

image segmentationfinite volume methodlevel set methodsemi-implicit schemezebrafishcell microscopy imagessubjective surface method

Mathematics Subject Classification ID

Parallel numerical computation (65Y05) Biomedical imaging and signal processing (92C55) Computing methodologies for image processing (68U10) Nonlinear initial, boundary and initial-boundary value problems for nonlinear parabolic equations (35K61) Finite difference methods for initial value and initial-boundary value problems involving PDEs (65M06) Finite volume methods for initial value and initial-boundary value problems involving PDEs (65M08) Stability and convergence of numerical methods for initial value and initial-boundary value problems involving PDEs (65M12) Finite volume methods for boundary value problems involving PDEs (65N08)

Abstract: In this paper, we introduce and study a novel segmentation method for 4D images based on surface evolution governed by a nonlinear partial differential equation, the generalized subjective surface equation. The new method uses 4D digital image information and information from a thresholded 4D image in a local neighborhood. Thus, the 4D image segmentation is accomplished by defining the edge detector function's input as the weighted sum of the norm of gradients of presmoothed 4D image and norm of presmoothed thresholded 4D image in a local neighborhood. Additionally, we design and study a numerical method based on the finite volume approach for solving the new model. The reduced diamond cell approach is used for approximating the gradient of the solution. We use a semi-implicit finite volume scheme for the numerical discretization and show that our numerical scheme is unconditionally stable. The new 4D method was tested on artificial data and applied to real data representing 3D+time microscopy images of cell nuclei within the zebrafish pectoral fin and hind-brain. In a real application, processing 3D+time microscopy images amounts to solving a linear system with several billion unknowns and requires over $1000$ GB of memory; thus, it may not be possible to process these images on a serial machine without parallel implementation utilizing the MPI. Consequently, we develop and present in the paper OpenMP and MPI parallel implementation of designed algorithms. Finally, we include cell tracking results to show how our new method serves as a basis for finding trajectories of cells during embryogenesis.

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Cites work

• scientific article; zbMATH DE number 3685109 (Why is no real title available?)
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Cited in

(7)

• 4D numerical schemes for cell image segmentation and tracking
• Finite volume schemes for the generalized subjective surface equation in image segmentation
• Numerical algorithm for tracking cell dynamics in 4D biomedical images
• 3D image segmentation supported by a point cloud
• Finding space-time boundaries with deformable hypersurfaces
• Parallel algorithms for segmentation of cellular structures in 2D+time and 3D morphogenesis data
• 4D embryogenesis image analysis using PDE methods of image processing

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