Tuning for Tissue Image Segmentation Workflows for Accuracy and Performance

• Published in: arXiv.org
• Main Authors: Taveira, Luis F R, Kurc, Tahsin, Alba C M A Melo, Kong, Jun, Bremer, Erich, Saltz, Joel H, Teodoro, George
• Format: Paper
• Language: English
• Published: Ithaca Cornell University Library, arXiv.org 05.10.2018
• Subjects: Accuracy; Algorithms; Biomarkers; Computing time; Image analysis; Image quality; Image segmentation; Markov analysis; Nuclei (cytology); Optimization; Parameters; Pipelining (computers); Simulation; Software; System effectiveness; Tuning; Workflow

We propose a software platform that integrates methods and tools for multi-objective parameter auto- tuning in tissue image segmentation workflows. The goal of our work is to provide an approach for improving the accuracy of nucleus/cell segmentation pipelines by tuning their input parameters. The shape, size and texture features of nuclei in tissue are important biomarkers for disease prognosis, and accurate computation of these features depends on accurate delineation of boundaries of nuclei. Input parameters in many nucleus segmentation workflows affect segmentation accuracy and have to be tuned for optimal performance. This is a time-consuming and computationally expensive process; automating this step facilitates more robust image segmentation workflows and enables more efficient application of image analysis in large image datasets. Our software platform adjusts the parameters of a nuclear segmentation algorithm to maximize the quality of image segmentation results while minimizing the execution time. It implements several optimization methods to search the parameter space efficiently. In addition, the methodology is developed to execute on high performance computing systems to reduce the execution time of the parameter tuning phase. Our results using three real-world image segmentation workflows demonstrate that the proposed solution is able to (1) search a small fraction (about 100 points) of the parameter space, which contains billions to trillions of points, and improve the quality of segmentation output by 1.20x, 1.29x, and 1.29x, on average; (2) decrease the execution time of a segmentation workflow by up to 11.79x while improving output quality; and (3) effectively use parallel systems to accelerate parameter tuning and segmentation phases.