研究目的
To provide an approach for improving the accuracy of nucleus/cell segmentation pipelines by tuning their input parameters, thereby facilitating more robust image segmentation workflows and enabling more efficient application of image analysis in large image datasets.
研究成果
The proposed multi-objective optimization framework significantly improves the quality of segmentation results and reduces the execution time of segmentation workflows. It demonstrates the potential for enabling more efficient application of image analysis in large image datasets and facilitating more robust image segmentation workflows.
研究不足
The study acknowledges the high cost of evaluating a point in the search space due to the compute expensive nature of the segmentation workflow and the difficulty of manually evaluating the search space and the quality of a segmentation result.
1:Experimental Design and Method Selection:
The study integrates a suite of methods and tools for automatic parameter tuning in analysis algorithms that segment nuclei in digitized images of tissue specimens. It employs multi-objective optimization algorithms to search the parameter space efficiently.
2:Sample Selection and Data Sources:
The experiments used 15 image tiles extracted from Glioblastoma multiforme (GBM) WSIs and manually segmented by a pathologist.
3:List of Experimental Equipment and Materials:
The experiments were conducted on the Stampede-distributed memory machine. Each node on Stampede has dual Intel Xeon E5-2680 processors, an Intel Xeon Phi SE10P co-processor, and 32 GB RAM.
4:Experimental Procedures and Operational Workflow:
The auto-tuning methods are deployed in the region templates (RTs) for efficient execution of image analysis pipelines on parallel machines. The integration of applications or workflows with RT for tuning is performed using an interface in which the user exports the parameters to be tuned and their value ranges.
5:Data Analysis Methods:
The quality of segmentation results was quantified with the average Dice coefficient, which ranges from 0.0 to 1.0, in which higher values mean a better agreement with ground-truth segmentation.
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