GPU-Accelerated RSF Level Set Evolution for Large-Scale Microvascular Segmentation

Microvascular networks are challenging to model because these structures are currently near the diffraction limit for most advanced three-dimensional imaging modalities, including confocal and light sheet microscopy. This makes semantic segmentation difficult, because individual components of these networks fluctuate within the confines of individual pixels. Level set methods are ideally suited to solve this problem by providing surface and topological constraints on the resulting model, however these active contour techniques are extremely time intensive and impractical for terabyte-scale images. We propose a reformulation and implementation of the region-scalable fitting (RSF) level set model that makes it amenable to three-dimensional evaluation using both single-instruction multiple data (SIMD) and single-program multiple-data (SPMD) parallel processing. This enables evaluation of the level set equation on independent regions of the data set using graphics processing units (GPUs), making large-scale segmentation of high-resolution networks practical and inexpensive. We tested this 3D parallel RSF approach on multiple data sets acquired using state-of-the-art imaging techniques to acquire microvascular data, including micro-CT, light sheet fluorescence microscopy (LSFM) and milling microscopy. To assess the performance and accuracy of the RSF model, we conducted a Monte-Carlo-based validation technique to compare results to other segmentation methods. We also provide a rigorous profiling to show the gains in processing speed leveraging parallel hardware. This study showcases the practical application of the RSF model, emphasizing its utility in the challenging domain of segmenting large-scale high-topology network structures with a particular focus on building microvascular models.

Evaluating DTW Measures via a Synthesis Framework for Time-Series Data

Time-series data originate from various applications that describe specific observations or quantities of interest over time. Their analysis often involves the comparison across different time-series data sequences, which in turn requires the alignment of these sequences. Dynamic Time Warping (DTW) is the standard approach to achieve an optimal alignment between two temporal signals. Different variations of DTW have been proposed to address various needs for signal alignment or classifications. However, a comprehensive evaluation of their performance in these time-series data processing tasks is lacking. Most DTW measures perform well on certain types of time-series data without a clear explanation of the reason. To address that, we propose a synthesis framework to model the variation between two time-series data sequences for comparison. Our synthesis framework can produce a realistic initial signal and deform it with controllable variations that mimic real-world scenarios. With this synthesis framework, we produce a large number of time-series sequence pairs with different but known variations, which are used to assess the performance of a number of well-known DTW measures for the tasks of alignment and classification. We report their performance on different variations and suggest the proper DTW measure to use based on the type of variations between two time-series sequences. This is the first time such a guideline is presented for selecting a proper DTW measure. To validate our conclusion, we apply our findings to real-world applications, i.e., the detection of the formation top for the oil and gas industry and the pattern search in streamlines for flow visualization.