scholarly journals Parallel Raster Scan for Euclidean Distance Transform

Symmetry ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 1808
Author(s):  
Juan Carlos Elizondo-Leal ◽  
José Gabriel Ramirez-Torres ◽  
Jose Hugo Barrón-Zambrano ◽  
Alan Diaz-Manríquez ◽  
Marco Aurelio Nuño-Maganda ◽  
...  

Distance transform (DT) and Voronoi diagrams (VDs) have found many applications in image analysis. Euclidean distance transform (EDT) can generate forms that do not vary with the rotation, because it is radially symmetrical, which is a desirable characteristic in distance transform applications. Recently, parallel architectures have been very accessible and, particularly, GPU-based architectures are very promising due to their high performance, low power consumption and affordable prices. In this paper, a new parallel algorithm is proposed for the computation of a Euclidean distance map and Voronoi diagram of a binary image that mixes CUDA multi-thread parallel image processing with a raster propagation of distance information over small fragments of the image. The basic idea is to exploit the throughput and the latency in each level of memory in the NVIDIA GPU; the image is set in the global memory, and can be accessed via texture memory, and we divide the problem into blocks of threads. For each block we copy a portion of the image and each thread applies a raster scan-based algorithm to a tile of m×m pixels. Experiment results exhibit that our proposed GPU algorithm can improve the efficiency of the Euclidean distance transform in most cases, obtaining speedup factors that even reach 3.193.

2018 ◽  
Author(s):  
Sebastian Daberdaku

Protein pockets and cavities usually coincide with the active sites of biological processes, and their identification is significant since it constitutes an important step for structure-based drug design and protein-ligand docking applications. This paper presents a novel purely geometric algorithm for the detection of ligand binding protein pockets and cavities based on the Euclidean Distance Transform (EDT). The EDT can be used to compute the Solvent-Excluded surface for any given probe sphere radius value at high resolutions and in a timely manner. The algorithm is adaptive to the specific candidate ligand: it computes two voxelised protein surfaces using two different probe sphere radii depending on the shape of the candidate ligand. The pocket regions consist of the voxels located between the two surfaces, which exhibit a certain minimum depth value from the outer surface. The distance map values computed by the EDT algorithm during the second surface computation can be used to elegantly determine the depth of each candidate pocket and to rank them accordingly. Cavities on the other hand, are identified by scanning the inside of the protein for voids. The algorithm determines and outputs the best k candidate pockets and cavities, i.e. the ones that are more likely to bind to the given ligand. The method was applied to a representative set of protein-ligand complexes and their corresponding unbound protein structures to evaluate its ligand binding site prediction capabilities, and was shown to outperform most of the previously developed purely geometric pocket and cavity search methods.


Author(s):  
JULIO CESAR TORELLI ◽  
RICARDO FABBRI ◽  
GONZALO TRAVIESO ◽  
ODEMIR MARTINEZ BRUNO

The Euclidean distance transform (EDT) is used in various methods in pattern recognition, computer vision, image analysis, physics, applied mathematics and robotics. Until now, several sequential EDT algorithms have been described in the literature, however they are time- and memory-consuming for images with large resolutions. Therefore, parallel implementations of the EDT are required specially for 3D images. This paper presents a parallel implementation based on domain decomposition of a well-known 3D Euclidean distance transform algorithm, and analyzes its performance on a cluster of workstations. The use of a data compression tool to reduce communication time is investigated and discussed. Among the obtained performance results, this work shows that data compression is an essential tool for clusters with low-bandwidth networks.


Author(s):  
Luis Fernando Segalla ◽  
Alexandre Zabot ◽  
Diogo Nardelli Siebert ◽  
Fabiano Wolf

Author(s):  
Kuryati Kipli ◽  
Mohammed Enamul Hoque ◽  
Lik Thai Lim ◽  
Tengku Mohd Afendi Zulcaffle ◽  
Siti Kudnie Sahari ◽  
...  

2018 ◽  
Vol 08 (01) ◽  
Author(s):  
Ismet Sahin ◽  
Yu Zhang ◽  
Florencia McAllister

Sign in / Sign up

Export Citation Format

Share Document