Robust Adaptive 3-D Segmentation of Vessel Laminae From Fluorescence Confocal Microscope Images and Parallel GPU Implementation

Arunachalam Narayanaswamy, Saritha Dwarakapuram, Christopher S. Bjornsson, Barbara M. Cutler, William Shain, Badrinath Roysam
Department of Electrical, Computer and Systems Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180 USA
IEEE Transactions on Medical Imaging, 2008


   title={Robust Adaptive 3-D Segmentation of Vessel Laminae from Fluorescence Confocal Microscope Images & Parallel GPU Implementation},

   author={Narayanaswamy, A. and Dwarakapuram, S. and Bjornsson, C. and Cutler, BM and Shain, W. and Roysam, B.},

   journal={Microscopy and Microanalysis},






   publisher={Cambridge Univ Press}


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This paper presents robust 3-D algorithms to segment vasculature that is imaged by labeling laminae, rather than the lumenal volume. The signal is weak, sparse, noisy, nonuniform, low-contrast, and exhibits gaps and spectral artifacts, so adaptive thresholding and Hessian filtering based methods are not effective. The structure deviates from a tubular geometry, so tracing algorithms are not effective. We propose a four step approach. The first step detects candidate voxels using a robust hypothesis test based on a model that assumes Poisson noise and locally planar geometry. The second step performs an adaptive region growth to extract weakly labeled and fine vessels while rejecting spectral artifacts. To enable interactive visualization and estimation of features such as statistical confidence, local curvature, local thickness, and local normal, we perform the third step. In the third step, we construct an accurate mesh representation using marching tetrahedra, volume-preserving smoothing, and adaptive decimation algorithms. To enable topological analysis and efficient validation, we describe a method to estimate vessel centerlines using a ray casting and vote accumulation algorithm which forms the final step of our algorithm. Our algorithm lends itself to parallel processing, and yielded an 8x speedup on a graphics processor (GPU). On synthetic data, our meshes had average error per face (EPF) values of (0.1-1.6) voxels per mesh face for peak signal-to-noise ratios from (110-28 dB). Separately, the error from decimating the mesh to less than 1% of its original size, the EPF was less than 1 voxel/face. When validated on real datasets, the average recall and precision values were found to be 94.66% and 94.84%, respectively.
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