Streaming level set algorithm for 3D segmentation of confocal microscopy images

We present a high performance variant of the popular geodesic active contours which are used for splitting cell clusters in microscopy images. Previously, we implemented a linear pipelined version that incorporates as many cues as possible into developing a suitable level-set speed function so that an evolving contour exactly segments a cell/nuclei blob. We use image gradients, distance maps, multiple channel information and a shape model to drive the evolution. We also developed a dedicated seeding strategy that uses the spatial coherency of the data to generate an over complete set of seeds along with a quality metric which is further used to sort out which seed should be used for a given cell. However, the computational performance of any level-set methodology is quite poor when applied to thousands of 3D data-sets each containing thousands of cells. Those data-sets are common in confocal microscopy. In this work, we explore methods to stream the algorithm in shared memory, multi-core environments. By partitioning the input and output using spatial data structures we insure the spatial coherency needed by our seeding algorithm as well as improve drastically the speed without memory overhead. Our results show speed-ups up to a factor of six.