Neural Process Reconstruction from Sparse User Scribbles


Mike Roberts; Won-Ki Jeong; Amelio Vazquez-Reina; Markus Unger; Horst Bischof; Jeff Lichtman; Hanspeter Pfister


We present a novel semi-automatic method for segmenting neural processes in large, highly anisotropic EM (electron microscopy) image stacks. Our method takes advantage of sparse scribble annotations provided by the user to guide a 3D variational segmentation model, thereby allowing our method to globally optimally enforce 3D geometric constraints on the segmentation. Moreover, we leverage a novel algorithm for propagating segmentation constraints through the image stack via optimal volumetric pathways, thereby allowing our method to compute highly accurate 3D segmentations from very sparse user input. We evaluate our method by reconstructing 16 neural processes in a 1024x1024x50 nanometer-scale EM image stack of a mouse hippocampus. We demonstrate that, on average, our method is 68% more accurate than previous state-of-the-art semi-automatic methods.

BibTex entry

@proceedings { 303, title = {Neural Process Reconstruction from Sparse User Scribbles}, year = {2011}, author = {Mike Roberts and Won-Ki Jeong and Amelio Vazquez-Reina and Markus Unger and Horst Bischof and Jeff Lichtman and Hanspeter Pfister} }