SOFTWARE ORIGINAL ARTICLE NeuroMorph: A Toolset for the Morphometric Analysis and Visualization of 3D Models Derived from Electron Microscopy Image Stacks

Abstract Serial electron microscopy imaging is crucial for exploring the structure of cells and tissues. The develop-ment of block face scanning electron microscopy methods and their ability to capture large image stacks, some with near isotropic voxels, is proving particularly useful for the exploration of brain tissue. This has led to the creation of numerous algorithms and software for segmenting out dif-ferent features from the image stacks. However, there are few tools available to view these results and make detailed morphometric analyses on all, or part, of these 3D models. We have addressed this issue by constructing a collection of software tools, called NeuroMorph, with which users can view the segmentation results, in conjunction with the orig