2015/11/03 by Philipp Hanslovsky, Hanslovsky, Philipp, John Bogovic +3 · 1 citation
Biochemistry, Genetics and Molecular Biology · #Advanced Electron Microscopy Techniques and Applications #Advanced Fluorescence Microscopy Techniques #Cell Image Analysis Techniques #Computer Vision and Pattern Recognition (cs.CV) #FOS: Computer and information sciences
paper · pdf · doi:10.48550/arxiv.1511.01161
openalex publication_date 2015/11/03 · openalex created_date 2022/10/01 · openalex updated_date 2026/07/28
Motivation: Serial section microscopy is an established method for detailed\nanatomy reconstruction of biological specimen. During the last decade, high\nresolution electron microscopy (EM) of serial sections has become the de-facto\nstandard for reconstruction of neural connectivity at ever increasing scales\n(EM connectomics). In serial section microscopy, the axial dimension of the\nvolume is sampled by physically removing thin sections from the embedded\nspecimen and subsequently imaging either the block-face or the section series.\nThis process has limited precision leading to inhomogeneous non-planar sampling\nof the axial dimension of the volume which, in turn, results in distorted image\nvolumes. This includes that section series may be collected and imaged in\nunknown order.\n Results: We developed methods to identify and correct these distortions\nthrough image-based signal analysis without any additional physical apparatus\nor measurements. We demonstrate the efficacy of our methods in proof of\nprinciple experiments and application to real world problems.\n Availability and Implementation: We made our work available as libraries for\nthe ImageJ distribution Fiji and for deployment in a high performance parallel\ncomputing environment. Our sources are open and available at\nhttp://github.com/saalfeldla/section-sort,\nhttp://github.com/saalfeldlab/em-thickness-estimation, and\nhttp://github.com/saalfeldlab/z-spacing-spark.\n Contact: [email protected]\n