Image-Based Correction of Continuous and Discontinuous Non-Planar Axial Distortion in Serial Section Microscopy

TL;DR

This paper introduces image-based methods to correct axial distortions in serial section microscopy, improving the accuracy of 3D reconstructions without additional hardware, and provides open-source tools for the community.

Contribution

The authors developed novel image analysis techniques to identify and correct non-planar axial distortions in serial section microscopy, enabling more accurate biological volume reconstructions.

Findings

Effective correction of axial distortions demonstrated in experiments

Tools implemented in Fiji and parallel computing environments

Open-source code available for community use

Abstract

Motivation: Serial section microscopy is an established method for detailed anatomy reconstruction of biological specimen. During the last decade, high resolution electron microscopy (EM) of serial sections has become the de-facto standard for reconstruction of neural connectivity at ever increasing scales (EM connectomics). In serial section microscopy, the axial dimension of the volume is sampled by physically removing thin sections from the embedded specimen and subsequently imaging either the block-face or the section series. This process has limited precision leading to inhomogeneous non-planar sampling of the axial dimension of the volume which, in turn, results in distorted image volumes. This includes that section series may be collected and imaged in unknown order. Results: We developed methods to identify and correct these distortions through image-based signal analysis without any additional physical apparatus or measurements. We demonstrate the efficacy of our methods in proof of principle experiments and application to real world problems. Availability and Implementation: We made our work available as libraries for the ImageJ distribution Fiji and for deployment in a high performance parallel computing environment. Our sources are open and available at http://github.com/saalfeldla/section-sort, http://github.com/saalfeldlab/em-thickness-estimation, and http://github.com/saalfeldlab/z-spacing-spark. Contact: saalfelds@janelia.hhmi.org