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Restoring drifted electron microscope volumes using synaptic vesicles at sub-pixel accuracy.

ABSTRACT: Imaging ultrastructures in cells using Focused Ion Beam Scanning Electron Microscope (FIB-SEM) yields section-by-section images at nano-resolution. Unfortunately, we observe that FIB-SEM often introduces sub-pixel drifts between sections, in the order of 2.5?nm. The accumulation of these drifts significantly skews distance measures and geometric structures, which standard image registration techniques fail to correct. We demonstrate that registration techniques based on mutual information and sum-of-squared-distances significantly underestimate the drift since they are agnostic to image content. For neuronal data at nano-resolution, we discovered that vesicles serve as a statistically simple geometric structure, making them well-suited for estimating the drift with sub-pixel accuracy. Here, we develop a statistical model of vesicle shapes for drift correction, demonstrate its superiority, and provide a self-contained freely available application for estimating and correcting drifted datasets with vesicles.

SUBMITTER: Stephensen HJT

PROVIDER: S-EPMC7035423 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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Restoring drifted electron microscope volumes using synaptic vesicles at sub-pixel accuracy.

Stephensen Hans Jacob Teglbjærg HJT Darkner Sune S Sporring Jon J

Communications biology 20200221 1

Imaging ultrastructures in cells using Focused Ion Beam Scanning Electron Microscope (FIB-SEM) yields section-by-section images at nano-resolution. Unfortunately, we observe that FIB-SEM often introduces sub-pixel drifts between sections, in the order of 2.5 nm. The accumulation of these drifts significantly skews distance measures and geometric structures, which standard image registration techniques fail to correct. We demonstrate that registration techniques based on mutual information and su ...[more]

PMID: 32081999

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Dataset Information

Restoring drifted electron microscope volumes using synaptic vesicles at sub-pixel accuracy.

Publications

Restoring drifted electron microscope volumes using synaptic vesicles at sub-pixel accuracy.

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