Estimation of Z-Thickness and XY-Anisotropy of Electron Microscopy Images using Gaussian Processes

@article{Ambegoda2020EstimationOZ,
  title={Estimation of Z-Thickness and XY-Anisotropy of Electron Microscopy Images using Gaussian Processes},
  author={Thanuja D. Ambegoda and Julien N. P. Martel and Jozef Adamcik and Matthew Cook and Richard H. R. Hahnloser},
  journal={ArXiv},
  year={2020},
  volume={abs/2002.00228}
}
Serial section electron microscopy (ssEM) is a widely used technique for obtaining volumetric information of biological tissues at nanometer scale. However, accurate 3D reconstructions of identified cellular structures and volumetric quantifications require precise estimates of section thickness and anisotropy (or stretching) along the XY imaging plane. In fact, many image processing algorithms simply assume isotropy within the imaging plane. To ameliorate this problem, we present a method for… 

References

SHOWING 1-10 OF 36 REFERENCES
Image-based correction of continuous and discontinuous non-planar axial distortion in serial section microscopy.
TLDR
Methods to identify and correct distortions through image-based signal analysis without any additional physical apparatus or measurements are developed and demonstrated in proof of principle experiments and application to real world problems.
Estimating the thickness of ultra thin sections for electron microscopy by image statistics
TLDR
The standard deviation of the difference between pixel values as a function of distance is used to give an extremely simple, linear algorithm, and it is shown that these images with high certainty belong to the required statistical class, and that the reconstructions are valid.
Image-based correction of continuous and discontinuous non-planar axial distortion in serial section microscopy
TLDR
This work developed methods to identify and correct distortions through image‐based signal analysis without any additional physical apparatus or measurements that results in distorted image volumes.
Post-acquisition image based compensation for thickness variation in microscopy section series
TLDR
This work has developed a method to estimate the relative z-position of each individual section as a function of signal change across the section series in serial section Microscopy.
Electron tomography : methods for three-dimensional visualization of structures in the cell
Introduction: Principles of Electron Tomography.- Sample Shrinkage and Radiation Damage of Plastic Sections.- Electron Tomography of Frozen-hydrated Sections of Cells and Tissues.- The Electron
Cylindrical diameters method for calibrating section thickness in serial electron microscopy
TLDR
The cylindrical diameters method gives the same answer as that obtained by the minimal folds method, and improves the accuracy of section thickness as inferred from the colour of sections floating in water.
Candidate Sampling for Neuron Reconstruction from Anisotropic Electron Microscopy Volumes
TLDR
This paper proposes to replace the heuristic set of candidates used in previous methods with samples drawn from a conditional random field (CRF) that is trained to label sections of neural tissue that produce 30% less reconstruction errors than current candidate generation methods.
Thin sections. I. A study of section thickness and physical distortion produced during microtomy.
TLDR
The thicknesses of sections of n-butyl methacrylate polymer were determined by ellipsometry, and correlated with the color shown in reflected light, and agree well with optical theory and with previous published data for thin films.
Elastic volume reconstruction from series of ultra-thin microscopy sections
TLDR
This work developed a method to reassemble a continuous volume from such large section series that explicitly minimizes artificial deformation by applying a global elastic constraint.
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