Dataset Information

Image-based correction of continuous and discontinuous non-planar axial distortion in serial section microscopy.

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/saalfeldlab/section-sort, http://github.com/saalfeldlab/z-spacing and http://github.com/saalfeldlab/z-spacing-spark.

Contact

saalfelds@janelia.hhmi.org.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Hanslovsky P

PROVIDER: S-EPMC5860381 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature

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Publications

Image-based correction of continuous and discontinuous non-planar axial distortion in serial section microscopy.

Hanslovsky Philipp P Bogovic John A JA Saalfeld Stephan S

Bioinformatics (Oxford, England) 20170501 9

<h4>Motivation</h4>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 ei ...[more]

PMID: 28453669

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Project description:To investigate the feasibility of using an image-based method to correct for distortions induced by various artifacts in the x-ray spectrum recorded with photon-counting detectors for their application in breast computed tomography (CT).The polyenergetic incident spectrum was simulated with the tungsten anode spectral model using the interpolating polynomials (TASMIP) code and carefully calibrated to match the x-ray tube in this study. Experiments were performed on a Cadmium-Zinc-Telluride (CZT) photon-counting detector with five energy thresholds. Energy bins were adjusted to evenly distribute the recorded counts above the noise floor. BR12 phantoms of various thicknesses were used for calibration. A nonlinear function was selected to fit the count correlation between the simulated and the measured spectra in the calibration process. To evaluate the proposed spectral distortion correction method, an empirical fitting derived from the calibration process was applied on the raw images recorded for polymethyl methacrylate (PMMA) phantoms of 8.7, 48.8, and 100.0 mm. Both the corrected counts and the effective attenuation coefficient were compared to the simulated values for each of the five energy bins. The feasibility of applying the proposed method to quantitative material decomposition was tested using a dual-energy imaging technique with a three-material phantom that consisted of water, lipid, and protein. The performance of the spectral distortion correction method was quantified using the relative root-mean-square (RMS) error with respect to the expected values from simulations or areal analysis of the decomposition phantom.The implementation of the proposed method reduced the relative RMS error of the output counts in the five energy bins with respect to the simulated incident counts from 23.0%, 33.0%, and 54.0% to 1.2%, 1.8%, and 7.7% for 8.7, 48.8, and 100.0 mm PMMA phantoms, respectively. The accuracy of the effective attenuation coefficient of PMMA estimate was also improved with the proposed spectral distortion correction. Finally, the relative RMS error of water, lipid, and protein decompositions in dual-energy imaging was significantly reduced from 53.4% to 6.8% after correction was applied.The study demonstrated that dramatic distortions in the recorded raw image yielded from a photon-counting detector could be expected, which presents great challenges for applying the quantitative material decomposition method in spectral CT. The proposed semi-empirical correction method can effectively reduce these errors caused by various artifacts, including pulse pileup and charge sharing effects. Furthermore, rather than detector-specific simulation packages, the method requires a relatively simple calibration process and knowledge about the incident spectrum. Therefore, it may be used as a generalized procedure for the spectral distortion correction of different photon-counting detectors in clinical breast CT systems.

Dataset Information

Image-based correction of continuous and discontinuous non-planar axial distortion in serial section microscopy.

Motivation

Results

Availability and implementation

Contact

Supplementary information

Publications

Image-based correction of continuous and discontinuous non-planar axial distortion in serial section microscopy.

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