Estimating the thickness of ultra thin sections for electron microscopy by image statistics

Sporring, Jon; Khanmohammadi, Mahdieh; Darkner, Sune; Nava, Nicoletta; Nyengaard, Jens Rondel; Jensen, Eva Bjorn Wedel

doi:10.1109/isbi.2014.6867833

Cited by 6 publications

(22 citation statements)

References 5 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Due to lack of ground truth data, the validity of this method can only be assessed through synthetic experiments and by visual inspection of 3D surfaces (Sporring et al . ()). Thus, the issue is whether the assumptions in the synthetic experiments are valid for the real data.…”

Section: Discussionmentioning

confidence: 94%

“…To establish the relation between the sections in the z ‐direction, we estimated the thickness of each section using (Sporring et al . ()): the distance between two registered images was estimated by first normalizing the average intensity value to be 0 and the standard deviation to be 1 for each image. Then, the standard deviation of the difference between pixel values as a function of distance between the pixels for each image was calculated, and these two scaling functions were averaged.…”

Section: Methodsmentioning

confidence: 99%

“…We use a newly presented method for estimating the section thickness using image statistics only (Sporring et al . ()), and we present a novel method for estimating the densities of vesicles taking into account the projection uncertainty. We previously showed that the acute FS‐stress significantly increases the number of docked vesicles in mPFC as compared to sham stress (Nava et al .…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

3D analysis of synaptic vesicle density and distribution after acute foot‐shock stress by using serial section transmission electron microscopy

Khanmohammadi

Darkner

Nava

et al. 2016

Journal of Microscopy

View full text Add to dashboard Cite

Behavioural stress has shown to strongly affect neurotransmission within the neocortex. In this study, we analysed the effect of an acute stress model on density and distribution of neurotransmitter-containing vesicles within medial prefrontal cortex. Serial section transmission electron microscopy was employed to compare two groups of male rats: (1) rats subjected to foot-shock stress and (2) rats with sham stress as control group. Two-dimensional (2D) density measures are common in microscopic images and are estimated by following a 2D path in-section. However, this method ignores the slant of the active zone and thickness of the section. In fact, the active zone is a surface in three-dimension (3D) and the 2D measures do not accurately reflect the geometric configuration unless the active zone is perpendicular to the sectioning angle. We investigated synaptic vesicle density as a function of distance from the active zone in 3D. We reconstructed a 3D dataset by estimating the thickness of all sections and by registering all the image sections into a common coordinate system. Finally, we estimated the density as the average number of vesicles per area and volume and modelled the synaptic vesicle distribution by fitting a one-dimensional parametrized distribution that took into account the location uncertainty due to section thickness. Our results showed a clear structural difference in synaptic vesicle density and distribution between stressed and control group with improved separation by 3D measures in comparison to the 2D measures. Our results showed that acute foot-shock stress exposure significantly affected both the spatial distribution and density of the synaptic vesicles within the presynaptic terminal.

show abstract

Section: Discussionmentioning

confidence: 94%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

3D analysis of synaptic vesicle density and distribution after acute foot‐shock stress by using serial section transmission electron microscopy

Khanmohammadi

Darkner

Nava

et al. 2016

Journal of Microscopy

View full text Add to dashboard Cite

show abstract

“…A concrete example of this situation may be found in Sporring et al (2014) where ultra thin electron microscopy sections are analysed.…”

Section: Introductionmentioning

confidence: 99%

“…This procedure has been applied with success in Sporring et al (2014). In the present paper, we study the statistical properties of the resulting estimator of h. Under the tractable, yet flexible class of Lévy-based random field models, we derive an approximate variance of the estimator.…”

Section: Introductionmentioning

confidence: 99%

Estimation of Sample Spacing in Stochastic Processes

Rønn-Nielsen¹,

Sporring²,

Hahn³

2017

Image Anal Stereol

Self Cite

View full text Add to dashboard Cite

Motivated by applications in electron microscopy, we study the situation where a stationary and isotropic random field is observed on two parallel planes with unknown distance. We propose an estimator for this distance. Under the tractable, yet flexible class of Lévy-based random field models, we derive an approximate variance of the estimator. The estimator and the approximate variance perform well in two simulation studies.

show abstract

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

2016

View full text Add to dashboard Cite

MotivationSerial 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.ResultsWe 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 ImplementationWe 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.Supplementary information Supplementary data are available at Bioinformatics online

show abstract

Estimating the thickness of ultra thin sections for electron microscopy by image statistics

Cited by 6 publications

References 5 publications

3D analysis of synaptic vesicle density and distribution after acute foot‐shock stress by using serial section transmission electron microscopy

3D analysis of synaptic vesicle density and distribution after acute foot‐shock stress by using serial section transmission electron microscopy

Estimation of Sample Spacing in Stochastic Processes

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

Contact Info

Product

Resources

About