A guide to analysis and reconstruction of serial block face scanning electron microscopy data
Summary
Serial block face scanning electron microscopy (SBF‐SEM) is a relatively new technique that allows the acquisition of serially sectioned, imaged and digitally aligned ultrastructural data. There is a wealth of information that can be obtained from the resulting image stacks but this presents a new challenge for researchers – how to computationally analyse and make best use of the large datasets produced. One approach is to reconstruct structures and features of interest in 3D. However, the software programmes can appear overwhelming, time‐consuming and not intuitive for those new to image analysis. There are ...
Source: Journal of Microscopy - January 1, 2018 Category: Laboratory Medicine Authors: E. COCKS, M. TAGGART, F.C. RIND, K. WHITE Tags: Original Article Source Type: research
Analogous on ‐axis interference topographic phase microscopy (AOITPM)
Summary
The refractive index (RI) of a sample as an endogenous contrast agent plays an important role in transparent live cell imaging. In tomographic phase microscopy (TPM), 3D quantitative RI maps can be reconstructed based on the measured projections of the RI in multiple directions. The resolution of the RI maps not only depends on the numerical aperture of the employed objective lens, but also is determined by the accuracy of the quantitative phase of the sample measured at multiple scanning illumination angles. This paper reports an analogous on‐axis interference TPM, where the interference angle between the sample...
Source: Journal of Microscopy - January 1, 2018 Category: Laboratory Medicine Authors: P. XIU, Q. LIU, X. ZHOU, Y. XU, C. KUANG, X. LIU Tags: Original Article Source Type: research
On the influence of lipid ‐induced optical anisotropy for the bioimaging of exo‐ or endocytosis with interference microscopic imaging
Summary
Some implementations of interference microscopy imaging use digital holographic measurements of complex scattered fields to reconstruct three‐dimensional refractive index maps of weakly scattering, semi‐transparent objects, frequently encountered in biological investigations. Reconstruction occurs through application of the object scattering potential which assumes an isotropic refractive index throughout the object. Here, we demonstrate that this assumption can in some circumstances be invalid for biological imaging due to the presence of lipid‐induced optical anisotropy. We show that the nanoscale organizat...
Source: Journal of Microscopy - January 1, 2018 Category: Laboratory Medicine Authors: D. MARQUES, A. MIRANDA, A.G. SILVA, P.R.T. MUNRO, P.A.A. DE BEULE Tags: Original Article Source Type: research
An optical configuration for fastidious STEM detector calibration and the effect of the objective ‐lens pre‐field
Summary
In the scanning transmission electron microscope, an accurate knowledge of detector collection angles is paramount in order to quantify signals on an absolute scale. Here we present an optical configuration designed for the accurate measurement of collection angles for both image‐detectors and energy‐loss spectrometers. By deflecting a parallel electron beam, carefully calibrated using a diffraction pattern from a known material, we can directly observe the projection‐distortion in the post‐specimen lenses of probe‐corrected instruments, the 3‐fold caustic when an image‐corrector is fitted, and any mi...
Source: Journal of Microscopy - January 1, 2018 Category: Laboratory Medicine Authors: L. JONES, A. VARAMBHIA, H. SAWADA, P.D. NELLIST Tags: Original Article Source Type: research
Segmentation of clustered cells in negative phase contrast images with integrated light intensity and cell shape information
In this study, the emphasis was put on the segmentation of clustered cells in negative phase contrast images. A new method was proposed to combine both light intensity and cell shape information through the construction of grey‐weighted distance transform (GWDT) within preliminarily segmented areas. With the constructed GWDT, the clustered cells can be detected and then separated with a modified region skeleton‐based method. Moreover, a contour expansion operation was applied to get optimised detection of cell boundaries. In this paper, the working principle and detailed procedure of the proposed method are described, ...
Source: Journal of Microscopy - December 27, 2017 Category: Laboratory Medicine Authors: Y. WANG, C. WANG, Z. ZHANG Tags: Original Article Source Type: research
Segmentation of clustered cells in negative phase contrast images with integrated light intensity and cell shape information
Journal of Microscopy, EarlyView. (Source: Journal of Microscopy)
Source: Journal of Microscopy - December 27, 2017 Category: Laboratory Medicine Source Type: research
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Journal of Microscopy, Ahead of Print. (Source: Journal of Microscopy)
Source: Journal of Microscopy - December 27, 2017 Category: Laboratory Medicine Source Type: research
Multipoint scanning dual ‐detection confocal microscopy for fast 3D volumetric measurement
Summary
We propose a multipoint scanning dual‐detection confocal microscopy (MS‐DDCM) system for fast 3D volumetric measurements. Unlike conventional confocal microscopy, MS‐DDCM can accomplish surface profiling without axial scanning. Also, to rapidly obtain 2D images, the MS‐DDCM employs a multipoint scanning technique, with a digital micromirror device used to produce arrays of effective pinholes, which are then scanned. The MS‐DDCM is composed of two CCDs: one collects the conjugate images and the other collects nonconjugate images. The ratio of the axial response curves, measured by the two detectors, provid...
Source: Journal of Microscopy - December 18, 2017 Category: Laboratory Medicine Authors: D. LEE, D. ‐G. GWEON, H. YOO Tags: Original Article Source Type: research
Multipoint scanning dual ‐detection confocal microscopy for fast 3D volumetric measurement
Journal of Microscopy, EarlyView. (Source: Journal of Microscopy)
Source: Journal of Microscopy - December 18, 2017 Category: Laboratory Medicine Source Type: research
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Journal of Microscopy, Ahead of Print. (Source: Journal of Microscopy)
Source: Journal of Microscopy - December 18, 2017 Category: Laboratory Medicine Source Type: research
Three ‐dimensional digital reconstruction of skin epidermis and dermis
This study describes how three‐dimensional (3D) human skin tissue is reconstructed, and provides digital anatomical data for the physiological structure of human skin tissue based on large‐scale thin serial sections. Human skin samples embedded in paraffin were cut serially into thin sections and then stained with hematoxylin‐eosin. Images of serial sections obtained from lighting microscopy were scanned and aligned by the scale‐invariant feature transform algorithm. 3D reconstruction of the skin tissue was generated using Mimics software. Fibre content, porosity, average pore diameter and specific surface area of ...
Source: Journal of Microscopy - December 14, 2017 Category: Laboratory Medicine Authors: P. Liu, J. ‐Y. ZHU, B. TANG, Z.‐C. HU Tags: Original Article Source Type: research
Structure and composition of Unio pictorum shell: arguments for the diversity of the nacroprismatic arrangement in molluscs
Journal of Microscopy, EarlyView. (Source: Journal of Microscopy)
Source: Journal of Microscopy - December 14, 2017 Category: Laboratory Medicine Source Type: research
Three ‐dimensional digital reconstruction of skin epidermis and dermis
Journal of Microscopy, EarlyView. (Source: Journal of Microscopy)
Source: Journal of Microscopy - December 14, 2017 Category: Laboratory Medicine Source Type: research
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Journal of Microscopy, Ahead of Print. (Source: Journal of Microscopy)
Source: Journal of Microscopy - December 14, 2017 Category: Laboratory Medicine Source Type: research
