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Journal of Microscopy

An international and interdisciplinary forum for publication, discussion & education for scientists and technologists who use any form of microscopy or image analysis.

Journal_Aug 2014.jpgThe Journal of Microscopy publishes quality original research articles, review articles, Hot Topic papers, and letters to the Editor, covering all aspects of microscopy and analysis. This includes cutting-edge technology and innovative applications in physics, chemistry, material and biological sciences.

The Journal is for scientists and technologists who develop, advance or apply any form of microscopy, spatially resolved spectroscopy, compositional mapping & image analysis.

The Journal of Microscopy is particularly interested in papers on original applications & developments in microscopy.


Impact Factor: 2.15

ISI Journal Citation Reports © Ranking: 2013: 3/11 (Microscopy)
Frequency: Monthly
Print ISSN: 0022-2720 / Online ISSN: 1365-2818

Aims & Scope

The Journal of Microscopy is for scientists and technologists that use any form of microscopy, spatially resolved spectroscopy, compositional mapping and image analysis. This includes technology and applications in physics, chemistry, material and biological sciences.

The Journal of Microscopy is published by Wiley on the Wiley Online Library on behalf of the Royal Microscopical Society.

Latest Early View Papers available online

The following early view papers are available now at Wiley online.

A novel segmentation approach for noisy medical images using Intuitionistic fuzzy divergence with neighbourhood-based membership function
A. Jati, G. Singh, S. Koley, A. Konar, A.K. Ray and C. Chakraborty

Image thresholding remains always a challenging task in image segmentation irrespective of all different types of applications. Biomedical image analytics require more precise image segmentation for analysing specially shape and size of the region of interest. More specifically, it plays an important role in digital pathology and radiology for providing better characterization and visualization of cells, tissues, tumours etc. In view of this, medical image segmentation demands higher segmentation accuracy especially when the images are affected by noise. There are various situations where noise becomes inherent in the medical images. For example, segmentation of the breast micro-calcifications/lesions in X-Ray mammogram images still suffers from diagnostic precision due to noise and overlapping heterogeneous intensity variation. In pathological evaluation, the microscopic images get also affected by noises in hospital facilities. Under such situation, improvement on diagnostic precision necessitates development of automated segmentation approach. This work focuses on developing a novel and generic technique to delineate objects from medical images efficiently using an intuitionistic fuzzy divergence based thresholding. A neighbourhood based membership function is defined here. It is observed that the proposed intuitionistic fuzzy divergence based image thresholding technique yields lesser degradation of segmentation performance in noisy environment. It works efficiently in both additive and multiplicative noise-based images. In order to show its novelty and generality, the proposed methodology has been tested on three types of medical applications. The results show that the proposed methodology is effective, more accurate and efficient for segmenting noisy images in comparison with ground truths. In addition, the results clearly validate the efficacy of the proposed algorithm in handling noise that corrupts the images as opposed to the conventional practice of filtering the images prior to the segmentation phase.


Methods to calibrate and scale axial distances in confocal microscopy as a function of refractive index
T.H. Besseling, J. Jose and A. Van Blaaderen

When a confocal microscope is used to construct a 3D image of a sample, distances in the (axial) z-direction are not effected in the same way as in the (lateral) xy-direction. The first reason for this is that the resolution in the z-direction is typically three times worse than in the xy-direction. Therefore, objects of several micrometers or smaller seem elongated or smeared out in the z-direction. Additionally, the light used for imaging has to pass through the immersion fluid, a glass container wall and the sample itself, which almost always have different refractive indices. This mismatch in refractive index results, amongst others, in elongated z-distances. Accurate calibration of the z-distances in confocal microscopy therefore remain cumbersome. In this paper we present two methods to calibrate the z-distances that are both practical and easy to employ. With one of these methods we measured the axial or z-distance scaling as a function of refractive index mismatch and compared it to theoretical predictions. Accurate distance measurement in 3D confocal microscopy is important for quantitative analysis, volume visualization and image restoration processes.


Grain-oriented segmentation of images of porous structures using ray casting and curvature energy minimization
Hyun-Gyu Lee, Min-Kook Choi and Sang-Chul Lee

The analysis of microscope images of porous structures is a key part of the assessment of grain quality in materials for medical applications and self-assembled materials, which are becoming increasingly important. A common method of analysis is to consider the pattern of grain in the material as a two-dimensional signal, and characterize that in terms of frequencies. But this is not effective with scanning electron microscope (SEM) images, which tend to have many defects: the boundaries between grains of material are indistinct; grain sizes are variable; and the brightness of the image varies from one location to another. We take a new approach for analysis. First we process an SEM image by looking at its contrast: we compare each of the dots that make up the image with a locally determined level of brightness, and hence classify each dot either as part of the interior of a grain, or as part of a grain boundary. Because the original image was defective, this classification is only provisional, and at this stage the grain boundaries actually consist of many disconnected pieces. So now we construct a grid of points that covers the processed image and, from each point on this grid, we probe outwards with little sunbursts of radial lines, or 'rays', and find the first piece of grain boundary struck by each ray. We discard very long rays, which probably missed the boundary of the grain in which the ray started. After these over-long rays have been eliminated, some of these little sunbursts will be good approximations to the shape of a grain; others will not, largely depending on the location of the grid point from which the rays originated. So we assess the smoothness of the approximate grain produced by each sunburst, and accept the very smoothest grain. We can now use this grain to make a small correction to the processed image that contains the incomplete grain boundaries. Then the process of finding the most plausible grain is repeated, and the image on which we are working is repeatedly updated with new grains, until there are no more sunbursts of rays which produce plausible grains, and the image is filled with completed grains. We show that this process outperforms five other state-of-the-art techniques for recognizing grain boundaries, in terms of both speed and accuracy, on SEM images of anodized Ti and alumina.


Calcium silicate cement-induced remineralisation of totally demineralised dentine in comparison with glass ionomer cement: tetracycline labelling and two-photon fluorescence microscopy
A.R. Atmeh, E.Z. Chong, G. Richard, A. Boyde, F. Festy and T.F. Watson

Dentine demineralisation is the earliest stage of dental caries that cause mineral loss from the dental tissues such as dentine. For the management of dental caries, damaged and demineralised dentine is usually cut by the dentist and removed before placing an appropriate restorative material. This procedure could be extensive leaving minimal dentine to support the restoration, which may affect the durability and functionality of the restored tooth. Recently, more conservative approaches have been adopted that suggest leaving the demineralised dentine and encouraging the deposition of minerals back into its organic matrix (remineralisation). Calcium silicate cements, known as Portland cement, has been used for dental applications for more than two decades, but not much evidence exists on their ability to induce the remineralisation of demineralised dentine. Although different technique has been applied to evaluate dentine remineralisation, their ability to detect mineralisation is limited to surface characterisation, which does not enable high resolution observation of the mineralisation process within the structure of the organic matrix. The two-photon fluorescence microscopy is a subsurface imaging technique that allows imaging of deep tissues with high resolution. Combining this technique with a fluorescent mineralisation labelling dye, such as tetracycline, could provide an improved mineralisation imaging technique. This study evaluated the potential of calcium-silicate based dental restorative material (BiodentineTM) to induce remineralisation of totally demineralised dentine using two-photon fluorescence microscopy with tetracycline labelling.

Latest Short Invited Reviews available online

Electron microscopy of quantum dots
Thomas Walther

What environmental transmission electron microscopy measures and how this links to diffusivity: thermodynamics versus kinetics
Thomas Walther

Wavelets: on the virtues and applications of the mathematical microscope
Michael Unser

Biological applications of cryo-soft X-ray tomography
E. Duke, K. Dent, M. Razi and L. M. Collinson

Nonlinear optical microscopy with vibrational contrast
M. J. Winterhalder and A. Zumbusch

Focused ion beam scanning electron microscopy in biology
C. Kizilyaprak, J. Daraspe and B.M. Humbel

Lay Descriptions

In order to make the science we publish more accessible, a second abstract or lay description in easy to understand non-technical language has been developed. Lay Descriptions for papers published through the Journal of Microsopy will be included in infocus and here on the RMS website.

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