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Virtual reality is increasingly used in medicine for diagnostics, for visualisation of complex structures and for preoperative planning. In interventional radiology, minimally invasive approach could be described with a target point representing the desired needle tip position and an array of all possible trajectories leading to it resembling irregular “cone” or “pyramid”. We present a pilot study of planning a minimally invasive posterior infrazygomatic and suprazygomatic approaches into the pterygopalatine fossa using a solid angle as a measure of size of the approach in five virtually reconstructed heads. The minimally invasive approaches were planned by manually drawing the edges of “pyramids” that described each approach in 3D using virtual reality program Tracer. For each head, a transverse diameter was measured and for each approach a solid angle size, average edge length and estimated area on the skin from where the target point could be reached were calculated. We found that, the solid angle of posterior infrazygomatic approach was significantly larger than suprazygomatic approach (p0.001). Furthermore, the transverse head diameter and solid angle in posterior infrazygomatic approach were negatively correlated (ρ=-0.55, p=0.0002), while transverse head diameter and the estimated area on the skin from where the target point could be reached in the suprazygomatic approach were positively correlated (ρ=0.37, p=0.0206). In conclusion, our findings provide important preliminary evidence on the feasibility of evaluating and comparing different minimally invasive approaches using virtual reality systems, and affirm the validity of solid angle as a measure of the size of the approach.

Filtration of super-resolved microscopic images brings often troubles with removing undesired image parts like, e.g., noise, inhomogenous background and reconstruction artifacts. Standard filtration techniques, e.g., convolution- or Fourier transform-based methods are not always appropriate, since they may lower image resolution that was acquired by hi-tech and expensive microscopy systems. Thus, in this article it is proposed to filter such images using discrete wavelet transform (DWT). Newly developed Wavelet_Denoise plugin for free available Fiji software package demonstrates important possibilities of applying DWT to images: Decomposition of a filtered picture using various wavelet filters and levels of details with showing decomposed images and visualization of effects of back transformation of the picture with chosen level of suppression or denoising of wavelet coefficients. The Fiji framework allows, for example, using a plethora of various microscopic image formats for data opening, users can easily install the plugin through a menu command and the plugin supports processing 3D images in Z-stacks. The application of the plugin for removal of reconstruction artifacts and undesirable background in images acquired by super-resolved structured illumination microscopy is demonstrated as well.

The main objective of this study was to find out whether the selected chloroplast characteristics measured in the mesophyll layer nearest to the needle surface (i.e., the first mesophyll layer) could be representative for the whole needle cross section. Two chloroplast sampling approaches were applied on Norway spruce needles during the investigation of the effects of different levels of air CO2 concentration and irradiance: (i) sampling only from the first mesophyll layer, and (ii) systematic uniform random (SUR) sampling. The selected characteristics were: (i) chloroplast area, (ii) starch grain area, and (iii) starch areal density on median chloroplast cross sections, and (iv) chloroplast number per unit of needle volume. It was shown that the first mesophyll layer was not representative for estimating all evaluated characteristics except the chloroplast area. Sampling only there caused obtaining slightly biased results, while SUR sampling gave unbiased estimations at the cost of longer measuring time. The major effect of studied factors was in starch areal density and starch grain area, which were larger in sun needles in elevated CO2 concentration in comparison with sun needles in ambient CO2 concentration. In conclusion, it was demonstrated that the first layer of mesophyll is not always representative for the needle cross section. If technically feasible, SUR is recommended for analysis of chloroplast ultrastructure. The simplified sampling design can be applied, e.g., for comparisons of many different treatments. However, it should be combined with other approaches to characterize the chloroplast function and the results carefully considered and interpreted.

The present paper deals with the problem of volume estimation of individual objects from a single 2D view. Our main application is volume estimation of pancreatic (Langerhans) islets and the single 2D view constraint comes from the time and equipment limitations of the standard clinical procedure. Two main approaches are followed in this paper. First, two regression-based methods are proposed, using a set of simple shape descriptors of the segmented image of the islet. Second, two example-based methods are proposed, based on a database of islets with known volume. For training and evaluation, islet volumes were determined by OPT microscopy and a semi-automatical stereological volume estimation using the so-called Fakir probes. The performance of the single image volume estimation methods is studied on a set of 99 islets from human donors. Further experiments were also performed on a stone dataset and on synthetic 3D shapes, generated using a flexible stochastic particle model. The proposed methods are fast and the experimental results show that in most situations the proposed methods perform significantly better than the methods currently used in clinical practice, which are based on simple spherical or ellipsoidal models.

The effect of ageing on the capillary network in skeletal muscles has produced conflicting results in both, human and animals studies. Some of the inconsistencies are due to non-comparable and biased methods that were applied on thin transversal sections, especially in muscles with complicated morphological structures, such as in human masseter muscle. We present a new immunohistochemical method for staining capillaries and muscle fibres in 100 µm thick sections as well as novel approach to 3D visualization of capillaries and muscle fibres. Applying confocal microscopy and virtual 3D stereological grids, or tracing capillaries in virtual reality, length of capillaries within a muscle volume or length of capillaries adjacent to muscle fibre per fibre length, fibre surface or fibre volume were evaluated in masseter muscle of young and old subjects by an unbiased approach. Our findings show that anatomic capillarity is well maintained in masseter muscle in old subjects; however, vascular remodelling occurs with age, which could be a response to changed muscle function and age-related muscle fibre type transformations.

The microvascular bed of the human term placenta is located in the mature intermediate and terminal villi. Despite repeated studies, a commonly accepted model of its spatial organization is not yet available. In the present study, the 3-D arrangement of vessels in mature intermediate and terminal placental villi was examined using the combination of confocal microscopy and image processing. Fixed and paraffin embedded placental samples were cut into 120 μm thick sections. Serial optical sections were captured by a confocal microscope and used as an initial data for 3-D reconstruction. The reconstructed segments of the villous tree show parallel vessels of mature intermediate villi giving rise to the capillaries of terminal villi. The signs of longitudinal and sprouting capillary growth as well as growth of new villi were observed. The presented method allowed us to visualize large parts of peripheral placental villi, which is useful for elucidating the arrangement of their vascular bed.

Image analysis techniques for preprocessing, segmentation and estimation of geometrical characteristics of fiber-like structures from 2-D or 3-D images captured by a confocal microscope are presented. Methods are demonstrated on fiber-like biological structure: endoplasmic reticulum (ER) of tobacco cells. In the presented analysis of 2-D images of ER before and after the treatment of latrunculin B, ER and ER tubules were segmented and the area density of ER as well as the length density of ER tubules in the cell cortical layer were estimated by automatic image analysis algorithms. Images of 3-D arrangement of ER were reconstructed and rendered by various visualization techniques.

Periodic spatial grids can be used for unbiased estimation of length and surface area of objects by counting or measuring intersections of the objects with the grids. The estimators are theoretically based on discrete approximation of well established integral geometric formulas. The variance of the estimates depends on properties of both the grid and the measured objects. Main results of the theory of variance of the isotropic uniform random (IUR) volume estimation by spatial grids, especially a formula relating the variance of the volume estimator with the object surface area and the grid constant, are recapitulated. To identify main features of length and surface area IUR estimates the variance due to rotation and simple asymptotic formulas for the residual variance of estimates of selected model objects is calculated. Surface area estimates by multiple grids of parallel lines in 3D and of the variance of length estimates by periodic grids of planes or spheres in ddimensional space are studied.

The volume tensor provides a robust estimate of the shape and orientation of an object in space. In this paper, we introduce Fakir method for estimating the tensor of an object in 3D data set based on the intersections of objects boundary with virtual lines. We calculate the precision of shape estimates by predicting the variance of estimators of integrals based on systematic sampling. To demonstrate the ability of the Fakir method, we measure changes in shape and orientation of compartments in the pheasant brain during development.

The integral of a smooth function with bounded support over a set with finite perimeter in Euclidean space ℝd is estimated using a periodic grid in an isotropic uniform random position. Extension term in the estimator variance is proportional to the integral of the squared modulus of the function over the object boundary and to the grid scaling factor raised to the power of d+1. Our result generalizes the Kendall-Hlawka-Matheron formula for the variance of the isotropic uniform systematic estimator of volume.