Automatic method of analysis of OCT images in assessing the severity degree of glaucoma and the visual field loss

Introduction: In many practical aspects of ophthalmology, it is necessary to assess the severity degree of glaucoma in cases where, for various reasons, it is impossible to perform a visual field test - static perimetry. These are cases in which the visual field test result is not reliable, e.g. advanced AMD (Age-related Macular Degeneration). In these cases, there is a need to determine the severity of glaucoma, mainly on the basis of optic nerve head (ONH) and retinal nerve fibre layer (RNFL) structure. OCT is one of the diagnostic methods capable of analysing changes in both, ONH and RNFL in glaucoma. Material and method: OCT images of the eye fundus of 55 patients (110 eyes) were obtained from the SOCT Copernicus (Optopol Tech. SA, Zawiercie, Poland). The authors proposed a new method for automatic determination of the RNFL (retinal nerve fibre layer) and other parameters using: mathematical morphology and profiled segmentation based on morphometric information of the eye fundus. A quantitative ratio of the quality of the optic disk and RNFL – BGA (biomorphological glaucoma advancement) was also proposed. The obtained results were compared with the results obtained from a static perimeter. Results: Correlations between the known parameters of the optic disk as well as those suggested by the authors and the results obtained from static perimetry were calculated. The result of correlation with the static perimetry was 0.78 for the existing methods of image analysis and 0.86 for the proposed method. Practical usefulness of the proposed ratio BGA and the impact of the three most important features on the result were assessed. The following results of correlation for the three proposed classes were obtained: cup/disk diameter 0.84, disk diameter 0.97 and the RNFL 1.0. Thus, analysis of the supposed visual field result in the case of glaucoma is possible based only on OCT images of the eye fundus. Conclusions: The calculations and analyses performed with the proposed algorithm and BGA ratio confirm that it is possible to calculate supposed mean defect (MD) of the visual field test based on OCT images of the eye fundus

Analysis of microtomographic images in automatic defect localization and detection

The paper presents a fast method of fully automatic localization and classification of defects in aluminium castings based on computed microtomography images. In the light of current research and based on available publications, where such analysis is made on the basis of images obtained from standard radiography (x-ray), this is a new approach which uses microtomographic images (μ-CT). In addition, the above-mentioned solutions most often analyze a pre-separated portion of an image, which requires the initial operator interference. The authors’ own pre-processing methods, which allow to separate the element area and potential defect areas from μ-CT images, and methods of extraction of selected features describing these areas have been proposed in the solution discussed here. A neural network trained using the Levenberg–Marquardt method with error backpropagation has been used as a classifier. The optimal network structure 20–4–1 and a set of 20 features describing the analysed areas have been determined as a result of performed tests. The applied solutions have provided 89% correct detection for any defect size and 96.73% for large defects, which is comparable to the results obtained from methods using x-ray images. This has confirmed that it is possible to use μ-CT images in automatic defect localization in 3D. Thanks to this method, quantitative analysis of aluminium castings can be carried out without user interaction and fully automated

Automatyczne metody analizy orientacji mikrotubul

A microtubule is a fibrous structure of 25 nm diameter and 10—25 μm length, which is created as a result of the polymerization of the tubulin protein. The orientation of microtubules in relation to the cell axis changes due to both internal factors (associated with intracellular processes) and external ones (the gravitational field, light intensity, mechanical stresses, an electric field, etc.). In order to evaluate these changes, the inclination angle to the cell axis is usually measured. In this monograph three developed algorithms for measuring the inclination angle to the cell axis are presented. The algorithms allowed determining a histogram of microtubule inclination angles which takes into consideration the area of microtubules. Additionally, the work covers the employment of the developed algorithms to the analysis of inclination angle variability as a kind of a trend in a cell. The authors present a spatial, three-dimensional reconstruction of microtubules based on a sequence of images obtained with a fluorescence microscope, using the depth-of-focus change feature. The monograph also contains an analysis of the protofilaments present in cross-sectional images of microtubules. Various possible approaches to this issue are shown. The authors hope that their monograph will be particularly useful for biologists and confirm them in the belief that many laborious measurements can be performed with a profiled image analysis application, leaving to them the analysis of the obtained results only

Automatic analysis of selected choroidal diseases in OCT images of the eye fundus

Introduction: This paper describes a method for automatic analysis of the choroid in OCT images of the eye fundus in ophthalmology. The problem of vascular lesions occurs e.g. in a large population of patients having diabetes or macular degeneration. Their correct diagnosis and quantitative assessment of the treatment progress are a critical part of the eye fundus diagnosis.Material and method: The study analysed about 1'000 OCT images acquired using SOCT Copernicus (Optopol Tech. SA, Zawiercie, Poland). The proposed algorithm for image analysis enabled to analyse the texture of the choroid portion located beneath the RPE (Retinal Pigment Epithelium) layer. The analysis was performed using the profiled algorithm based on morphological analysis and texture analysis and a classifier in the form of decision trees.Results: The location of the centres of gravity of individual objects present in the image beneath the RPE layer proved to be important in the evaluation of different types of images. In addition, the value of the standard deviation and the number of objects in a scene were equally important. These features enabled classification of three different forms of the choroid that were related to retinal pathology: diabetic edema (the classification gave accuracy ACC1 = 0.73), ischemia of the inner retinal layers (ACC2 = 0.83) and scarring fibro vascular tissue (ACC3 = 0.69). For the cut decision tree the results were as follows: ACC1 = 0.76, ACC2 = 0.81, ACC3 = 0.68.Conclusions: The created decision tree enabled to obtain satisfactory results of the classification of three types of choroidal imaging. In addition, it was shown that for the assumed characteristics and the developed classifier, the location of B-scan does not significantly affect the results. The image analysis method for texture analysis presented in the paper confirmed its usefulness in choroid imaging. Currently the application is further studied in the Clinical Department of Ophthalmology in the District Railway Hospital in Katowice, Medical University of Silesia, Poland

Automatic method of analysis of OCT images in the assessment of the tooth enamel surface after orthodontic treatment with fixed braces

Introduction: Fixed orthodontic appliances, despite years of research and development, still raise a lot of controversy because of its potentially destructive influence on enamel. Therefore, it is necessary to quantitatively assess the condition and therein the thickness of tooth enamel in order to select the appropriate orthodontic bonding and debonding methodology as well as to assess the quality of enamel after treatment and clean-up procedure in order to choose the most advantageous course of treatment. One of the assessment methods is computed tomography where the measurement of enamel thickness and the 3D reconstruction of image sequences can be performed fully automatically. Material and method: OCT images of 180 teeth were obtained from the Topcon 3D OCT-2000 camera. The images were obtained in vitro by performing sequentially 7 stages of treatment on all the teeth: before any interference into enamel, polishing with orthodontic paste, etching and application of a bonding system, orthodontic bracket bonding, orthodontic bracket removal, cleaning off adhesive residue. A dedicated method for the analysis and processing of images involving median filtering, mathematical morphology, binarization, polynomial approximation and the active contour method has been proposed. Results: The obtained results enable automatic measurement of tooth enamel thickness in 5 seconds using the Core i5 CPU M460 @ 2.5GHz 4GB RAM. For one patient, the proposed method of analysis confirms enamel thickness loss of 80 μm (from 730 ± 165 μm to 650 ± 129 μm) after polishing with paste, enamel thickness loss of 435 μm (from 730 ± 165 μm to 295±55 μm) after etching and bonding resin application, growth of a layer having a thickness of 265 μm (from 295 ± 55 μm to 560 ± 98 μm after etching) which is the adhesive system. After removing an orthodontic bracket, the adhesive residue was 105 μm and after cleaning it off, the enamel thickness was 605 μm. The enamel thickness before and after the whole treatment decreased by about 125 μm. Conclusions: This paper presents an automatic quantitative method for the assessment of tooth enamel thickness. This method has proven to be an effective diagnostic tool that allows evaluation of the surface and cross section of tooth enamel after orthodontic treatment with fixed thin-arched braces and proper selection of the methodology and course of treatment

Preservation and sterilization methods of the meniscal allografts : literature review

Nowadays, there are four types of meniscal allografts known: fresh, cryopreserved, deep-frozen and lyophilized ones but only two of them are widely used in clinical practice. Use of different types of meniscal allografts still remains controversial due to preparation method, their biomechanical properties as well as cost which is connected with processing and storage. The main aim of this review is to present the current status of knowledge concerning meniscal allograft preservation and sterilization, especially the advantages and disadvantages of each method. Authors wanted to show a broad spectrum of methods used and conceptions presented by other authors. The second aim is to gather available information about meniscal preservation and sterilization methods in one paper. Deep-frozen and cryopreserved meniscal allografts are the most frequently used ones in the clinical practice. The use of fresh grafts stays controversial but also has many followers. Lyophilized grafts in turn are not applied at present due to some serious drawbacks including reduction of tensile strength, poor rehydration, graft shrinkage and post-transplantation joint effusion as well as increased risk of meniscal size reduction. An application of sterilizing agents make the meniscal allograft free from the bacteria and viruses, but also it may cause serious structure changes. Therefore, choosing just one ideal method of meniscal allograft preservation and sterilization is complicated and should be based on broad knowledge and experience of surgeon performing the transplantation

Calibration and segmentation of skin areas in hyperspectral imaging for the needs of dermatology

Introduction: Among the currently known imaging methods, there exists hyperspectral imaging. This imaging fills the gap in visible light imaging with conventional, known devices that use classical CCDs. A major problem in the study of the skin is its segmentation and proper calibration of the results obtained. For this purpose, a dedicated automatic image analysis algorithm is proposed by the paper's authors. Material and method: The developed algorithm was tested on data acquired with the Specim camera. Images were related to different body areas of healthy patients. The resulting data were anonymized and stored in the output format, source dat (ENVI File) and raw. The frequency. of the data obtained ranged from 397 to 1030 nm. Each image was recorded every 0.79 nm, which in total gave 800 2D images for each subject. A total of 36' 000 2D images in dat format and the same number of images in the raw format were obtained for 45 full hyperspectral measurement sessions. As part of the paper, an image analysis algorithm using known analysis methods as well as new ones developed by the authors was proposed. Among others, filtration with a median filter, the Canny filter, conditional opening and closing operations and spectral analysis were used. The algorithm was implemented in Matlab and C and is used in practice. Results: The proposed method enables accurate segmentation for 36' 000 measured 2D images at the level of 7.8%. Segmentation is carried out fully automatically based on the reference ray spectrum. In addition, brightness calibration of individual 2D images is performed for the subsequent wavelengths. For a few segmented areas, the analysis time using Intel Core i5 CPU RAM [email protected] 4GB does not exceed 10 s. Conclusions: The obtained results confirm the usefulness of the applied method for image analysis and processing in dermatological practice. In particular, it is useful in the quantitative evaluation of skin lesions. Such analysis can be performed fully automatically without operator's intervention

X-ray microtomography analysis of the aluminum alloy composite reinforced by SiC after Friction Stir Processing

Despite many years of using friction stir processing (FSP), there are many unexplained aspects concerning the processes which appear during FSP: determining the direction of flow and mixing of the materials and the degree of mixing and microstructure fragmentation in specific areas. This paper presents the impact of FSP on the micro- and macrostructure of the composite with hypo-eutectic Si matrix reinforced by SiC particles. The analysis of the structure of the processed area in FSP in the relation to the microstructure of the base material has been made using x-ray microtomography. The results of these studies have been juxtaposed with studies using microscopic methods (light microscopy and SEM). The microtomography images revealed an additional separation on the advancing side and the weld nugget, where on the basis of a 3D reconstruction a layer microstructure on the direction of linear movement of the tool has been demonstrated. The analyses have revealed a limited flow of the material above the weld nugget. The main advantages of the research method applied were the possibility to show the invisible or barely visible elements of the microstructure using standard test methods and the ability to analyze the microstructure changes uninterruptedly in different directions in the volume of the material

Methods of measuring the iridocorneal angle in tomographic images of the anterior segment of the eye

Introduction: This paper presents the problem of automatic measurement of the iridocorneal angle in tomographic images of the anterior segment of the eye. It includes the results of the comparison of well-known methods for measuring the iridocorneal angle with new methods, proposed in this paper. All these methods concern tomographic image analysis and processing.Material and method: In total, approximately 100'000 tomographic images (from about 6'000 patients) were analysed. They were obtained using two devices: SOCT Copernicus (Optopol Tech. SA, Zawiercie, Poland) and Visante OCT (Carl Zeiss Meditec, Inc, Dublin, California, USA). The patients, aged 12 to 78 years with varying degrees of the iridocorneal angle pathology, were from the region of Silesia, Poland. The images were in DICOM or RAW formats and analysed in the software developed by the authors for the purposes of this study.Results: The results indicate that the measurement method proposed by the authors, which is based on the calculation of the minimum distance between the iris and the cornea in the adopted area, is the most accurate. For this method sensitivity was 0.88, specificity 0.89 and the area under the Receiver Operating Characteristic curve (AUC) was 0.88. The other known methods for measuring the iridocorneal angle gave worse results, that is, for example, for the measurement of the distance between the iris and the cornea AUC = 0.87, sensitivity = 0.86 and specificity = 0.71. For another well-known method of measuring the iridocorneal angle AUC = 0.77, sensitivity = 0.82 and specificity = 0.61.Conclusions: The study proved that the proposed method of measuring the minimum distance between the iris and the cornea within the adopted area is the most effective in the classification of the iridocorneal angle in patients with a high degree of pathology of all the compared measurement methods based on tomographic images. However, it requires fully automated measurement

Automatic analysis of 2D polyacrylamide gels in the diagnosis of DNA polymorphisms

Introduction: The analysis of polyacrylamide gels is currently carried out manually or automatically. In the automatic method, there are limitations related to the acceptable degree of distortion of lane and band continuity. The available software cannot deal satisfactorily with this type of situations. Therefore, the paper presents an original image analysis method devoid of the aforementioned drawbacks.Material: This paper examines polyacrylamide gel images from Li-Cor DNA Sequencer 4300S resulting from the use of the electrophoretic separation of DNA fragments. The acquired images have a resolution dependent on the length of the analysed DNA fragments and typically it is MG×NG=3806×1027 pixels. The images are saved in TIFF format with a grayscale resolution of 16 bits/pixel. The presented image analysis method was performed on gel images resulting from the analysis of DNA methylome profiling in plants exposed to drought stress, carried out with the MSAP (Methylation Sensitive Amplification Polymorphism) technique.Results: The results of DNA polymorphism analysis were obtained in less than one second for the Intel Core™ 2 Quad CPU [email protected], 8GB RAM. In comparison with other known methods, specificity was 0.95, sensitivity = 0.94 and AUC (Area Under Curve) = 0.98.Conclusions: It is possible to carry out this method of DNA polymorphism analysis on distorted images of polyacrylamide gels. The method is fully automatic and does not require any operator intervention. Compared with other methods, it produces the best results and the resulting image is easy to interpret. The presented method of measurement is used in the practical analysis of polyacrylamide gels in the Department of Genetics at the University of Silesia in Katowice, Poland