Ontology-Driven Process-Based Laboratory Information Management System

In this study, authors focus on the Laboratory Information Management System (LIMS) development. Taditionally, the LIMS is implemented to organize the medical laboratory processes, from specimen access through laboratory analysis to issuing reports to physicians. The LIMS is to automate laboratory processes and is compatible with laboratory tools and quality control instruments. Authors present the enterprise architecture (EA) of pathomorphology diagnosis unit (PDU), covering the LIMS applications and processes. Further, they formulate the system\u27s knowledge model. Authors propose an OWL ontology for the IoTDT-BPMN (Internet of Things Digital Twin – Business Process Model and Notation) metamodel for the PDU. Authors conclude that ontology elements related to the processes of PDU facilitate the LIMS development and usage, particularly to support the federated learning realized by selected labs

Measuring Respiratory Motion for Supporting the Minimally Invasive Destruction of Liver Tumors

Objective: Destroying liver tumors is a challenge for contemporary interventional radiology. The aim of this work is to compare different techniques used for the measurement of respiratory motion, as this is the main hurdle to the effective implementation of this therapy. Methods: Laparoscopic stereoscopic reconstruction of point displacements on the surface of the liver, observation of breathing using external markers placed on the surface of the abdominal cavity, and methods for registration of the surface of the abdominal cavity during breathing were implemented and evaluated. Results: The following accuracies were obtained: above 4 mm and 0.5 mm, and below 8 mm for laparoscopic, skin markers, and skin surface registration methods, respectively. Conclusions: The clinical techniques and accompanying imaging modalities employed to destroy liver tumors, as well as the advantages and limitations of the proposed methods, are presented. Further directions for their development are also indicated

Automatic liver segmentation in computed tomography using general-purpose shape modeling methods

Abstract Background Liver segmentation in computed tomography is required in many clinical applications. The segmentation methods used can be classified according to a number of criteria. One important criterion for method selection is the shape representation of the segmented organ. The aim of the work is automatic liver segmentation using general purpose shape modeling methods. Methods As part of the research, methods based on shape information at various levels of advancement were used. The single atlas based segmentation method was used as the simplest shape-based method. This method is derived from a single atlas using the deformable free-form deformation of the control point curves. Subsequently, the classic and modified Active Shape Model (ASM) was used, using medium body shape models. As the most advanced and main method generalized statistical shape models, Gaussian Process Morphable Models was used, which are based on multi-dimensional Gaussian distributions of the shape deformation field. Results Mutual information and sum os square distance were used as similarity measures. The poorest results were obtained for the single atlas method. For the ASM method in 10 analyzed cases for seven test images, the Dice coefficient was above 55$$\%$$ % , of which for three of them the coefficient was over 70$$\%$$ % , which placed the method in second place. The best results were obtained for the method of generalized statistical distribution of the deformation field. The DICE coefficient for this method was 88.5$$\%$$ % Conclusions This value of 88.5 $$\%$$ % Dice coefficient can be explained by the use of general-purpose shape modeling methods with a large variance of the shape of the modeled object—the liver and limitations on the size of our training data set, which was limited to 10 cases. The obtained results in presented fully automatic method are comparable with dedicated methods for liver segmentation. In addition, the deforamtion features of the model can be modeled mathematically by using various kernel functions, which allows to segment the liver on a comparable level using a smaller learning set

Akwizycja i analiza danych dla celów biopsji z wykorzystaniem obrazów fotodynamicznych

Biopsy is the main criterion for cancer diagnosis, especially in early histopatological stage. The success of such examination strongly depends on a proper choice of the tissue acquisition. In this paper a semi-automated method of the ROI extraction in photodynamical images is presented.Biopsja jest głównym kryterium w początkowym stadium w diagnostyce raka. Skuteczność zależy od poprawnego wyboru miejsca akwizycji tkanki. Artykuł prezentuje proces akwizycji i analizy danych, której celem jest półautomatyczne wyznaczenie potencjalnego obszaru biopsji

Modeling of Respiratory Motion to Support the Minimally Invasive Destruction of Liver Tumors

Objective: Respiratory movements are a significant factor that may hinder the use of image navigation systems during minimally invasive procedures used to destroy focal lesions in the liver. This article aims to present a method of estimating the displacement of the target point due to respiratory movements during the procedure, working in real time. Method: The real-time method using skin markers and non-rigid registration algorithms has been implemented and tested for various classes of transformation. The method was validated using clinical data from 21 patients diagnosed with liver tumors. For each patient, each marker was treated as a target and the remaining markers as target position predictors, resulting in 162 configurations and 1095 respiratory cycles analyzed. In addition, the possibility of estimating the respiratory phase signal directly from intraoperative US images and the possibility of synchronization with the 4D CT respiratory sequence are also presented, based on ten patients. Results: The median value of the target registration error (TRE) was 3.47 for the non-rigid registration method using the combination of rigid transformation and elastic body spline curves, and an adaptation of the assessing quality using image registration circuits (AQUIRC) method. The average maximum distance was 3.4 (minimum: 1.6, maximum 6.8) mm. Conclusions: The proposed method obtained promising real-time TRE values. It also allowed for the estimation of the TRE at a given geometric margin level to determine the estimated target position. Directions for further quantitative research and the practical possibility of combining both methods are also presented

Semi-automatic measurements and description of the geometry of vascular tree based on Bézier spline curves: application to cerebral arteries

Abstract Background The geometry of the vessels is easy to assess in novel 3D studies. It has significant influence on flow patterns and this way the evolution of vascular pathologies such as aneurysms and atherosclerosis. It is essential to develop robust system for vascular anatomy measurement and digital description allowing for assessment of big numbers of vessels. Methods A semiautomatic, robust, integrated method for vascular anatomy measurements and mathematical description are presented. Bezier splines of 6th degree and continuity of C3 was proposed and distribution of control points was dependent on local radius. Due to main interest of our institution, the system was primarily used for the assessment of the geometry of the intracranial arteries, especially the first Medial Cerebral Artery division. Results 1359 synthetic figures were generated: 381 torus and 978 spirals. Experimental verification of the proposed methodology was conducted on 400 Middle Cerebral Artery divisions. Conclusions In difference to other described solution all proposed methodology steps were integrated allows analysis of variability of geometrical parameters among big number of Medial Cerebral Artery bifurcations using single application. This allows for determination of significant trends in the parameters variability with age and in contrary almost no differences between men and women

Computer aided sentiment analysis of anorexia nervosa patients’ vocabulary

Abstract Background Diagnosing and treating anorexia nervosa is an important challenge for modern psychiatry. Taking into account a connection between the mental state of a person and the characteristics of their language, this paper presents developed and tested method for analyzing the written statements of patients with anorexia nervosa and healthy individuals, including the identification of keywords. Methods Due to the short nature of the texts, which is related to the difficulty of expressing oneself about one’s body when suffering from anorexia, the bag of words approach was used for documents’ information representation. The document is represented as a vector, where its various elements indicate the number of individual words. Then, a rule-based model was created, where as a collection of rules, dictionary files were used corresponding to three groups of positive, negative and neutral sounds for each subcategory. Next in the analyzed texts were searched and counted keywords. Based on the keywords found, each of the documents was categorized into one of the groups in every subcategory. Results It is possible to indicate a set of characteristics sentiment for every person. Additionally, the results of specific patient could be analyzed in six specific subcategories: self-esteem, acceptance of the assessment of the environment, emotions, autoimmune, functioning of the body and body image. Conclusions The described analysis indicates the existence of a relationship between the mental state of the author’s textual health and the vocabulary he or she uses. It is possible to indicate a set of characteristic sentiment terms specific to a given group of people. Their presence is related to the author’s mental state and their body image. It could help focus on specific topics during therapy

Methods and Tools Supporting the Learning and Teaching of Mathematics Dedicated to Students with Blindness

Teaching mathematics to blind people is a challenge of modern educational methods. This article presents a method of preparing the adapted material and its usage in the learning process of mathematics by blind people, as well as the results of evaluating the proposed approach. The presented results were obtained based on a mathematical analysis course conducted in two classes—with and without using the developed method. The developed method uses the conceptualization of knowledge as a graph. The learning process is supported by feedback processes that consider the mechanisms of knowledge and error vectors, on which a personalized adaptation of the learning path is made for each particular student. The evaluation process has shown a statistically significant improvement in learning results achieved by blind students. The average final test score in the group working with the platform during learning increased by 14%. In addition, there was an increase in cooperation between blind students who had the opportunity to take on the role of a teacher, which was observed in 27% of the participants. Our results indicate the effectiveness of the developed approach and motivate us to evaluate the method in a broader group of students. The engagement of students indirectly indicates overcoming the barriers known from the state of the art: uncertainty, poor motivation, and difficulties in consolidating the acquired skills

Planowanie chirurgicznych zabiegów ortopedycznych z użyciem drukowanych modeli 3D

Traditionally, pre-planned orthopedic surgery is based on a patient’s CT and MRI images of patients. While these images can illustrate a patient’s organ from different angles, they might not show all injuries that could cause possible complications. Besides, only visualizations with 3D models are not sufficient because they do not allow to fit and adjust necessary tools and components.In the paper the pre-surgical planning with the use of a printed 3D bone model is presented. On the basis of this case all the stages of preparation and printing the 3D model have been described in detail. The potential benefits from the use of the 3D printing technology have been collected.Tradycyjnie, ortopedyczne zabiegi chirurgiczne wykorzystują do planowania obrazy tomografii komputerowej lub rezonansu magnetycznego pacjenta. Umożliwiają one wizualizację struktur anatomicznych w różnych płaszczyznach, jednak na ich podstawie nie jest możliwe pokazanie wszystkich możliwych położeń anatomicznych oraz potencjalnych powikłań z nimi związanych. Zastosowanie wyłącznie wirtualnych modeli trójwymiarowych nie pozwala na zaplanowanie położenia wybranych struktur oraz narzędzi chirurgicznych podczas zabiegu.W artykule przedstawiono etapy powstawania drukowanego modelu 3D do planowania zabiegu ortopedycznego oraz potencjalne korzyści wynikające z użycia technologii druku 3D