Automated analysis of polarimetric images for the diagnostics of gastric biopsies

2021 ◽  
Author(s):  
Hee Ryung Lee ◽  
Myeongseop Kim ◽  
Aude Jobart-Malfait ◽  
Dominique Lamarque ◽  
Tatiana Novikova
Keyword(s):  
Automated Analysis ◽  
Gastric Biopsies

Accidental gastric biopsies with the ayre brush

1956 ◽  
Vol 30 (4) ◽  
pp. 686-689 ◽  
Author(s):  
Melvin Rossman ◽  
Julius Wolf
Keyword(s):  
Gastric Biopsies

Development and study of a method for cell separation during white blood cell segmentation on images of bone marrow preparations in information and measurement systems for diagnostics of acute leukemia

2020 ◽  
pp. 68-72
Author(s):  
V.G. Nikitaev ◽  
A.N. Pronichev ◽  
V.V. Dmitrieva ◽  
E.V. Polyakov ◽  
A.D. Samsonova ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Blood Cell ◽  
Acute Leukemia ◽  
White Blood Cell ◽  
Cell Separation ◽  
Large Scale ◽  
Bone Marrow Cells ◽  
Automated Analysis ◽  
Cell Segmentation ◽  
Measurement Systems

The issues of using of information and measurement systems based on processing of digital images of microscopic preparations for solving large-scale tasks of automating the diagnosis of acute leukemia are considered. The high density of leukocyte cells in the preparation (hypercellularity) is a feature of microscopic images of bone marrow preparations. It causes the proximity of cells to eachother and their contact with the formation of conglomerates. Measuring of the characteristics of bone marrow cells in such conditions leads to unacceptable errors (more than 50%). The work is devoted to segmentation of contiguous cells in images of bone marrow preparations. A method of cell separation during white blood cell segmentation on images of bone marrow preparations under conditions of hypercellularity of the preparation has been developed. The peculiarity of the proposed method is the use of an approach to segmentation of cell images based on the watershed method with markers. Key stages of the method: the formation of initial markers and builds the lines of watershed, a threshold binarization, shading inside the outline. The parameters of the separation of contiguous cells are determined. The experiment confirmed the effectiveness of the proposed method. The relative segmentation error was 5 %. The use of the proposed method in information and measurement systems of computer microscopy for automated analysis of bone marrow preparations will help to improve the accuracy of diagnosis of acute leukemia.

The Orientation of Gastric Biopsy Samples Improves the Interobserver Agreement of the OLGA Staging System

2017 ◽  
Vol 26 (4) ◽  
pp. 351-356 ◽  
Author(s):  
Bogdan Cotruta ◽  
Cristian Gheorghe ◽  
Razvan Iacob ◽  
Mona Dumbrava ◽  
Cristina Radu ◽  
...  
Keyword(s):  
Intestinal Metaplasia ◽  
Lamina Propria ◽  
Case Series ◽  
Gastric Biopsy ◽  
Gastric Atrophy ◽  
Observer Agreement ◽  
Gastric Body ◽  
Kappa Index ◽  
Gastric Biopsies

Background & Aims: Evaluation of severity and extension of gastric atrophy and intestinal metaplasia is recommended to identify subjects with a high risk for gastric cancer. The inter-observer agreement for the assessment of gastric atrophy is reported to be low. The aim of the study was to evaluate the inter-observer agreement for the assessment of severity and extension of gastric atrophy using oriented and unoriented gastric biopsy samples. Furthermore, the quality of biopsy specimens in oriented and unoriented samples was analyzed.Methods: A total of 35 subjects with dyspeptic symptoms addressed for gastrointestinal endoscopy that agreed to enter the study were prospectively enrolled. The OLGA/OLGIM gastric biopsies protocol was used. From each subject two sets of biopsies were obtained (four from the antrum, two oriented and two unoriented, two from the gastric incisure, one oriented and one unoriented, four from the gastric body, two oriented and two unoriented). The orientation of the biopsy samples was completed using nitrocellulose filters (Endokit®, BioOptica, Milan, Italy). The samples were blindly examined by two experienced pathologists. Inter-observer agreement was evaluated using kappa statistic for inter-rater agreement. The quality of histopathology specimens taking into account the identification of lamina propria was analyzed in oriented vs. unoriented samples. The samples with detectable lamina propria mucosae were defined as good quality specimens. Categorical data was analyzed using chi-square test and a two-sided p value <0.05 was considered statistically significant.Results: A total of 350 biopsy samples were analyzed (175 oriented / 175 unoriented). The kappa index values for oriented/unoriented OLGA 0/I/II/III and IV stages have been 0.62/0.13, 0.70/0.20, 0.61/0.06, 0.62/0.46, and 0.77/0.50, respectively. For OLGIM 0/I/II/III stages the kappa index values for oriented/unoriented samples were 0.83/0.83, 0.88/0.89, 0.70/0.88 and 0.83/1, respectively. No case of OLGIM IV stage was found in the present case series. Good quality histopathology specimens were described in 95.43% of the oriented biopsy samples, and in 89.14% of the unoriented biopsy samples, respectively (p=0.0275).Conclusion: The orientation of gastric biopsies specimens improves the inter-observer agreement for the assessment of gastric atrophy.Key words:  –  –  – .Abbreviations: H. pylori: Helicobacter pylori; OLGA: operative link for gastritis assessment; OLGIM: operative link on intestinal metaplasia assessment.

Software including the functions of automated analysis of electric power consumption in pipeline oil transportation

2011 ◽  
Vol 8 (1) ◽  
pp. 233-238
Author(s):  
R.M. Bogdanov ◽  
S.V. Lukin
Keyword(s):  
Power Consumption ◽  
Electric Power ◽  
Data Model ◽  
Automated Analysis ◽  
Petroleum Products ◽  
Electric Power Consumption ◽  
Scientific Center ◽  
Relational Data Model ◽  
Oil Transportation ◽  
Academy Of Sciences

Oil and petroleum products transportation is characterized by a significant cost of electric power. Correct oil and petroleum products accounting and forecasting requires knowledge of many factors. The software for norms of electric power consumption analysis for the planned period was developed at the Ufa Scientific Center of the Russian Academy of Sciences. Based on the principles of the relational data model, a schematic diagram/arrangement for the main oil transportation objects was developed, which allows to hold the initial data and calculated parameters in a structured manner.

Advances in the Prediction of Protein Subcellular Locations with Machine Learning

2019 ◽  
Vol 14 (5) ◽  
pp. 406-421 ◽  
Author(s):  
Ting-He Zhang ◽  
Shao-Wu Zhang
Keyword(s):  
Machine Learning ◽  
Feature Fusion ◽  
Protein Sequences ◽  
Subcellular Location ◽  
Automated Analysis ◽  
Cellular Level ◽  
Machine Learning Algorithms ◽  
Feature Representation ◽  
Protein Subcellular Location ◽  
Protein Subcellular Locations

Background: Revealing the subcellular location of a newly discovered protein can bring insight into their function and guide research at the cellular level. The experimental methods currently used to identify the protein subcellular locations are both time-consuming and expensive. Thus, it is highly desired to develop computational methods for efficiently and effectively identifying the protein subcellular locations. Especially, the rapidly increasing number of protein sequences entering the genome databases has called for the development of automated analysis methods. Methods: In this review, we will describe the recent advances in predicting the protein subcellular locations with machine learning from the following aspects: i) Protein subcellular location benchmark dataset construction, ii) Protein feature representation and feature descriptors, iii) Common machine learning algorithms, iv) Cross-validation test methods and assessment metrics, v) Web servers. Result & Conclusion: Concomitant with a large number of protein sequences generated by highthroughput technologies, four future directions for predicting protein subcellular locations with machine learning should be paid attention. One direction is the selection of novel and effective features (e.g., statistics, physical-chemical, evolutional) from the sequences and structures of proteins. Another is the feature fusion strategy. The third is the design of a powerful predictor and the fourth one is the protein multiple location sites prediction.

Analysis of babA, cagE and cagA Genes in Helicobacter pylori from Upper Gastric Patients in the North of Iran

2019 ◽  
Vol 19 (3) ◽  
pp. 274-278 ◽  
Author(s):  
Saba Fakhrieh Asl ◽  
Mehrnaz Pourvahedi ◽  
Ali Mojtahedi ◽  
Mohammad Shenagari
Keyword(s):  
Helicobacter Pylori ◽  
Gastric Diseases ◽  
Specific Primers ◽  
The North ◽  
Different Types ◽  
North Of Iran ◽  
Gastric Biopsies ◽  
Pcr Method ◽  
Non Ulcer Dyspepsia ◽  
H Pylori

Objective:Helicobacter pylori is a Gram-negative bacterium which has a serious effect on up to half of the world’s population and has been related to different gastric diseases. The goal of this study was to assess the frequency of babA, cagE and cagA genotypes among H. pylori strains isolated from gastric biopsies of endoscopic patients in the north of Iran.Methods:The present study was performed on 90 strains of H. pylori isolated from patients with gastric diseases (Gastric ulcer (GU), Duodenal ulcer (DU), Gastritis (G), Non-ulcer dyspepsia (NUD) and Gastric adenocarcinoma (GC)). DNA was extracted from all isolated strains and PCR method was performed to detect the prevalence of babA2, cagE and cagA genes using specific primers.Results:Among 90 samples of H. pylori, babA2, cagE, and cagA genes were detected in 42.2%, 30% and 82.2% of strains respectively. The statistical analysis showed that the prevalence of cagA gene in GU, G, DU, and NUD was significantly higher than other genes. Moreover, cagA, and babA2 genes were significantly more prevalent in GC patients compared to cagE gene. Our isolates exhibited 8 distinct arrangements of virulence patterns. The occurrence of cagA (35.6%) was the most prevalent pattern followed by cagA/babA2 (20%) and cagA/babA2/cagE (14.4%).Conclusion:In summary, as first report from Guilan province in the north of Iran, we showed significant association between the presence of babA2, cagE, and cagA genes in different types of gastric disorders.

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