• Applied Microscopy
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• 제51권
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• pp.4.1-4.12
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• 2021

Fluorescence in situ hybridization (FISH) is a technique to visualize specific DNA/RNA sequences within the cell nuclei and provide the presence, location and structural integrity of genes on chromosomes. A confocal Whole Slide Imaging (WSI) scanner technology has superior depth resolution compared to wide-field fluorescence imaging. Confocal WSI has the ability to perform serial optical sections with specimen imaging, which is critical for 3D tissue reconstruction for volumetric spatial analysis. The standard clinical manual scoring for FISH is labor-intensive, time-consuming and subjective. Application of multi-gene FISH analysis alongside 3D imaging, significantly increase the level of complexity required for an accurate 3D analysis. Therefore, the purpose of this study is to establish automated 3D FISH scoring for z-stack images from confocal WSI scanner. The algorithm and the application we developed, SHIMARIS PAFQ, successfully employs 3D calculations for clear individual cell nuclei segmentation, gene signals detection and distribution of break-apart probes signal patterns, including standard break-apart, and variant patterns due to truncation, and deletion, etc. The analysis was accurate and precise when compared with ground truth clinical manual counting and scoring reported in ten lymphoma and solid tumors cases. The algorithm and the application we developed, SHIMARIS PAFQ, is objective and more efficient than the conventional procedure. It enables the automated counting of more nuclei, precisely detecting additional abnormal signal variations in nuclei patterns and analyzes gigabyte multi-layer stacking imaging data of tissue samples from patients. Currently, we are developing a deep learning algorithm for automated tumor area detection to be integrated with SHIMARIS PAFQ.

• 대한의생명과학회지
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• 제29권2호
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• pp.53-57
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• 2023

The main objective of pathologists is to achieve accurate lesion diagnoses, which has become increasingly challenging due to the growing number of pathological slides that need to be examined. However, using digital technology has made it easier to complete this task compared to older methods. Digital pathology is a specialized field that manages data from digitized specimen slides, utilizing image processing technology to automate and improve analysis. It aims to enhance the precision, reproducibility, and standardization of pathology-based researches, preclinical, and clinical trials through the sophisticated techniques it employs. The advent of whole slide imaging (WSI) technology is revolutionizing the pathology field by replacing glass slides as the primary method of pathology evaluation. Image processing technology that utilizes WSI is being implemented to automate and enhance analysis. Artificial intelligence (AI) algorithms are being developed to assist pathologic diagnosis and detection and segmentation of specific objects. Application of AI-based digital pathology in biomedical researches is classified into four areas: diagnosis and rapid peer review, quantification, prognosis prediction, and education. AI-based digital pathology can result in a higher accuracy rate for lesion diagnosis than using either a pathologist or AI alone. Combining AI with pathologists can enhance and standardize pathology-based investigations, reducing the time and cost required for pathologists to screen tissue slides for abnormalities. And AI-based digital pathology can identify and quantify structures in tissues. Lastly, it can help predict and monitor disease progression and response to therapy, contributing to personalized medicine.

• 한국컴퓨터그래픽스학회논문지
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• 제29권3호
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• pp.127-135
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• 2023

조직병리에서 전체 슬라이드 영상의 정확한 분할은 질병 진단과 치료 계획에 매우 중요한 작업이다. 그러나 전체 슬라이드 영상은 크기가 크고 조직의 형태, 염색 및 촬영 조건이 다양하기 때문에 기존의 자동 영상 분할 알고리즘을 항상 적용하는 것은 어렵다. 최근 인간의 전문 지식과 알고리즘을 결합한 대화형 영상 분할 기술의 발전은 전체 슬라이드 영상 분할의 효율 성과 정확성을 개선할 수 있는 가능성을 보여주었다. 그러나 이러한 접근 방식은 동시에 어려운 과제를 제기하기도 했다. 본 논문에서는 다중 해상도 전체 슬라이드 영상을 활용하는 새로운 대화형 분할 방법인 ZoomISEG를 제안한다. 기존의 단일 스케일 방법과의 비교 및 ablation study를 통해 제안된 방법의 효율성과 성능을 입증한다. 실험 결과, 제안된 방법은 사람의 개입을 줄이면서도 최고 해상도 데이터를 사용하는 방식에 필적하는 정확도를 달성함을 확인했다.

• Biomolecules & Therapeutics
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• 제30권2호
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• pp.179-183
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• 2022

Traditionally, pathologists microscopically examine tissue sections to detect pathological lesions; the many slides that must be evaluated impose severe work burdens. Also, diagnostic accuracy varies by pathologist training and experience; better diagnostic tools are required. Given the rapid development of computer vision, automated deep learning is now used to classify microscopic images, including medical images. Here, we used a Inception-v3 deep learning model to detect mouse lung metastatic tumors via whole slide imaging (WSI); we cropped the images to 151 by 151 pixels. The images were divided into training (53.8%) and test (46.2%) sets (21,017 and 18,016 images, respectively). When images from lung tissue containing tumor tissues were evaluated, the model accuracy was 98.76%. When images from normal lung tissue were evaluated, the model accuracy ("no tumor") was 99.87%. Thus, the deep learning model distinguished metastatic lesions from normal lung tissue. Our approach will allow the rapid and accurate analysis of various tissues.

• 시스템엔지니어링학술지
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• 제15권2호
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• pp.72-78
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• 2019

Pathology is the motor that drives healthcare to understand diseases. The way pathologists diagnose diseases, which involves manual observation of images under a microscope has been used for the last 150 years, it's time to change. This paper is specifically based on tumor detection using deep learning techniques. Pathologist examine the specimen slides from the specific portion of body (e-g liver, breast, prostate region) and then examine it under the microscope to identify the effected cells among all the normal cells. This process is time consuming and not sufficiently accurate. So, there is a need of a system that can detect tumor automatically in less time. Solution to this problem is computational pathology: an approach to examine tissue data obtained through whole slide imaging using modern image analysis algorithms and to analyze clinically relevant information from these data. Artificial Intelligence models like machine learning and deep learning are used at the molecular levels to generate diagnostic inferences and predictions; and presents this clinically actionable knowledge to pathologist through dynamic and integrated reports. Which enables physicians, laboratory personnel, and other health care system to make the best possible medical decisions. I will discuss the techniques for the automated tumor detection system within the new discipline of computational pathology, which will be useful for the future practice of pathology and, more broadly, medical practice in general.