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介绍整个幻灯片图像文件的框架巴贝尔鱼:基于OCR的文件标签工具

Nils Englert¹, Constantin Schwab², Maximilian Legnar¹

¹Section Computational Pathology Heidelberg, Institute of Pathology Heidelberg, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany.

Journal of pathology informatics

|December 5, 2024

概括

本研究介绍了Babel fish,这是一种自动化工具,可以从整个幻灯片图像中提取元数据. 它准确地检索幻灯片信息,简化数字幻灯片管理和与实验室系统的集成.

科学领域:

数字病理学数字病理学
计算病理学计算病理学
医疗信息学医疗信息学

背景情况:

从整个幻灯片图像中手动提取元数据是耗时的.
准确的元数据对于组织数字幻灯片和将其与患者数据联系起来至关重要.

研究的目的:

开发一个自动化工具,巴贝尔鱼,用于从扫描的幻灯片宏观图像中提取元数据.
为了提高管理和分析数字病理幻灯片的效率.

主要方法:

巴贝尔鱼工具使用光学字符识别 (OCR) 来提取元数据.
它使用easyOCR进行初级提取,并使用pytesseract用于具有挑战性的案例,例如区块号码检测.
该工具是在342个和110个幻灯片的数据集上开发和测试的.

主要成果:

巴贝尔鱼工具在获取幻灯片元数据方面实现了0.982的整体准确度.
个别元数据组件,如案件号和年份,以1000准确度提取.
区块号检测准确度为0.982.2. 区块号检测准确度为0.982.

结论:

巴贝尔鱼自动从整个幻灯片图像中提取必要的元数据 (案例号,年份,块ID,染色).
这种工具可以显著帮助大批量图像文件的更名,并且对DICOM转换管道有价值.
自动化元数据提取增强了数字幻灯片的组织和与实验室信息系统的集成.

关键词:

自动化自动化自动化自动化迪科姆公司 (DICOM)数字病理学数字病理学这是光学字符识别系统.

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FISH - Fluorescent In-situ Hybridization

FISH - Fluorescent In-situ Hybridization

Fluorescence in situ hybridization, or FISH, was developed in the early 1980s and has quickly become one of the most widely used techniques in cytogenetics. Labeled probes are used to bind complementary DNA or RNA sequences on a chromosome or in a region within a cell. Earlier, the probes could only be obtained by cloning or reverse transcription of a DNA template. Currently, the probe oligonucleotides can be synthesized synthetically. Additionally, with the advancement of optical techniques,...