CN109003659A - Stomach Helicobacter pylori infects pathological diagnosis and supports system and method - Google Patents
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Abstract
本发明公开了一种基于大数据深度学习的胃幽门螺旋杆菌感染病理诊断支持系统和方法,该系统包括:图像数据获得单元,用于获得胃正常切片图像和已确诊的胃幽门螺旋杆菌感染病例的病理切片图像作为已输入图像数据;图像数据标注单元,用于对已输入图像数据进行标注;图像数据库构建单元,用于对图像数据标注单元提供的已标注图像数据分类、整理,构建病理图像数据库;卷积神经网络(CNN)构造单元,用于构造第一卷积神经网络模型;以及卷积神经网络模型训练单元,获得理想的卷积神经网络模型。通过本发明的胃幽门螺旋杆菌感染病理诊断支持系统和方法可实现精准和高效的智能读片,以辅助临床上胃幽门螺旋杆菌感染的病理诊断工作,提高其准确率、工作效率及工作持续状态。
The invention discloses a pathological diagnosis support system and method for gastric Helicobacter pylori infection based on big data deep learning. The system includes: an image data acquisition unit, which is used to obtain images of normal gastric slices and diagnosed cases of gastric Helicobacter pylori infection The pathological slice image is used as the input image data; the image data labeling unit is used to label the input image data; the image database construction unit is used to classify and organize the labeled image data provided by the image data labeling unit, and construct the pathological image database; a convolutional neural network (CNN) construction unit, used to construct a first convolutional neural network model; and a convolutional neural network model training unit, to obtain an ideal convolutional neural network model. Through the support system and method for the pathological diagnosis of gastric Helicobacter pylori infection of the present invention, accurate and efficient intelligent film reading can be realized to assist the clinical pathological diagnosis of gastric Helicobacter pylori infection, and improve its accuracy, work efficiency and work continuity .
Description
技术领域technical field
本发明涉及一种基于大数据深度学习的胃幽门螺旋杆菌感染病理诊断支持系统和方法。The invention relates to a support system and method for pathological diagnosis of gastric Helicobacter pylori infection based on big data deep learning.
背景技术Background technique
深度学习是目前人工智能领域用于图像识别和语音分析的最契合、应用最广泛的算法,其灵感来自于人类大脑的工作机制,是通过建立卷积神经网络对外部输入的数据进行自动化特征提取,从而能够使机器理解学习数据,获得信息并输出。目前,基于深度学习的人工智能已应用于各个行业领域,包括语音识别、人脸识别、车标识别、手写汉字识别等。近年来人工智能辅助医疗技术的产品研发也取得重大进展,如由谷歌大脑及Verily公司研发的用于乳腺癌病理诊断的人工智能产品可达到89%的肿瘤定位准确率;浙江大学附属第一医院利用人工智能实现快速分析甲状腺B超中结节区域的位置和良恶性。Deep learning is currently the most suitable and widely used algorithm for image recognition and speech analysis in the field of artificial intelligence. Its inspiration comes from the working mechanism of the human brain. It is to automatically extract features from externally input data by establishing a convolutional neural network. , so that the machine can understand the learning data, obtain information and output. At present, artificial intelligence based on deep learning has been applied in various industries, including speech recognition, face recognition, car logo recognition, handwritten Chinese character recognition, etc. In recent years, the product research and development of artificial intelligence-assisted medical technology has also made significant progress. For example, the artificial intelligence product developed by Google Brain and Verily for the pathological diagnosis of breast cancer can achieve an accuracy rate of 89% of tumor location; the First Affiliated Hospital of Zhejiang University Using artificial intelligence to quickly analyze the location and benign and malignant of nodules in thyroid B-ultrasound.
在医疗诊断过程中,病理组织切片检查需要极高的规范化和精确度。目前绝大部分的病理组织切片是由人工制作,并由病理医生结合自身长期积累的临床诊断经验来分析和判断。现代医学证明,胃幽门螺杆菌(Helicobacter pylori,HP)是慢性胃炎、消化性溃疡、胃癌的重要致病因子,已被国际癌症研究机构(IARC)列为I类致癌物之一。因此,早期检测HP感染对于及时根除HP、治疗HP相关性疾病具有重要的临床意义。临床上,通过胃镜钳取胃黏膜组织,石蜡包埋切片、染色进行组织学镜检检测HP,对有经验的病理医师来说是诊断该菌感染的“金标准”。相较于其他HP检测方法,采用病理组织学方法直接检测HP具有以下优势:①在胃镜取材时明确胃内的大体病变,如溃疡、胃癌;②在明确HP感染的同时,确定胃内炎症的程度和类型;③对接受HP根除治疗后复查的患者,可明确胃十二指肠病变的转归;④临床应用在胃窦取1块足够大的标本即能诊断98%的HP感染,提供HP存在的直接证据。病理切片可采用改良的Warthern-Starry银染法,于40X镜下观察可见淡黄色背景上呈棕色或褐色弯曲状或短棒状物,长5μm,结合HP多位于胃小凹或固有腺内的特点,易于辨认,阳性率较高。尽管随着现代医学技术的发展,快速尿素酶试验方法(RUT)和非侵入性检测方法如血清学检测、尿素呼气试验等检测方法应用更加广泛,但上述方法只能间接反映HP感染的情况,且各有局限性,比如RUT检测结果容易受患者用药史(如近期应用抗生素、铋剂或质子泵抑制剂可导致假阴性结果)、胃镜下取材部位、实验条件等多因素影响,且标本中要有104以上的细菌才显示阳性。In the process of medical diagnosis, pathological tissue biopsy requires extremely high standardization and precision. At present, the vast majority of pathological tissue sections are made manually, and are analyzed and judged by pathologists based on their long-term accumulated clinical diagnosis experience. Modern medicine has proved that gastric Helicobacter pylori (HP) is an important pathogenic factor of chronic gastritis, peptic ulcer and gastric cancer, and has been listed as one of the class I carcinogens by the International Agency for Research on Cancer (IARC). Therefore, early detection of HP infection has important clinical significance for timely eradication of HP and treatment of HP-related diseases. Clinically, gastric mucosal tissue is obtained by gastroscope forceps, paraffin-embedded, sectioned, and stained for histological microscopic examination to detect HP. For experienced pathologists, it is the "gold standard" for diagnosing HP infection. Compared with other HP detection methods, the direct detection of HP by pathological histology has the following advantages: ① When gastroscopy is used, the gross lesions in the stomach, such as ulcers and gastric cancer, can be identified; degree and type; ③Reexamination of patients who received HP eradication therapy can clarify the outcome of gastroduodenal lesions; ④Clinical application can diagnose 98% of HP infections by taking a large enough specimen from the gastric antrum. Direct evidence for the existence of HP. The pathological section can adopt the modified Warthern-Starry silver staining method. Under the 40X microscope, brown or brown curved or short rod-shaped objects can be seen on a light yellow background, with a length of 5 μm. Combined with the characteristics that HP is mostly located in gastric pits or intrinsic glands , easy to identify, high positive rate. Although with the development of modern medical technology, rapid urease test (RUT) and non-invasive detection methods such as serological detection, urea breath test and other detection methods are more widely used, but the above methods can only indirectly reflect the situation of HP infection , and each has limitations. For example, the RUT test results are easily affected by multiple factors such as the patient's medication history (such as recent use of antibiotics, bismuth or proton pump inhibitors can lead to false negative results), the location of the sample under the gastroscope, and the experimental conditions. There must be more than 10 4 bacteria in the test to show positive.
因此病理组织学方法检测HP作为一种能直观查见病原体的敏感且特异的检测手段,对于HP感染及相关性疾病的诊断、治疗和随访仍具有十分重要的临床价值。因此,病理组织学人工检测HP感染的缺点主要是:病理玻片的结果判断是由病理医生肉眼观察所得,这种人工阅片方法与病理医生自身经验、工作状态等主观因素密切相关,容易产生误差。尽管改良W-S染色下幽门螺杆菌的形态清晰,但对于细菌数量少、切片质量参差不齐、胃黏膜病变复杂多样甚至可能干扰病原体观察等复杂情况下,经验不足的病理医生容易漏诊、误诊。同时,病理医生要负责检查切片上的所有可见的生物组织,而每个病人都会有许多切片,在进行40倍放大时每个切片都有100多亿的像素,因此人工阅片的工作量极大,容易受阅片者主观情绪和疲劳阅片等因素的影响。而且,不同的病理学家对同一病人可能给出相当不同的诊断结论。因此,这种高度依赖人为因素的病理组织学诊断方法具有主观差异性,加上其工作强度大、时间成本高且诊断不一致性等缺点,很大程度上会影响HP感染的早期诊治从而影响患者预后。另外,培养合格专业的病理医生需要进行长期的专业培训和实践过程,培养周期长,且易受当前社会经济、文化等社会因素的影响,意味着我国乃至全世界病理医生数量“供不应求”、职业缺口大的严峻形势亟需解决。Therefore, the histopathological detection of HP, as a sensitive and specific detection method that can visually detect pathogens, still has very important clinical value for the diagnosis, treatment and follow-up of HP infection and related diseases. Therefore, the shortcomings of manual detection of HP infection in pathological histology are mainly: the results of pathological slides are judged by pathologists' naked eyes. error. Although the morphology of Helicobacter pylori is clear under improved W-S staining, inexperienced pathologists are likely to miss and misdiagnose complicated cases such as small number of bacteria, uneven section quality, complex and diverse gastric mucosal lesions, and even interference with pathogen observation. At the same time, pathologists are responsible for checking all visible biological tissues on the slices, and each patient has many slices, and each slice has more than 10 billion pixels when magnified by 40 times, so the workload of manual reading is extremely high. Large, easily affected by factors such as the reader's subjective emotions and fatigue reading. Furthermore, different pathologists may come to quite different diagnostic conclusions for the same patient. Therefore, this pathological and histological diagnosis method, which is highly dependent on human factors, has subjective differences, coupled with its shortcomings such as high work intensity, high time cost, and inconsistency in diagnosis, which will largely affect the early diagnosis and treatment of HP infection and thus affect patients. prognosis. In addition, cultivating qualified professional pathologists requires long-term professional training and practice. The training cycle is long and is easily affected by social factors such as the current socio-economic and cultural factors. This means that the number of pathologists in my country and the world is in short supply. The severe situation with a large gap needs to be resolved urgently.
发明内容Contents of the invention
针对病理组织学人工阅片的缺点,本发明拟通过计算机对大量胃幽门螺旋杆菌感染病理图像进行深度学习,来建立智能化的胃幽门螺旋杆菌感染病理诊断数学模型,搭建基于大数据及深度学习算法的胃幽门螺旋杆菌感染辅助病理诊断人工智能平台,从而实现高准确率和高效率的智能读片,以辅助临床上胃幽门螺旋杆菌感染的病理诊断工作,提高其准确率、工作效率及工作持续状态。Aiming at the shortcomings of manual reading in pathological histology, this invention intends to use a computer to conduct deep learning on a large number of pathological images of gastric Helicobacter pylori infection to establish an intelligent mathematical model for the pathological diagnosis of gastric Helicobacter pylori infection, and to build a model based on big data and deep learning. The artificial intelligence platform for gastric Helicobacter pylori infection-assisted pathological diagnosis based on algorithms can realize high-accuracy and high-efficiency intelligent film reading to assist clinical pathological diagnosis of gastric Helicobacter pylori infection and improve its accuracy, work efficiency and work efficiency. persistent state.
基于此,本发明的目的在于克服上述现有技术的不足之处而提供一种可提高临床诊断胃幽门螺旋杆菌感染时的效率、降低医疗成本的胃幽门螺旋杆菌感染病理诊断支持系统。Based on this, the object of the present invention is to overcome the shortcomings of the above-mentioned prior art and provide a support system for pathological diagnosis of gastric Helicobacter pylori infection that can improve the efficiency of clinical diagnosis of gastric Helicobacter pylori infection and reduce medical costs.
为实现上述目的,本发明采取的技术方案为:一种基于大数据深度学习的胃幽门螺旋杆菌感染病理诊断支持系统,所述支持系统包括:图像数据获得单元,用于获得胃正常切片图像和已确诊的胃幽门螺旋杆菌感染病例的病理切片图像作为已输入图像数据;图像数据标注单元,用于对所述已输入图像数据进行标注,以及保证图像的标签和图像的真实病理诊断结果一致;图像数据库构建单元,用于对所述图像数据标注单元提供的已标注图像数据分类、整理,构建病理图像数据库;卷积神经网络构造单元,用于构造第一卷积神经网络模型;以及卷积神经网络模型训练单元,利用所述病理图像数据库的图像数据对所述第一卷积神经网络模型的参数进行调节,以及训练所述第一卷积神经网络模型,获得可用于检测患者病理图像数据的第二卷积神经网络模型。In order to achieve the above object, the technical solution adopted by the present invention is: a support system for pathological diagnosis of gastric Helicobacter pylori infection based on big data deep learning, the support system includes: an image data acquisition unit for obtaining normal slice images of the stomach and The pathological slice image of the confirmed gastric Helicobacter pylori infection case is used as the input image data; the image data labeling unit is used to label the input image data and ensure that the label of the image is consistent with the real pathological diagnosis result of the image; The image database construction unit is used to classify and organize the marked image data provided by the image data labeling unit to construct a pathological image database; the convolutional neural network construction unit is used to construct the first convolutional neural network model; and convolution The neural network model training unit adjusts the parameters of the first convolutional neural network model by using the image data of the pathological image database, and trains the first convolutional neural network model to obtain pathological image data that can be used to detect patients The second convolutional neural network model.
由此,医生可结合所述支持设备针对输入的患者病理图像给出的分类结果和相应的概率,以及医生的专业知识和经验快速地诊断出该患者的是否患有胃幽门螺旋杆菌感染,显著提高临床诊断的效率,从而降低医疗成本;其中,为了保证收集到的图像数据准确无误,可以利用图像标注工具ASAP,对每张病理切片图像进行标注,以保证图像的标签和真实值一致;为了加快训练网络模型的速度,可以使用具有高速并行计算的GPU来代替CPU进行训练;为了加快卷积神经网络模型的检测速度,基于卷积神经网络训练单元,可以将训练好的网络模型重新建模为可变步长的CNN分类模型结构,以用于实际操作中的检测方法;该模型将对巨大的全切片图像进行分块化处理,将预选出的活体组织区域分割成大小相同的ROI分块,由于分块间的检测可以高度并行化,使得检测的速度在多GPU的并行下得到显著提升,然后通过可变步长的CNN分类模型的检测,生成预测概率分布图像;图像数据库将病理图像数据分为训练集、测试集和校验集等;第一卷积神经网络模型的参数包括学习速率、训练次数和多少层网络等网络参数,训练指在寻求最优解时,自动调节参数的过程。Thus, the doctor can quickly diagnose whether the patient suffers from gastric Helicobacter pylori infection by combining the classification results and corresponding probabilities given by the support device for the input patient pathological images, as well as the doctor's professional knowledge and experience. Improve the efficiency of clinical diagnosis, thereby reducing medical costs; Among them, in order to ensure the accuracy of the collected image data, you can use the image annotation tool ASAP to annotate each pathological slice image to ensure that the label of the image is consistent with the real value; To speed up the training of the network model, you can use the GPU with high-speed parallel computing instead of the CPU for training; in order to speed up the detection speed of the convolutional neural network model, based on the convolutional neural network training unit, you can remodel the trained network model It is a CNN classification model structure with a variable step size, which is used in the detection method in the actual operation; the model will block the huge full-slice image, and divide the pre-selected living tissue area into ROI points of the same size. block, because the detection between blocks can be highly parallelized, the speed of detection is significantly improved under the parallelism of multiple GPUs, and then the prediction probability distribution image is generated through the detection of the CNN classification model with variable step size; the image database will pathological Image data is divided into training set, test set and verification set, etc.; the parameters of the first convolutional neural network model include network parameters such as learning rate, number of training times, and how many layers of the network. Training refers to automatically adjusting parameters when seeking the optimal solution the process of.
优选地,所述支持系统还包括卷积神经网络模型检验单元,用于获得理想的卷积神经网络模型。应当说明的是,此处“理想”是指卷积神经网络模型的准确率高,以及“鲁棒”。Preferably, the support system further includes a convolutional neural network model checking unit, configured to obtain an ideal convolutional neural network model. It should be noted that "ideal" here refers to the high accuracy and "robustness" of the convolutional neural network model.
优选地,所述卷积神经网络模型检验单元包括卷积神经网络模型校验单元和卷积神经网络模型测试单元,所述卷积神经网络模型校验单元用于检测所述第二卷积神经网络模型的准确率;所述卷积神经网络模型测试单元,用于检测所述第二卷积神经网络模型是否过拟合,以筛选出鲁棒的第三卷积神经网络模型;应当说明的是,如若模型在测试集上的准确率与校验集训练中的准确率相差较大,则说明模型过拟合,此时,可返回卷积神经网络训练单元中,调节网络结构或参数,进行再次训练以获得更好的网络模型;如若在测试集上的准确率与校验集训练中的准确率十分接近,则说明该模型较为鲁棒。Preferably, the convolutional neural network model verification unit includes a convolutional neural network model verification unit and a convolutional neural network model testing unit, and the convolutional neural network model verification unit is used to detect the second convolutional neural network The accuracy rate of the network model; the convolutional neural network model testing unit is used to detect whether the second convolutional neural network model is overfitting, so as to screen out a robust third convolutional neural network model; it should be explained Yes, if the accuracy rate of the model on the test set is significantly different from the accuracy rate in the verification set training, it means that the model is overfitting. At this time, you can return to the convolutional neural network training unit and adjust the network structure or parameters. Retrain to get a better network model; if the accuracy on the test set is very close to the accuracy in the validation set training, the model is more robust.
优选地,所述支持系统还包括卷积神经网络模型预训练单元,用于当所述图像数据获得单元收集到的已输入图像数据不足时,对所述第一卷积神经网络模型进行预训练。Preferably, the support system further includes a convolutional neural network model pre-training unit, configured to perform pre-training on the first convolutional neural network model when the input image data collected by the image data acquisition unit is insufficient .
优选地,所述支持系统还包括病理图像数据预处理单元,用于筛选和示出患者病理图像中的待检测区域。Preferably, the supporting system further includes a pathological image data preprocessing unit, which is used for screening and displaying the region to be detected in the patient's pathological image.
优选地,为了确保检测的有效性,所述预处理单元采用自适应阈值法筛选出所述待检测区域。Preferably, in order to ensure the validity of the detection, the preprocessing unit uses an adaptive threshold method to filter out the region to be detected.
优选地,所述卷积神经网络训练单元采用微调法训练所述第一卷积神经网络模型。Preferably, the convolutional neural network training unit uses a fine-tuning method to train the first convolutional neural network model.
作为本发明的另一方面,本发明还提供了一种胃幽门螺旋杆菌感染的病理诊断支持方法,所述支持方法包括以下步骤:As another aspect of the present invention, the present invention also provides a method for supporting the pathological diagnosis of gastric Helicobacter pylori infection, the supporting method comprising the following steps:
图像数据获得:获得胃正常切片图像和已确诊的胃幽门螺旋杆菌感染病例的病理切片图像作为已输入图像数据;Image data acquisition: Obtain images of normal gastric slices and pathological slice images of confirmed cases of gastric Helicobacter pylori infection as input image data;
图像数据标注:对所述已输入图像数据进行标注,以及保证图像的标签和图像的真实病理诊断结果一致;Image data labeling: labeling the input image data, and ensuring that the label of the image is consistent with the real pathological diagnosis result of the image;
图像数据库构建:对所述图像数据标注单元提供的已标注图像数据分类、整理,构建病理图像数据库;Image database construction: classifying and sorting the labeled image data provided by the image data labeling unit, and constructing a pathological image database;
卷积神经网络构造:构造第一卷积神经网络模型;以及Convolutional neural network construction: constructing a first convolutional neural network model; and
卷积神经网络模型训练:利用所述病理图像数据库的图像数据对所述第一卷积神经网络模型的参数进行调节,以及训练所述第一卷积神经网络模型,获得可用于检测患者病理图像数据的第二卷积神经网络模型。Convolutional neural network model training: use the image data of the pathological image database to adjust the parameters of the first convolutional neural network model, and train the first convolutional neural network model to obtain pathological images that can be used to detect patients The second convolutional neural network model for the data.
应当说明的是,图像数据标注和图像数据库构建可以看作病理图像数据库构建阶段。优选地,所述支持方法还包括卷积神经网络模型检验步骤:获得理想的卷积神经网络模型;所述卷积神经网络模型检验步骤包括卷积神经网络模型校验和卷积神经网络模型测试,所述卷积神经网络模型校验用于检测所述第二卷积神经网络模型的准确率;所述卷积神经网络模型测试,用于检测所述第二卷积神经网络模型是否过拟合,以筛选出鲁棒的第三卷积神经网络模型。应当说明的是,卷积神经网络构造、卷积神经网络模型训练和卷积神经网络模型检验可看作卷积神经网络的训练阶段,用于获得理想的卷积神经网络模型。It should be noted that image data annotation and image database construction can be regarded as the stage of pathological image database construction. Preferably, the supporting method also includes a convolutional neural network model verification step: obtaining an ideal convolutional neural network model; the convolutional neural network model verification step includes convolutional neural network model verification and convolutional neural network model testing , the convolutional neural network model verification is used to detect the accuracy of the second convolutional neural network model; the convolutional neural network model test is used to detect whether the second convolutional neural network model is overfitting combined to screen out a robust third convolutional neural network model. It should be noted that the convolutional neural network construction, convolutional neural network model training, and convolutional neural network model verification can be regarded as the training phase of the convolutional neural network, which is used to obtain an ideal convolutional neural network model.
作为本发明的第三个方面,本发明还涉及上述支持系统在病理诊断胃幽门螺旋杆菌感染中的临床应用。As the third aspect of the present invention, the present invention also relates to the clinical application of the above support system in the pathological diagnosis of gastric Helicobacter pylori infection.
综上所述,本发明的有益效果为:In summary, the beneficial effects of the present invention are:
与现有的病理医生人工阅片相比较,本发明基于大数据和深度学习算法的胃幽门螺旋杆菌感染病理诊断的支持设备具有准确率高、耗时短且工作持续时间长的优点,且此发明在各大医院包括三甲、基层医院的推广和云端服务化将有助于解决医疗资源分配不均匀、实现远程优质医疗等,为广大患者提供更便捷、更准确的病理诊断服务;上述优点的实现是因为本发明的设备和方法利用深度学习算法在图像识别的优势,让计算机进行大数据级别的胃幽门螺旋杆菌感染病理切片的深度学习,从而训练出能模拟病理医生阅片并与之媲美的智能化神经网络模型,经过不断学习和验证,该神经网络模型可以实现对胃幽门螺旋杆菌感染病理切片的智能阅片、快速识别并得出科学结论。Compared with the existing manual reading by pathologists, the supporting equipment for the pathological diagnosis of gastric Helicobacter pylori infection based on big data and deep learning algorithms in the present invention has the advantages of high accuracy, short time-consuming and long working duration, and this The promotion and cloud service of the invention in major hospitals, including the top three and grassroots hospitals, will help to solve the uneven distribution of medical resources, realize remote high-quality medical care, etc., and provide more convenient and accurate pathological diagnosis services for the majority of patients; the advantages of the above This is achieved because the device and method of the present invention utilize the advantages of deep learning algorithms in image recognition, allowing the computer to perform deep learning of pathological sections of gastric Helicobacter pylori infection at the large data level, so as to train a pathological doctor who can simulate the reading of slices and is comparable to it. The intelligent neural network model, after continuous learning and verification, the neural network model can realize the intelligent reading, rapid identification and scientific conclusion of the pathological sections of gastric Helicobacter pylori infection.
附图说明Description of drawings
图1为本发明的胃幽门螺旋杆菌感染病理诊断支持系统的结构框图;Fig. 1 is the block diagram of structure of gastric Helicobacter pylori infection pathological diagnosis support system of the present invention;
图2为本发明实施例二的胃幽门螺旋杆菌感染病理诊断支持方法的流程图;2 is a flow chart of a method for supporting pathological diagnosis of gastric Helicobacter pylori infection according to Example 2 of the present invention;
图3为对胃幽门螺旋杆菌感染切片图;Fig. 3 is the slice diagram of gastric Helicobacter pylori infection;
图4为本发明的实施例二的快速检测模型的原理图;Fig. 4 is the schematic diagram of the rapid detection model of the second embodiment of the present invention;
图5为本发明的胃幽门螺旋杆菌感染病理诊断支持系统在应用时的流程图;Fig. 5 is the flowchart of the application of the gastric Helicobacter pylori infection pathological diagnosis support system of the present invention;
其中,1、胃幽门螺旋杆菌感染病理诊断支持系统,2、图像数据获得单元,3、图像数据标注单元,4、卷积神经网络构造单元,5、卷积神经网络模型训练单元,6、卷积神经网络模型检验单元,7、图像数据库构建单元,8、病理图像数据预处理单元,9、输入终端,10、输出终端。Among them, 1. Gastric Helicobacter pylori infection pathological diagnosis support system, 2. Image data acquisition unit, 3. Image data labeling unit, 4. Convolutional neural network construction unit, 5. Convolutional neural network model training unit, 6. Volume 7. Image database construction unit, 8. Pathological image data preprocessing unit, 9. Input terminal, 10. Output terminal.
具体实施方式Detailed ways
为更好的说明本发明的目的、技术方案和优点,下面将结合附图和具体实施例对本发明作进一步说明。In order to better illustrate the purpose, technical solutions and advantages of the present invention, the present invention will be further described below in conjunction with the accompanying drawings and specific embodiments.
实施例1Example 1
参见图1,本发明的胃幽门螺旋杆菌感染病理诊断支持系统1的一种实施例,其包括:Referring to Fig. 1, a kind of embodiment of gastric Helicobacter pylori infection pathological diagnosis support system 1 of the present invention, it comprises:
图像数据获得单元2,用于获得胃正常切片图像和已确诊的胃幽门螺旋杆菌感染病例的病理切片图像作为已输入图像数据;The image data obtaining unit 2 is used to obtain the normal slice image of the stomach and the pathological slice image of the confirmed gastric Helicobacter pylori infection case as the input image data;
图像数据标注单元3,用于对已输入图像数据进行标注,以及保证图像的标签和图像的真实病理诊断结果一致;An image data labeling unit 3, configured to label the input image data, and ensure that the label of the image is consistent with the real pathological diagnosis result of the image;
图像数据库构建单元7,用于对图像数据标注单元提供的已标注图像数据分类、整理,构建病理图像数据库;The image database construction unit 7 is used to classify and organize the labeled image data provided by the image data labeling unit, and construct a pathological image database;
卷积神经网络构造单元4,用于构造第一卷积神经网络模型;A convolutional neural network construction unit 4, configured to construct a first convolutional neural network model;
卷积神经网络模型训练单元5,利用病理图像数据库的图像数据对第一卷积神经网络模型的参数进行调节,以及训练第一卷积神经网络模型,获得可用于检测患者病理图像数据的第二卷积神经网络模型;The convolutional neural network model training unit 5 uses the image data of the pathological image database to adjust the parameters of the first convolutional neural network model, and trains the first convolutional neural network model to obtain the second convolutional neural network model that can be used to detect the patient's pathological image data. Convolutional neural network model;
卷积神经网络模型检验单元6,用于获得理想的卷积神经网络模型,包括卷积神经网络模型校验单元(图中未显示)和卷积神经网络模型测试单元(图中未显示),卷积神经网络模型校验单元用于检测第二卷积神经网络模型的准确率;卷积神经网络模型测试单元,用于检测第二卷积神经网络模型是否过拟合,以筛选出鲁棒的第三卷积神经网络模型。The convolutional neural network model verification unit 6 is used to obtain an ideal convolutional neural network model, including a convolutional neural network model verification unit (not shown in the figure) and a convolutional neural network model test unit (not shown in the figure), The convolutional neural network model check unit is used to detect the accuracy of the second convolutional neural network model; the convolutional neural network model test unit is used to detect whether the second convolutional neural network model is overfitting, to screen out robust The third convolutional neural network model.
卷积神经网络模型预训练单元(图中未显示),用于当图像数据获得单元收集到的已输入图像数据不足时,对第一卷积神经网络模型进行预训练;以及Convolutional neural network model pre-training unit (not shown in the figure), used for pre-training the first convolutional neural network model when the input image data collected by the image data acquisition unit is insufficient; and
病理图像数据预处理单元8,用于筛选和示出患者病理图像中的待检测区域。The pathological image data preprocessing unit 8 is used for screening and showing the region to be detected in the patient's pathological image.
其中,病理图像数据预处理单元8采用自适应阈值法筛选出待检测区域;卷积神经网络模型训练单元5采用微调(fine-tune)法训练第一卷积神经网络模型;数据库中包括以下四类数据集:训练集、消验集、测试集以及常规的已公开病理图像数据集。Wherein, the pathological image data preprocessing unit 8 adopts the self-adaptive threshold method to filter out the area to be detected; the convolutional neural network model training unit 5 adopts the fine-tuning (fine-tune) method to train the first convolutional neural network model; the database includes the following four Class datasets: training set, validation set, test set, and regular published pathology image datasets.
另外,输入终端9用于将现有的胃正常切片图像和已确诊的胃幽门螺旋杆菌感染病例的病理切片图像输入图像数据获得单元2,并且,这些输入的数据最后将由图像数据库构建单元7分类收集,用于支持后续的临床诊断工作;In addition, the input terminal 9 is used to input the existing normal gastric slice images and pathological slice images of confirmed gastric Helicobacter pylori infection cases into the image data acquisition unit 2, and these input data will be finally classified by the image database construction unit 7 Collected to support subsequent clinical diagnosis;
以及将待检测的患者的病理切片图像输入病理图像数据预处理单元8;And input the pathological slice image of the patient to be detected into the pathological image data preprocessing unit 8;
输出终端10,用于将由卷积神经网络模型训练单元5获得的鲁棒的卷积神经网络模型对输入病理图像数据预处理单元8的待检测的患者的病理切片图像分类检测的结果(病理类型和相应的概率)呈现给医生,以供临床诊断参考。The output terminal 10 is used for the result of the pathological slice image classification detection (pathological type) of the patient to be detected by the robust convolutional neural network model obtained by the convolutional neural network model training unit 5 input to the pathological image data preprocessing unit 8 and the corresponding probability) are presented to doctors for reference in clinical diagnosis.
实施例2Example 2
参见图2,本发明的胃幽门螺旋杆菌感染诊断支持方法的一种实施例,其包括如下步骤:Referring to Fig. 2, an embodiment of the diagnosis support method of gastric Helicobacter pylori infection of the present invention, it comprises the following steps:
(1)采集图像数据(1) Collect image data
以中山大学附属第六医院医学生物库数据为数据来源,采集14000张病理切片图像,包括7000张胃正常组织切片图像和7000张胃幽门螺旋杆菌感染组织切片,并分别按照训练集:校验集:测试集=3:1:1的数量比例进行随机分组。如下表1所示:Using the medical biobank data of the Sixth Affiliated Hospital of Sun Yat-sen University as the data source, 14,000 pathological slice images were collected, including 7,000 gastric normal tissue slice images and 7,000 gastric Helicobacter pylori infected tissue slices, and respectively according to the training set: verification set : test set = 3:1:1 ratio of the number of random groups. As shown in Table 1 below:
表1病理切片图像的具体数据。Table 1 Specific data of pathological slice images.
将所采集的图像进行数字化扫描储存、序号建档,创建胃幽门螺旋杆菌感染病理图像数据库。The collected images were digitally scanned and stored, serial numbered and archived to create a pathological image database of gastric Helicobacter pylori infection.
(2)标注图像信息(2) Annotate image information
利用现有的ASAP图像标注软件对步骤(1)所收集的训练集、校验集和测试集的病理切片图像进行数据标记。为保证信息标注的准确性,需在标注前对图像进行优化处理。对图像的标注工作主要包括:用不同颜色/粗细/虚实线条勾勒出图像中各种病理结构区域,根据胃内的大体病变,如溃疡、胃癌;HP感染的同时,确定胃内炎症的程度和类型;镜下观察可见淡黄色背景上呈棕色或褐色弯曲状或短棒状物;HP多位于胃小凹或固有腺内等情形,然后对图像分类并赋予分值,并将所勾勒的区域进行标签命名。将正确标注后的病理图像进行数字化存储,以进行下一步的网络模型训练和校验。图3为对胃幽门螺旋杆菌感染中不典型增生区域的标注图。Use the existing ASAP image labeling software to perform data labeling on the pathological slice images of the training set, verification set and test set collected in step (1). In order to ensure the accuracy of information labeling, it is necessary to optimize the image before labeling. The image labeling work mainly includes: outline various pathological structure areas in the image with different colors/thickness/virtual and solid lines, and determine the degree of inflammation and Type; under the microscope, brown or brown curved or short rod-shaped objects can be seen on a light yellow background; HP is mostly located in gastric pits or intrinsic glands. Tab naming. The correctly labeled pathological images are digitally stored for the next step of network model training and verification. Figure 3 is an annotated map of the atypical hyperplasia area in gastric Helicobacter pylori infection.
(3)训练卷积神经网络(3) Training convolutional neural network
①设计模型①Design model
(a)按照卷积层、最大采样层、非线性函数、全连接层级联的方式来构造卷积神经网络;(a) Construct a convolutional neural network according to the cascade of convolutional layers, maximum sampling layers, nonlinear functions, and fully connected layers;
(b)采用多层网络来增强网络的拟合能力;(b) Using a multi-layer network to enhance the fitting ability of the network;
(c)网络最后的全连接层的输出的通道数设为2,分别代表该图像是胃正常切片图像、胃幽门螺旋杆菌感染组织切片图像。(c) The number of channels of the output of the last fully connected layer of the network is set to 2, respectively representing that the image is a normal gastric slice image and a gastric Helicobacter pylori infected tissue slice image.
②训练网络② training network
(a)根据步骤(1)、(2)中收集到的图像数据,对卷积神经网络模型的参数进行调节,在校验集上观察分类的准确率;(a) According to the image data collected in steps (1), (2), the parameters of the convolutional neural network model are adjusted, and the accuracy of classification is observed on the verification set;
(b)为了加快训练网络的速度,使用具有高速并行计算的GPU来代替CPU进行训练;(b) In order to speed up the training network, use a GPU with high-speed parallel computing instead of a CPU for training;
(c)卷积神经网络权值参数的更新的方法使用SGD来求解,如若收敛速度较慢,使用Adadelta,Adam等优化方法来求解;(c) The method of updating the weight parameters of the convolutional neural network uses SGD to solve, if the convergence speed is slow, use Adadelta, Adam and other optimization methods to solve;
(d)如若步骤(1)收集到的训练数据(即图像数据)数目太少,卷积神经网络模型采用先在常规的公开病理图像数据集预训练,再将收集到的图像数据采用fine-tune(微调)的方法来训练卷积神经网络模型;(d) If the number of training data (i.e., image data) collected in step (1) is too small, the convolutional neural network model is first pre-trained on a conventional public pathological image data set, and then the collected image data is fine- tune (fine-tuning) method to train the convolutional neural network model;
(e)如在现有卷积神经网络模型上训练,分类的准确率无法上升,可以通过增加卷积神经网络网络模型的深度来增加卷积神经网络模型的拟合能力。(e) If training on the existing convolutional neural network model, the classification accuracy cannot be increased, the fitting ability of the convolutional neural network model can be increased by increasing the depth of the convolutional neural network model.
③设计快速检测模型(如图4所示)③ Design a rapid detection model (as shown in Figure 4)
1.为了提高检测效率,在预处理阶段采用自适应阈值法,从全切片图像中预选出活体组织区域,作为卷积神经网络的检测对象(如图4箭头101所示,代表预处理过程)。1. In order to improve the detection efficiency, an adaptive threshold method is used in the preprocessing stage to preselect the living tissue area from the whole slice image as the detection object of the convolutional neural network (as shown by the arrow 101 in Figure 4, representing the preprocessing process) .
2.为了提高检测的准确度以及灵活性,基于步骤(3),可以将训练好的卷积神经网络重新建模为可变步长的CNN分类模型,以用于实际操作中的检测方法;该模型将对巨大的全切片图像进行分块化处理,将预选出的活体组织区域分割成大小相同的ROI分块;由于分块间的检测可以高度并行化,使得检测的速度在多GPU的情况下得到有效的提升(如图4箭头102所示,代表模型快速检测过程)。通过卷积神经网络模型的检测,生成预测概率分布图像。2. In order to improve the accuracy and flexibility of detection, based on step (3), the trained convolutional neural network can be remodeled as a variable step-size CNN classification model for the detection method in actual operation; This model will block the huge full-slice image, and divide the pre-selected living tissue area into ROI blocks of the same size; since the detection between blocks can be highly parallelized, the detection speed is faster than that of multi-GPU. In this case, it is effectively improved (as shown by arrow 102 in FIG. 4 , which represents a fast model detection process). Through the detection of the convolutional neural network model, an image of the predicted probability distribution is generated.
3.基于第2步的预测概率分布图像,在后处理中,筛除零散点后,分析预测概率分布图,以得到最终全切片图像的预测结果(如图4箭头103所示,代表后处理过程)。3. Based on the predicted probability distribution image of step 2, in the post-processing, after screening out the scattered points, analyze the predicted probability distribution map to obtain the predicted result of the final full-slice image (as shown in Fig. 4 arrow 103, representing post-processing process).
(4)测试集验证(4) Test set verification
(a)基于步骤③的可变步长的分类模型结构,使用步骤(3)中训练好的卷积神经网络模型来对测试集测试,观察模型在测试集上的准确率。(a) Based on the variable step size classification model structure of step ③, use the convolutional neural network model trained in step (3) to test the test set, and observe the accuracy of the model on the test set.
(b)如若步骤(3)中训练好的卷积神经网络模型在测试集的上准确率与训练中的校验集的准确率相差较大,则说明模型过拟合;此时,可返回步骤(3)中,调节卷积神经网络模型网络结构或参数,获得更好的网络模型。(b) If the accuracy rate of the convolutional neural network model trained in step (3) on the test set is significantly different from the accuracy rate of the verification set in training, it means that the model is overfitting; at this time, return to In step (3), adjust the network structure or parameters of the convolutional neural network model to obtain a better network model.
(c)如若步骤(3)中训练好的卷积神经网络模型在测试集上的准确率与训练中的校验集的准确率十分接近,则说明该训练所得的卷积神经网络模型较为鲁棒,可作为合适的检测病患的病理图像的网络模型。(c) If the accuracy rate of the trained convolutional neural network model on the test set in step (3) is very close to the accuracy rate of the verification set in training, it means that the trained convolutional neural network model is relatively robust. Rod, can be used as a suitable network model for detecting pathological images of patients.
实施例3Example 3
本发明的胃幽门螺旋杆菌感染病理诊断支持系统的一种应用例,将待检测的病理图像通过输入终端9输入本发明的胃幽门螺旋杆菌感染诊断支持设备中的病理图像数据预处理单元8,之后的运行流程参见图5,其中,An application example of the gastric Helicobacter pylori infection pathological diagnosis support system of the present invention, the pathological image to be detected is input into the pathological image data preprocessing unit 8 in the gastric Helicobacter pylori infection diagnosis support device of the present invention through the input terminal 9, See Figure 5 for the subsequent operation process, in which,
(a)为了确保检测的有效性,在开始阶段采用自适应阈值法,从全切片图像中预选出活体组织区域,然后基于阈值结果区域中心框选出待检测区域(即患者病理组织区域);(a) In order to ensure the validity of the detection, an adaptive threshold method is used in the initial stage to pre-select the living tissue area from the whole slice image, and then select the area to be detected (ie the patient's pathological tissue area) based on the threshold result area center frame;
(b)之后,对患者病理组织区域图片进行预处理,预处理包括去噪、直方图均衡、归一化等步骤;(b) After that, preprocessing is performed on the image of the patient's pathological tissue area, and the preprocessing includes steps such as denoising, histogram equalization, and normalization;
(c)用先前训练好的卷积神经网络模型(即实施例1中第二卷积神经网络模型)对预处理后的图片中待检测区域进行分类检测,从而得出胃幽门螺旋杆菌感染的预测结果,包括该病理切片所属的胃幽门螺旋杆菌感染类别以及相应的概率。(c) Use the previously trained convolutional neural network model (i.e. the second convolutional neural network model in Example 1) to classify and detect the area to be detected in the preprocessed picture, thereby obtaining the infection rate of gastric Helicobacter pylori The prediction results include the category of gastric Helicobacter pylori infection to which the pathological section belongs and the corresponding probability.
实施例4本发明的胃幽门螺旋杆菌感染病理诊断支持方法与现有方法的比较Example 4 Comparison between the method for supporting the pathological diagnosis of gastric Helicobacter pylori infection of the present invention and existing methods
目前临床上病理诊断工作是由经过规范化培训的病理医生人工阅读病理组织切片,结合自身长期积累的临床诊断经验来作出分析和诊断。由于这种人工肉眼阅片方法与病理医生自身经验、工作状态、主观情绪等因素密切相关,故准确率不高,但耗时长,工作持续时间有限,容易产生漏诊、误诊及诊断不一致等情况。本发明则利用计算机对标准化的大量胃幽门螺旋杆菌感染病理图像的深度学习,对卷积神经网络进行参数调节和拟合训练,从而获得较为鲁棒的网络模型。这种基于大数据和深度学习的神经网络能模拟人工阅片,根据输入的新病理图像得出对应的输出值即病理诊断结论。再者,通过模型重建,在不影响检测准确度的情况下,极大提高了检测速度。At present, the clinical pathological diagnosis is performed by the pathologists who have undergone standardized training to manually read the pathological tissue slides, and combine their long-term accumulated clinical diagnosis experience to make analysis and diagnosis. Since this method of manual naked eye image reading is closely related to the pathologist's own experience, working status, subjective emotions and other factors, the accuracy rate is not high, but it takes a long time and the working duration is limited, which is prone to missed diagnosis, misdiagnosis and inconsistent diagnosis. The present invention uses a computer to perform deep learning on a large number of standardized pathological images of gastric Helicobacter pylori infection, and performs parameter adjustment and fitting training on the convolutional neural network, thereby obtaining a relatively robust network model. This kind of neural network based on big data and deep learning can simulate manual film reading, and obtain the corresponding output value, that is, the pathological diagnosis conclusion, according to the new pathological image input. Furthermore, through model reconstruction, the detection speed is greatly improved without affecting the detection accuracy.
选取30名具有3年以上胃幽门螺旋杆菌感染诊断与治疗经验的医生,分别每人提供40张疑似胃幽门螺旋杆菌感染的病理图像,判断其类型,然后计算准确率和平均时间,统计医生诊断状态,与本发明的诊断支持方法相比较,其结果如下表2所示。Select 30 doctors with more than 3 years of experience in the diagnosis and treatment of gastric Helicobacter pylori infection, each provide 40 pathological images of suspected gastric Helicobacter pylori infection, determine its type, then calculate the accuracy rate and average time, and count the doctor's diagnosis State, compared with the diagnostic support method of the present invention, the results are shown in Table 2 below.
表2胃幽门螺旋杆菌感染诊断结果的比较Table 2 Comparison of diagnostic results of gastric Helicobacter pylori infection
从上表2可知,采用本发明的方法阅读病理组织切片,其准确率比专业病理医生的水平更高,且耗时更短,工作持续时间长。It can be known from the above table 2 that the reading of pathological tissue slices by the method of the present invention has a higher accuracy rate than that of professional pathologists, and the time-consuming is shorter and the working duration is longer.
最后所应当说明的是,以上实施例仅用以说明本发明的技术方案而非对本发明保护范围的限制,尽管参照较佳实施例对本发明作了详细说明,本领域的普通技术人员应当理解,可以对本发明的技术方案进行修改或者等同替换,而不脱离本发明技术方案的实质和范围。Finally, it should be noted that the above embodiments are only used to illustrate the technical solutions of the present invention rather than limit the protection scope of the present invention. Although the present invention has been described in detail with reference to the preferred embodiments, those of ordinary skill in the art should understand that, The technical solution of the present invention can be modified or equivalently replaced without departing from the spirit and scope of the technical solution of the present invention.
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