WO2021115312A1 - Method for automatically sketching contour line of normal organ in medical image - Google Patents

Method for automatically sketching contour line of normal organ in medical image Download PDF

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WO2021115312A1
WO2021115312A1 PCT/CN2020/134840 CN2020134840W WO2021115312A1 WO 2021115312 A1 WO2021115312 A1 WO 2021115312A1 CN 2020134840 W CN2020134840 W CN 2020134840W WO 2021115312 A1 WO2021115312 A1 WO 2021115312A1
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normal
normal organ
segmentation
image
organs
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PCT/CN2020/134840
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Chinese (zh)
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魏军
沈烁
谢培梁
郑少逵
吕丽云
田孟秋
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广州柏视医疗科技有限公司
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    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06TIMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T7/00Image analysis
    • G06T7/10Segmentation; Edge detection
    • G06T7/11Region-based segmentation
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06NCOMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00Computing arrangements based on biological models
    • G06N3/02Neural networks
    • G06N3/04Architecture, e.g. interconnection topology
    • G06N3/045Combinations of networks
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06NCOMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00Computing arrangements based on biological models
    • G06N3/02Neural networks
    • G06N3/08Learning methods
    • G06N3/084Backpropagation, e.g. using gradient descent
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06TIMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T7/00Image analysis
    • G06T7/10Segmentation; Edge detection
    • G06T7/149Segmentation; Edge detection involving deformable models, e.g. active contour models
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06TIMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T7/00Image analysis
    • G06T7/10Segmentation; Edge detection
    • G06T7/194Segmentation; Edge detection involving foreground-background segmentation
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06TIMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T2207/00Indexing scheme for image analysis or image enhancement
    • G06T2207/10Image acquisition modality
    • G06T2207/10072Tomographic images
    • G06T2207/10081Computed x-ray tomography [CT]
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06TIMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T2207/00Indexing scheme for image analysis or image enhancement
    • G06T2207/10Image acquisition modality
    • G06T2207/10072Tomographic images
    • G06T2207/10104Positron emission tomography [PET]
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06TIMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T2207/00Indexing scheme for image analysis or image enhancement
    • G06T2207/20Special algorithmic details
    • G06T2207/20112Image segmentation details
    • G06T2207/20132Image cropping

Definitions

  • the invention relates to the technical field of medical image processing, in particular to a method for automatically delineating contour lines of normal organs in medical images.
  • Radiotherapy is currently one of the three important methods of clinical tumor treatment.
  • the delineation of target areas and organs at risk has a crucial influence on the accuracy of radiotherapy.
  • the contours of target areas and organs at risk are mainly obtained by doctors manually delineating the contours of the target areas and organs at risk in clinic.
  • Manual sketching by doctors has the following drawbacks: 1. The sketching efficiency is low; 2. It is heavily dependent on the doctor's clinical experience; 3. The reproducibility is poor, and the results of the sketching by different doctors at different times and different conditions are inconsistent. Therefore, there is an urgent need for accurate and fast automatic medical image segmentation algorithms to reduce the burden on doctors and improve the accuracy and automation of normal organ segmentation in medical images.
  • the atlas-based segmentation method is a popular method for automatic delineation of normal organs in medical imaging, especially in the medical imaging of head and neck tumors. Because the head and neck structure has a relatively fixed positional relationship, atlas-based segmentation The method has a good performance in the segmentation of normal organs of the head and neck. Atlas-based segmentation methods are generally divided into single atlas and multiple atlas methods. However, the single atlas segmentation method is very sensitive to the choice of atlas and the difference in the anatomical structure of the patient. When the target image is significantly different from the atlas, the single atlas method may fail to segment.
  • the multi-atlas segmentation method can reduce the sensitivity to the difference between atlas and patients, and has higher segmentation accuracy than single atlas, but the segmentation efficiency is lower.
  • the atlas-based segmentation method relies on image registration algorithms, which may introduce additional registration errors.
  • the atlas-based normal organ segmentation method has many defects and cannot meet clinical needs.
  • machine learning and deep learning, especially convolutional neural networks Convolutional Neural Network, CNN have achieved great success in the fields of image classification, computer vision, and target extraction. Many researchers also apply it to the segmentation of medical images.
  • Ibragimov, B and others proposed a head and neck normal organ segmentation method based on convolutional neural networks [Ibragimov B and Xing L 2017 Segmentation of organs-at-risks in head and neck CT images using convolutional neural networks ,Medical physics 44 547-57], and applied it to the automatic segmentation of 9 normal organs in head and neck medical imaging.
  • the method consists of the following steps: (1) Roughly determine the region of interest of the target normal organ according to the relative positional relationship between the normal brain organs and the center coordinates of the brain; (2) Based on the target pixel points and background in the target normal organ region of interest The image patch where the pixel is located is trained on a classification model based on a convolutional neural network; (3) Then, all pixels are classified on the region of interest of the target normal organ on the image to be segmented, so as to realize the normal organ in the image (4) Finally, use Markov random field to post-process the segmentation results to remove some over-segmented pixels.
  • This method uses the fixed position relationship of the normal organs of the brain to roughly determine the region of interest, and uses the results drawn by the doctor to train the normal organ segmentation model to realize the automatic segmentation of multiple normal organs in the head and neck.
  • this method Compared with the traditional normal organ segmentation method based on atlas, this method has higher segmentation accuracy on most normal organs, but the image segmentation method based on convolutional neural network is based on the characteristics of the data drawn by the doctor to learn the target. Therefore, the target area can be better recognized and segmented from the image, while the contrast of the image such as the optic nerve and the optic chiasm is low, and the smaller normal organs have less effective information on the image. Therefore, the conventional patch-based method still has low accuracy in segmentation on such normal organs.
  • the image contrast is low, which makes the image segmentation of small normal organs more dependent on the three-dimensional image environment, but the current hardware level is difficult to support the training of the convolutional neural network model under the large three-dimensional image matrix, so It is still a very challenging problem to segment the target normal organs of different sizes and different gray levels from clinical medical images.
  • embodiments of the present invention provide a method and system for automatically delineating the contour lines of normal organs in medical images.
  • an embodiment of the present invention provides a method for automatically delineating a contour line of a normal organ in a medical image, which includes the following steps:
  • Step S1 Obtain the patient image collected before the medical image, and preprocess it;
  • Step S2 Group all the normal organs to be segmented step by step, and use an iterative method to gradually locate the target normal organ sub-regions;
  • Step S3 Perform classification according to the segmentation difficulty of each normal organ in the determined normal organ sub-region; and use an iterative constrained normal organ segmentation model on the image corresponding to the determined normal organ sub-region to automatically perform the contour line of the target normal organ Delineate until all normal organs in all normal organ subdivisions are segmented.
  • the preprocessing of the patient image includes: resampling and normalization of the image gray level.
  • step S2 specifically includes the following steps:
  • step S22 The same partition when the normal organs as a target, the respective dimensions of the trimmed image obtained in step S21 is 2 n-1 times down-sampling, a convolutional neural network model based on 2 n-1 times the drop Perform normal organ partition recognition on the sampled image, and perform region cropping on the preprocessed image obtained in step S1 according to different normal organ partition recognition results to obtain images of each normal organ partition;
  • step S3 specifically includes the following steps:
  • step S31 Taking the image corresponding to the normal organ sub-division determined in step S2 as input, and segmenting the first-level normal organ based on the convolutional neural network model to obtain the first-level normal organ segmentation result;
  • step S32 Taking the first-level normal organ segmentation result obtained in step S31 and the image corresponding to the normal organ sub-region determined in step S2 as input, and restricting the second-level normal organ segmentation based on the volume
  • the product neural network model segmented the second-level normal organs to obtain the second-level normal organ segmentation results;
  • step S33 Iterate step by step, taking the segmentation results of all normal organs at the segmented level and the images corresponding to the normal organ sub-regions determined in step S2 as input, and constrain the segmentation of normal organs at the current level, and based on convolution
  • the neural network model segments the normal organs at the current segmentation level, and obtains the segmentation results of the normal organs at the current level until all normal organs are segmented.
  • the convolutional neural network model specifically includes the following steps:
  • the convolutional neural network model takes the segmentation results of patient images and other known normal organs as input, and the segmentation results as output;
  • the preprocessed patient image is used as the input of the convolutional neural network model, and the loss function of the current segmentation model is calculated according to the current output of the convolutional neural network model and the collected mask images of the normal organs outlined by the doctor, using back propagation
  • the method updates the parameters of the convolutional neural network model; iterates repeatedly, and when the preset number of model training iterations is reached or the loss function reaches the preset threshold, the convolutional neural network model training is completed and the model parameters are saved.
  • step S3 includes the following steps:
  • the mask image is a binary mask image.
  • an embodiment of the present invention provides a system for automatically delineating the contours of normal organs in medical images, including:
  • Patient image preprocessing module used to obtain and preprocess patient images collected before medical images
  • Normal organ grouping and target normal organ sub-region module used to group all normal organs to be segmented step by step, and use an iterative method to gradually locate the target normal organ sub-region;
  • Normal organ segmentation module used to classify the segmentation difficulty of each normal organ in the normal organ sub-division; and use the iterative constrained normal organ segmentation model on the image corresponding to the normal organ sub-division to automatically perform the contour line of the target normal organ Delineate until all normal organs in all normal organ subdivisions are segmented.
  • an embodiment of the present invention provides an electronic device, including a memory, a processor, and a computer program stored in the memory and capable of running on the processor.
  • the processor executes the program, the implementation is as described in the first aspect. Provides the steps of the method for automatically delineating the contour lines of normal organs in medical images.
  • an embodiment of the present invention provides a non-transitory computer-readable storage medium on which a computer program is stored.
  • the computer program is executed by a processor, the outline of a normal organ in a medical image as provided in the first aspect is realized.
  • the steps of the automatic line drawing method are realized.
  • the method and system for automatically delineating the contours of normal organs in medical images provided by the embodiments of the present invention are aimed at the problem of high hardware requirements for segmentation under large three-dimensional images, and adopts an iterative method to gradually reduce background areas and reduce volume-based
  • the computational complexity of the segmentation model of the product network greatly reduces its requirements for hardware devices.
  • normal organs are segmented from easy to difficult, and the normal organ segmentation results of the previous iteration are used to constrain The segmentation of normal organs in the next iteration improves the accuracy of segmentation.
  • FIG. 1 is a flowchart of a method for automatically delineating contour lines of normal organs in medical images according to an embodiment of the present invention
  • step S2 is a flowchart of step S2 in the method provided by an embodiment of the present invention.
  • FIG. 3 is a flowchart of step S3 in the method provided by an embodiment of the present invention.
  • FIG. 4 is a flowchart of a convolutional neural network model in a method provided by an embodiment of the present invention.
  • FIG. 5 is a flowchart of automatically delineating the contour line of the target normal organ in step S3 of the method provided by the embodiment of the present invention.
  • Fig. 6 is a schematic diagram of a system for automatically delineating the contours of normal organs in medical images according to an embodiment of the present invention
  • FIG. 7 is a framework diagram of iterative segmentation in the method provided by an embodiment of the present invention.
  • FIG. 8 is a block diagram of an iterative constrained normal organ segmentation model in the method provided by an embodiment of the present invention.
  • FIG. 9 is a physical structure diagram of an electronic device provided by an embodiment of the present invention.
  • Fig. 1 is a flow chart of a method for automatically delineating the contours of normal organs in medical images according to an embodiment of the present invention. As shown in Fig. 1, the method includes:
  • Step S1 Obtain patient images collected by medical images and preprocess them
  • Patient images include: CT (Computed Tomography), MR (magnetic resonance) or PET (Positron Emission Tomography), etc.
  • CT stands for electronic computer tomography, which uses precisely collimated X-ray beams, gamma rays, ultrasonic waves, etc., together with extremely sensitive detectors to scan a certain part of the human body one by one.
  • MR is a method of medical examination and a revolution in medical imaging.
  • Biological tissues can be penetrated by short-wave components in the electromagnetic spectrum such as X-rays, but can block mid-wave components such as ultraviolet, infrared and long waves. Human tissue allows long-wave components such as radio waves generated by magnetic resonance to pass through, which is one of the basic conditions for magnetic resonance in clinical applications.
  • PET is a relatively advanced clinical examination imaging technology in the field of nuclear medicine. Normal range PET is especially suitable for early diagnosis of disease, discovery of subclinical lesions and evaluation of treatment effect before there is no morphological change. At present, PET has shown particularly important value in the diagnosis and treatment of the three major types of diseases: tumor, coronary heart disease and brain disease.
  • preprocessing the patient image includes: resampling and image gray normalization.
  • Step S2 Divide all normal organs to be segmented into groups (for example: level 1: all normal organs; level 2: normal organs partition; level 3: normal organ sub-partitions; level 4: normal organs), and adopt an iterative method Gradually locate the target normal organ sub-region;
  • step S2 in the embodiment of the present invention specifically includes the following steps:
  • step S21 Regard all normal organs to be segmented as a target, perform 2 n times downsampling on each dimension of the preprocessed patient image obtained in step S1, based on the convolutional neural network model after 2 n times downsampling Recognize the target area on the image to obtain the rough positions of all target normal organs, and then crop the preprocessed image obtained in step S1 according to the prior information of the center coordinates of the target area and the size of the target normal organ to remove the image Most of the background area;
  • step S21 After normal organs when the same partition as a target, various dimensions of the cropped image obtained in step S21 is 2 n-1 times down-sampling, a convolutional neural network model based on the 2 n-1 times downsampling: S22 Perform normal organ partition recognition on the image of, and perform region cropping on the preprocessed image obtained in step S1 according to different normal organ partition recognition results to obtain images of each normal organ partition;
  • Step S3 Perform classification according to the division difficulty of each normal organ in the normal organ sub-division determined in step S2 (for example, level I: easy, level II: general, and level III: difficult).
  • the iterative constrained normal organ segmentation model as shown in Fig. 8 is used to automatically delineate the contour line of the target normal organ until all normal organs in all normal organ sub-divisions are The organ segmentation is complete.
  • step S3 specifically includes the following steps:
  • step S31 Taking the image corresponding to the normal organ sub-region determined in step S2 as input, and segmenting the normal organs of level I (level 1) based on the convolutional neural network model to obtain normal organs of level I (level 1) Segmentation result
  • step S32 The segmentation result of the normal organ of level I (level 1) obtained in step S31 and the image corresponding to the normal organ sub-region determined in step S2 are used as input, and the segmentation of the normal organ of level II (level 2) is constrained , Based on the convolutional neural network model, segment the normal organs of level II (level 2), and obtain the segmentation results of normal organs of level II (level 2);
  • step S33 Iterate step by step, taking the segmentation results of all normal organs at the segmented level and the images corresponding to the normal organ sub-regions determined in step S2 as input, and constraining the segmentation of normal organs at the current level, based on the convolutional neural network model , To segment the normal organs at the current segmentation level to obtain the segmentation results of the normal organs at the current level until all normal organs are segmented.
  • Figure 7 shows the frame diagram of iterative segmentation.
  • the convolutional neural network model used in step S2 and step S3 adopts a supervised learning method, based on pre-collected patient image data and sketched by experienced doctors.
  • the normal organ contour data and the known segmentation results of other normal organs are trained to obtain a stable normal organ detection model, normal organ sub-division detection model, and normal organ segmentation model corresponding to the sub-division, as shown in Figure 7.
  • the dashed part is shown.
  • the convolutional neural network model specifically includes three steps:
  • (A) Establish a convolutional neural network model.
  • the convolutional neural network model takes the patient image and the segmentation results of other known normal organs (if any) as input, and the segmentation results as output;
  • (B) Collect collected patient images (CT, MR or PET), and contour lines of normal organs drawn by experienced doctors. And pre-process the collected patient image resampling and image gray normalization, and then convert the contour line of each normal organ drawn by the doctor into a binary mask image with a target area of 1 and a background area of 0;
  • step (C) The patient image preprocessed in step (B) is used as the input of the convolutional neural network model, based on the current output of the convolutional neural network model and the masks of the normal organs drawn by the doctors collected in step (B) Model image, calculate the loss function of the current segmentation model, and use the back propagation method to update the parameters of the convolutional neural network model. Iterate repeatedly. When the preset number of model training iterations is reached or the loss function reaches the preset threshold, the convolutional neural network model training is completed and the model parameters are saved.
  • the automatic drawing of the contour line of the target normal organ in step S3 includes the following steps:
  • step (C) According to step (B), the mask image of the normal organ is converted into contour lines.
  • FIG. 6 is a schematic structural diagram of a system for automatically delineating the contours of normal organs in medical imaging according to an embodiment of the present invention, and the system includes:
  • Patient image preprocessing module used to obtain and preprocess patient images collected before medical images
  • Normal organ grouping and target normal organ sub-region module used to group all normal organs to be segmented step by step, and use an iterative method to gradually locate the target normal organ sub-region;
  • Normal organ segmentation module used to classify the segmentation difficulty of each normal organ in the normal organ sub-division; and use the iterative constrained normal organ segmentation model on the image corresponding to the normal organ sub-division to automatically perform the contour line of the target normal organ Delineate until all normal organs in all normal organ subdivisions are segmented.
  • the method and system for automatically delineating the contours of normal organs in medical images addresses the problem of high hardware requirements for segmentation under large three-dimensional images, and adopts an iterative method to gradually reduce the background area. Reduce the computational complexity of the segmentation model based on the convolutional network, so that its requirements for hardware devices are greatly reduced.
  • the iterative segmentation framework normal organs are segmented from easy to difficult, and the normal organ segmentation results of the previous iteration are used to constrain The segmentation of normal organs in the next iteration improves the accuracy of segmentation.
  • FIG. 9 is a schematic diagram of the physical structure of an electronic device provided by an embodiment of the present invention.
  • the electronic device may include: a processor 301, a communications interface 302, and a memory 303 And the communication bus 304, wherein the processor 301, the communication interface 302, and the memory 303 communicate with each other through the communication bus 304.
  • the processor 301 can call a computer program stored in the memory 303 and running on the processor 301 to execute the methods provided in the foregoing embodiments, for example, including:
  • All normal organs to be segmented are grouped step by step, and an iterative method is used to gradually locate the target normal organ sub-regions;
  • the classification is based on the difficulty of segmentation of each normal organ in the normal organ sub-division; and the iterative constrained normal organ segmentation model is used on the image corresponding to the normal organ sub-division to automatically delineate the contour line of the target normal organ until all normal organs are sub-division. All normal organs in the sub-area have been segmented.
  • the above-mentioned logical instructions in the memory 303 can be implemented in the form of a software functional unit and when sold or used as an independent product, they can be stored in a computer readable storage medium.
  • the technical solutions of the embodiments of the present invention can be embodied in the form of software products in essence or parts that contribute to the prior art or parts of the technical solutions, and the computer software products are stored in a storage medium.
  • Including several instructions to make a computer device (which can be a personal computer, a server, or a network device, etc.) execute all or part of the steps of the method described in each embodiment of the present invention.
  • the aforementioned storage media include: U disk, mobile hard disk, read-only memory (ROM, Read-Only Memory), random access memory (RAM, Random Access Memory), magnetic disks or optical disks and other media that can store program codes. .
  • the embodiment of the present invention also provides a non-transitory computer-readable storage medium on which a computer program is stored.
  • the computer program is implemented when executed by a processor to perform the methods provided in the foregoing embodiments, for example, including:
  • All normal organs to be segmented are grouped step by step, and an iterative method is used to gradually locate the target normal organ sub-regions;
  • the classification is based on the difficulty of segmentation of each normal organ in the normal organ sub-division; and the iterative constrained normal organ segmentation model is used on the image corresponding to the normal organ sub-division to automatically delineate the contour line of the target normal organ until all normal organs are sub-division. All normal organs in the sub-area have been segmented.
  • the device embodiments described above are merely illustrative.
  • the units described as separate components may or may not be physically separated, and the components displayed as units may or may not be physical units, that is, they may be located in One place, or it can be distributed to multiple network units.
  • Some or all of the modules can be selected according to actual needs to achieve the objectives of the solutions of the embodiments. Those of ordinary skill in the art can understand and implement it without creative work.
  • each implementation manner can be implemented by means of software plus a necessary general hardware platform, and of course, it can also be implemented by hardware.
  • the above technical solution essentially or the part that contributes to the existing technology can be embodied in the form of a software product, and the computer software product can be stored in a computer-readable storage medium, such as ROM/RAM, magnetic A disc, an optical disc, etc., include several instructions to make a computer device (which may be a personal computer, a server, or a network device, etc.) execute the methods described in each embodiment or some parts of the embodiment.

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Abstract

Disclosed are a method and system for automatically sketching a contour line of a normal organ in a medical image. The method comprises the following steps: S1, acquiring a patient image collected via a medical image, and preprocessing the patient image; S2, grouping, grade by grade, all normal organs to be segmented, and gradually positioning target normal organ sub-partitions using an iterative method; and S3, performing grading according to the segmentation difficulty of each normal organ in the determined normal organ sub-partitions, and automatically sketching a contour line of a target normal organ on an image corresponding to the determined normal organ sub-partitions using an iterative constraint type normal organ segmentation model until all the normal organs in all the normal organ sub-partitions have been segmented. By means of the method, the calculation complexity of a segmentation model based on a convolutional network is reduced, and the segmentation accuracy is improved.

Description

医学影像中正常器官的轮廓线自动勾画方法Method for automatically delineating contour lines of normal organs in medical imaging 技术领域Technical field
本发明涉及医学影像处理技术领域,尤其涉及一种医学影像中正常器官的轮廓线自动勾画方法。The invention relates to the technical field of medical image processing, in particular to a method for automatically delineating contour lines of normal organs in medical images.
背景技术Background technique
放射治疗是目前临床上肿瘤治疗的三大重要手段之一。在放射治疗中,靶区和危及器官的勾画对放射治疗的精确度有着至关重要的影响,而目前临床上靶区和危及器官的轮廓线主要通过医生手动勾画获得。由医生手动勾画存在以下几点缺陷:一、勾画效率低;二、严重依赖医生的临床经验;三、可重复性差,不同医生在不同时间不同状态下勾画的结果均不一致。因此,临床上亟需精确快速的医学影像自动分割算法来减轻医生的负担,提高医学影像中正常器官分割的精确度和自动化程度。Radiotherapy is currently one of the three important methods of clinical tumor treatment. In radiotherapy, the delineation of target areas and organs at risk has a crucial influence on the accuracy of radiotherapy. At present, the contours of target areas and organs at risk are mainly obtained by doctors manually delineating the contours of the target areas and organs at risk in clinic. Manual sketching by doctors has the following drawbacks: 1. The sketching efficiency is low; 2. It is heavily dependent on the doctor's clinical experience; 3. The reproducibility is poor, and the results of the sketching by different doctors at different times and different conditions are inconsistent. Therefore, there is an urgent need for accurate and fast automatic medical image segmentation algorithms to reduce the burden on doctors and improve the accuracy and automation of normal organ segmentation in medical images.
基于地图集(atlas)的分割方法是医学影像中的正常器官自动勾画的热门方法,尤其是头颈部肿瘤的医学影像中,由于头颈部结构具有相对固定的位置关系,因此基于atlas的分割方法在头颈部的正常器官的分割中有较好表现。基于atlas的分割方法一般分为单atlas和多atlas方法。但是,单atlas分割方法对atlas的选择和病人之间的解剖结构的差别非常敏感,当目标图像与atlas存在较大差异是,单atlas方法可能分割失败。而多atlas分割方法可以减低对atlas和病人间差异的敏感度,较单atlas具有更高的分割精度,但是分割效率更低。此外,基于atlas的分割方法依赖图像配准算法,其可能引入额外的配准误差。基于atlas的正常器官分割方法存在诸多缺陷,无法满足临床需求。近年来,机器学习和深度学习,尤其是卷积神经网络(Convolutional NeuralNetwork,CNN)在图像分类、计算机视觉和目标提取等领域上取得了巨大成功。许多研究者也将其应用于医学影像的分割。比如,Ibragimov,B等人 于2017年提出了一种基于卷积神经网络的头颈部正常器官分割方法[Ibragimov B and Xing L 2017Segmentation of organs-at-risks in head and neck CT images using convolutional neural networks,Medical physics 44 547-57],并将其应用于头颈部医学影像中的9种正常器官的自动分割。该方法由以下步骤组成:(1)根据脑部正常器官与脑部中心坐标的相对位置关系粗略确定目标正常器官的感兴趣区域;(2)基于目标正常器官感兴趣区域内目标像素点和背景像素点所在的图像块(patch)训练基于卷积神经网络的分类模型;(3)然后,在待分割图像上目标正常器官的感兴趣区域上对所有像素点进行分类,从而实现图像中正常器官的分割;(4)最后,再利用马尔科夫随机场对分割结果进行后处理,去除部分过分割像素。该方法利用脑部正常器官的固定位置关系粗略确定感兴趣区域,并利用医生勾画的结果训练正常器官分割模型,实现头颈部多个正常器官的自动分割。The atlas-based segmentation method is a popular method for automatic delineation of normal organs in medical imaging, especially in the medical imaging of head and neck tumors. Because the head and neck structure has a relatively fixed positional relationship, atlas-based segmentation The method has a good performance in the segmentation of normal organs of the head and neck. Atlas-based segmentation methods are generally divided into single atlas and multiple atlas methods. However, the single atlas segmentation method is very sensitive to the choice of atlas and the difference in the anatomical structure of the patient. When the target image is significantly different from the atlas, the single atlas method may fail to segment. The multi-atlas segmentation method can reduce the sensitivity to the difference between atlas and patients, and has higher segmentation accuracy than single atlas, but the segmentation efficiency is lower. In addition, the atlas-based segmentation method relies on image registration algorithms, which may introduce additional registration errors. The atlas-based normal organ segmentation method has many defects and cannot meet clinical needs. In recent years, machine learning and deep learning, especially convolutional neural networks (Convolutional Neural Network, CNN) have achieved great success in the fields of image classification, computer vision, and target extraction. Many researchers also apply it to the segmentation of medical images. For example, in 2017, Ibragimov, B and others proposed a head and neck normal organ segmentation method based on convolutional neural networks [Ibragimov B and Xing L 2017 Segmentation of organs-at-risks in head and neck CT images using convolutional neural networks ,Medical physics 44 547-57], and applied it to the automatic segmentation of 9 normal organs in head and neck medical imaging. The method consists of the following steps: (1) Roughly determine the region of interest of the target normal organ according to the relative positional relationship between the normal brain organs and the center coordinates of the brain; (2) Based on the target pixel points and background in the target normal organ region of interest The image patch where the pixel is located is trained on a classification model based on a convolutional neural network; (3) Then, all pixels are classified on the region of interest of the target normal organ on the image to be segmented, so as to realize the normal organ in the image (4) Finally, use Markov random field to post-process the segmentation results to remove some over-segmented pixels. This method uses the fixed position relationship of the normal organs of the brain to roughly determine the region of interest, and uses the results drawn by the doctor to train the normal organ segmentation model to realize the automatic segmentation of multiple normal organs in the head and neck.
相比较于传统的基于地图集的正常器官分割方法,该方法在大部分正常器官上具有更高分割精度,但基于卷积神经网络的图像分割方法是根据医生勾画好的数据学习目标的特征,从而能更好地从图像上识别和分割出目标区域,而如视神经、视交叉神经等图像对比度较低,体积较小的正常器官在图像上的有效信息较少。因此,常规的基于patch的方法在这类正常器官上的分割上精度仍较低。而且图像对比度较低,使得体积较小的正常器官在图像上的分割对三维图像环境的依赖较为严重,但目前的硬件水平较难支持大型三维图像矩阵下的卷积神经网络模型的训练,因此,从临床医学影像上分割出大小悬殊,灰度各异的目标正常器官,仍是一个极具挑战的问题。Compared with the traditional normal organ segmentation method based on atlas, this method has higher segmentation accuracy on most normal organs, but the image segmentation method based on convolutional neural network is based on the characteristics of the data drawn by the doctor to learn the target. Therefore, the target area can be better recognized and segmented from the image, while the contrast of the image such as the optic nerve and the optic chiasm is low, and the smaller normal organs have less effective information on the image. Therefore, the conventional patch-based method still has low accuracy in segmentation on such normal organs. Moreover, the image contrast is low, which makes the image segmentation of small normal organs more dependent on the three-dimensional image environment, but the current hardware level is difficult to support the training of the convolutional neural network model under the large three-dimensional image matrix, so It is still a very challenging problem to segment the target normal organs of different sizes and different gray levels from clinical medical images.
发明内容Summary of the invention
针对现有技术存在的问题,本发明实施例提供一种医学影像中正常器官的轮廓线自动勾画方法及系统。In view of the problems existing in the prior art, embodiments of the present invention provide a method and system for automatically delineating the contour lines of normal organs in medical images.
第一方面,本发明实施例提供一种医学影像中正常器官的轮廓线自动勾画方法,包括以下步骤:In the first aspect, an embodiment of the present invention provides a method for automatically delineating a contour line of a normal organ in a medical image, which includes the following steps:
步骤S1:获取医学影像前采集的病人影像,并对其进行预处理;Step S1: Obtain the patient image collected before the medical image, and preprocess it;
步骤S2:将所有待分割的正常器官逐级分组,并采用迭代式方法逐步定位目标正常器官子分区;Step S2: Group all the normal organs to be segmented step by step, and use an iterative method to gradually locate the target normal organ sub-regions;
步骤S3:根据确定的正常器官子分区内的各个正常器官的分割难度进行分级;并在确定的正常器官子分区对应的图像上采用迭代约束式正常器官分割模型对目标正常器官轮廓线的进行自动勾画,直至所有正常器官子分区内的所有正常器官分割完毕。Step S3: Perform classification according to the segmentation difficulty of each normal organ in the determined normal organ sub-region; and use an iterative constrained normal organ segmentation model on the image corresponding to the determined normal organ sub-region to automatically perform the contour line of the target normal organ Delineate until all normal organs in all normal organ subdivisions are segmented.
进一步地,病人影像的预处理包括:重采样和图像灰度归一化。Further, the preprocessing of the patient image includes: resampling and normalization of the image gray level.
进一步地,步骤S2具体包括以下步骤:Further, step S2 specifically includes the following steps:
S21:将所有待分割的正常器官当作为一个目标,对所述步骤S1所得到的预处理后的病人图像的各个维度进行2 n倍降采样,基于卷积神经网络模型在2 n倍降采样后的图像上进行目标区域识别,得到所有目标正常器官的粗略位置,再根据目标区域的中心坐标和目标正常器官大小的先验信息对所述步骤S1中所得到的预处理后的图像进行裁剪,去除图像中大部分的背景区域; S21: All When normal organ to be segmented as a target, various dimensions of the patient images preprocessed in the step S1 is obtained 2 n times down-sampling, a convolutional neural network model based on the 2 n times downsampling Perform target area recognition on the resulting image to obtain the rough positions of all target normal organs, and then crop the preprocessed image obtained in step S1 according to the prior information of the center coordinates of the target area and the size of the target normal organ , Remove most of the background area in the image;
S22:将同一分区的正常器官当作为一个目标,对所述步骤S21所得到的裁剪后的图像的各个维度进行2 n-1倍降采样,基于卷积神经网络模型在2 n-1倍降采样后的图像上进行正常器官分区的识别,根据不同的正常器官分区识别结果对所述步骤S1中所得到的预处理后的图像进行区域裁剪,得到各个正常器官分区的图像; S22: The same partition when the normal organs as a target, the respective dimensions of the trimmed image obtained in step S21 is 2 n-1 times down-sampling, a convolutional neural network model based on 2 n-1 times the drop Perform normal organ partition recognition on the sampled image, and perform region cropping on the preprocessed image obtained in step S1 according to different normal organ partition recognition results to obtain images of each normal organ partition;
S23:逐级迭代,直到定位出所有正常器官子分区的位置,并裁剪出各个正常器官子分区对应的图像。S23: Iterate step by step until the positions of all normal organ sub-divisions are located, and the images corresponding to each normal organ sub-division are cut out.
进一步地,步骤S3具体包括以下步骤:Further, step S3 specifically includes the following steps:
S31:将所述步骤S2所确定的正常器官子分区对应的图像作为输入,并基于卷积神经网络模型对第一级的正常器官进行分割,得到第一级正常器官的分割结果;S31: Taking the image corresponding to the normal organ sub-division determined in step S2 as input, and segmenting the first-level normal organ based on the convolutional neural network model to obtain the first-level normal organ segmentation result;
S32:将所述步骤S31得到的第一级正常器官的分割结果和所述步骤S2中所确定的正常器官子分区对应的图像作为输入,对第二级正常器官的分割进行约束,并基于卷积神经网络模型对第二级的正常器官进行分割,得到第 二级正常器官的分割结果;S32: Taking the first-level normal organ segmentation result obtained in step S31 and the image corresponding to the normal organ sub-region determined in step S2 as input, and restricting the second-level normal organ segmentation based on the volume The product neural network model segmented the second-level normal organs to obtain the second-level normal organ segmentation results;
S33:逐级迭代,将所有已分割级别的正常器官的分割结果和所述步骤S2中所确定的正常器官子分区对应的图像作为输入,对当前级正常器官的分割进行约束,并基于卷积神经网络模型对当前分割级的正常器官进行分割,得到当前级别正常器官的分割结果,直到分割出所有正常器官。S33: Iterate step by step, taking the segmentation results of all normal organs at the segmented level and the images corresponding to the normal organ sub-regions determined in step S2 as input, and constrain the segmentation of normal organs at the current level, and based on convolution The neural network model segments the normal organs at the current segmentation level, and obtains the segmentation results of the normal organs at the current level until all normal organs are segmented.
进一步地,卷积神经网络模型的具体包括以下步骤:Further, the convolutional neural network model specifically includes the following steps:
建立卷积神经网络模型,该卷积神经网络模型以病人图像和已知的其他正常器官的分割结果作为输入,以分割结果作为输出;Establish a convolutional neural network model. The convolutional neural network model takes the segmentation results of patient images and other known normal organs as input, and the segmentation results as output;
收集医学影像前采集的病人影像和由经验丰富的医生勾画好的正常器官轮廓线;并对收集的病人图像进行预处理,再将医生勾画的每一个正常器官的轮廓线转化为掩模图像;Collect patient images collected before medical imaging and outlines of normal organs drawn by experienced doctors; preprocess the collected patient images, and then convert the outlines of each normal organ drawn by doctors into mask images;
将预处理后的病人图像作为卷积神经网络模型的输入,根据卷积神经网络模型的当前输出和收集的医生勾画的对应正常器官的掩模图像计算当前分割模型的损失函数,采用反向传播方法对卷积神经网络模型的参数进行更新;反复迭代,当达到预设的模型训练迭代次数或损失函数达到预设阈值,卷积神经网络模型训练完成,保存模型参数。The preprocessed patient image is used as the input of the convolutional neural network model, and the loss function of the current segmentation model is calculated according to the current output of the convolutional neural network model and the collected mask images of the normal organs outlined by the doctor, using back propagation The method updates the parameters of the convolutional neural network model; iterates repeatedly, and when the preset number of model training iterations is reached or the loss function reaches the preset threshold, the convolutional neural network model training is completed and the model parameters are saved.
进一步地,步骤S3中对目标正常器官轮廓线的自动勾画包括以下步骤:Further, the automatic drawing of the contour line of the target normal organ in step S3 includes the following steps:
导入对应的已经训练好卷积神经网络模型;Import the corresponding trained convolutional neural network model;
将对应的图像和已知的其他正常器官的分割结果输入训练好的卷积神经网络模型,得到正常器官的掩模图像;Input the corresponding image and the segmentation results of other known normal organs into the trained convolutional neural network model to obtain the mask image of the normal organ;
根据得到的正常器官的掩模图像转化为轮廓线。According to the obtained mask image of normal organs, it is transformed into contour lines.
进一步地,掩模图像为二进制掩模图像。Further, the mask image is a binary mask image.
第二方面,本发明实施例提供一种医学影像中正常器官的轮廓线自动勾画系统,包括:In a second aspect, an embodiment of the present invention provides a system for automatically delineating the contours of normal organs in medical images, including:
病人影像预处理模块:用于获取医学影像前采集的病人影像,并对其进行预处理;Patient image preprocessing module: used to obtain and preprocess patient images collected before medical images;
正常器官分组及定位目标正常器官子分区模块:用于将所有待分割的正常器官逐级分组,并采用迭代式方法逐步定位目标正常器官子分区;Normal organ grouping and target normal organ sub-region module: used to group all normal organs to be segmented step by step, and use an iterative method to gradually locate the target normal organ sub-region;
正常器官分割模块:用于根据正常器官子分区内的各个正常器官的分割难度进行分级;并在正常器官子分区对应的图像上采用迭代约束式正常器官分割模型对目标正常器官轮廓线的进行自动勾画,直至所有正常器官子分区内的所有正常器官分割完毕。Normal organ segmentation module: used to classify the segmentation difficulty of each normal organ in the normal organ sub-division; and use the iterative constrained normal organ segmentation model on the image corresponding to the normal organ sub-division to automatically perform the contour line of the target normal organ Delineate until all normal organs in all normal organ subdivisions are segmented.
第三方面,本发明实施例提供一种电子设备,包括存储器、处理器及存储在存储器上并可在处理器上运行的计算机程序,所述处理器执行所述程序时实现如第一方面所提供的医学影像中正常器官的轮廓线自动勾画方法的步骤。In a third aspect, an embodiment of the present invention provides an electronic device, including a memory, a processor, and a computer program stored in the memory and capable of running on the processor. When the processor executes the program, the implementation is as described in the first aspect. Provides the steps of the method for automatically delineating the contour lines of normal organs in medical images.
第四方面,本发明实施例提供一种非暂态计算机可读存储介质,其上存储有计算机程序,该计算机程序被处理器执行时实现如第一方面所提供的医学影像中正常器官的轮廓线自动勾画方法的步骤。In a fourth aspect, an embodiment of the present invention provides a non-transitory computer-readable storage medium on which a computer program is stored. When the computer program is executed by a processor, the outline of a normal organ in a medical image as provided in the first aspect is realized. The steps of the automatic line drawing method.
本发明实施例提供的一种医学影像中正常器官的轮廓线自动勾画方法及系统针对大型三维图像下的分割对硬件水平要求较高的问题,采用迭代的方式,逐步减少背景区域,减少基于卷积网络的分割模型的计算复杂度,使得其对于硬件设备的要求大大降低。此外,针对图像对比度较低,体积较小的正常器官的分割精度低的问题,在迭代分割框架中,对正常器官实施由易到难的分割,并利用前次迭代的正常器官的分割结果约束下一次迭代的正常器官的分割,提高分割的准确度。The method and system for automatically delineating the contours of normal organs in medical images provided by the embodiments of the present invention are aimed at the problem of high hardware requirements for segmentation under large three-dimensional images, and adopts an iterative method to gradually reduce background areas and reduce volume-based The computational complexity of the segmentation model of the product network greatly reduces its requirements for hardware devices. In addition, for the problem of low image contrast and low segmentation accuracy of normal organs with small volumes, in the iterative segmentation framework, normal organs are segmented from easy to difficult, and the normal organ segmentation results of the previous iteration are used to constrain The segmentation of normal organs in the next iteration improves the accuracy of segmentation.
附图说明Description of the drawings
为了更清楚地说明本发明实施例或现有技术中的技术方案,下面将对实施例或现有技术描述中所需要使用的附图作简单地介绍,显而易见地,下面描述中的附图是本发明的一些实施例,对于本领域普通技术人员来讲,在不付出创造性劳动的前提下,还可以根据这些附图获得其他的附图。In order to explain the embodiments of the present invention or the technical solutions in the prior art more clearly, the following will briefly introduce the drawings that need to be used in the description of the embodiments or the prior art. Obviously, the drawings in the following description are For some of the embodiments of the present invention, those of ordinary skill in the art can obtain other drawings based on these drawings without creative work.
图1为本发明实施例提供的医学影像中正常器官的轮廓线自动勾画方法流程图;FIG. 1 is a flowchart of a method for automatically delineating contour lines of normal organs in medical images according to an embodiment of the present invention;
图2为本发明实施例提供的方法中步骤S2的流程图;2 is a flowchart of step S2 in the method provided by an embodiment of the present invention;
图3为本发明实施例提供的方法中步骤S3的流程图;FIG. 3 is a flowchart of step S3 in the method provided by an embodiment of the present invention;
图4为本发明实施例提供的方法中卷积神经网络模型的流程图;4 is a flowchart of a convolutional neural network model in a method provided by an embodiment of the present invention;
图5为本发明实施例提供的方法步骤S3中对目标正常器官轮廓线的自动勾画的流程图;FIG. 5 is a flowchart of automatically delineating the contour line of the target normal organ in step S3 of the method provided by the embodiment of the present invention;
图6本发明实施例提供的医学影像中正常器官的轮廓线自动勾画系统的原理图;Fig. 6 is a schematic diagram of a system for automatically delineating the contours of normal organs in medical images according to an embodiment of the present invention;
图7本发明实施例提供的方法中迭代分割框架图;FIG. 7 is a framework diagram of iterative segmentation in the method provided by an embodiment of the present invention;
图8本发明实施例提供的方法中迭代约束式正常器官分割模型框图;FIG. 8 is a block diagram of an iterative constrained normal organ segmentation model in the method provided by an embodiment of the present invention;
图9本发明实施例提供的一种电子设备的实体结构图。FIG. 9 is a physical structure diagram of an electronic device provided by an embodiment of the present invention.
具体实施方式Detailed ways
为使本发明实施例的目的、技术方案和优点更加清楚,下面将结合本发明实施例中的附图,对本发明实施例中的技术方案进行清楚、完整地描述,显然,所描述的实施例是本发明一部分实施例,而不是全部的实施例。基于本发明中的实施例,本领域普通技术人员在没有作出创造性劳动前提下所获得的所有其他实施例,都属于本发明保护的范围。In order to make the objectives, technical solutions, and advantages of the embodiments of the present invention clearer, the following will clearly and completely describe the technical solutions in the embodiments of the present invention with reference to the accompanying drawings in the embodiments of the present invention. Obviously, the described embodiments These are a part of the embodiments of the present invention, but not all of the embodiments. Based on the embodiments of the present invention, all other embodiments obtained by those of ordinary skill in the art without creative work shall fall within the protection scope of the present invention.
图1为本发明实施例提供的一种医学影像中正常器官的轮廓线自动勾画方法流程图,如图1所示,该方法包括:Fig. 1 is a flow chart of a method for automatically delineating the contours of normal organs in medical images according to an embodiment of the present invention. As shown in Fig. 1, the method includes:
步骤S1:获取医学影像采集的病人影像,并对其进行预处理;Step S1: Obtain patient images collected by medical images and preprocess them;
病人影像包括:CT(Computed Tomography)、MR(magnetic resonance)或PET(Positron Emission Tomography)等。其中,CT即电子计算机断层扫描,它是利用精确准直的X线束、γ射线、超声波等,与灵敏度极高的探测器一同围绕人体的某一部位作一个接一个的断面扫描。MR是医学检查的一种方法,也是医学影像学的一场革命,生物体组织能被电磁波谱中的短波成分如X线等穿透,但能阻挡中波成分如紫外线、红外线及长波。人体组织允许磁共振产生的长波成分如无线电波穿过,这是磁共振应用于临床的基本条件之一。PET是核医学领域比较先进的临床检查影像技术。正常范围PET特 别适用于在没有形态学改变之前,早期诊断疾病,发现亚临床病变以及评价治疗效果。目前,PET在肿瘤、冠心病和脑部疾病这三大类疾病的诊疗中尤其显示出重要的价值。Patient images include: CT (Computed Tomography), MR (magnetic resonance) or PET (Positron Emission Tomography), etc. Among them, CT stands for electronic computer tomography, which uses precisely collimated X-ray beams, gamma rays, ultrasonic waves, etc., together with extremely sensitive detectors to scan a certain part of the human body one by one. MR is a method of medical examination and a revolution in medical imaging. Biological tissues can be penetrated by short-wave components in the electromagnetic spectrum such as X-rays, but can block mid-wave components such as ultraviolet, infrared and long waves. Human tissue allows long-wave components such as radio waves generated by magnetic resonance to pass through, which is one of the basic conditions for magnetic resonance in clinical applications. PET is a relatively advanced clinical examination imaging technology in the field of nuclear medicine. Normal range PET is especially suitable for early diagnosis of disease, discovery of subclinical lesions and evaluation of treatment effect before there is no morphological change. At present, PET has shown particularly important value in the diagnosis and treatment of the three major types of diseases: tumor, coronary heart disease and brain disease.
本发明实施例的步骤S1中,对病人影像进行预处理包括:重采样和图像灰度归一化。In step S1 of the embodiment of the present invention, preprocessing the patient image includes: resampling and image gray normalization.
步骤S2:将所有待分割的正常器官逐级分组(如:1级:所有正常器官;2级:正常器官分区;3级:正常器官子分区;4级:正常器官),并采用迭代式方法逐步定位目标正常器官子分区;Step S2: Divide all normal organs to be segmented into groups (for example: level 1: all normal organs; level 2: normal organs partition; level 3: normal organ sub-partitions; level 4: normal organs), and adopt an iterative method Gradually locate the target normal organ sub-region;
如图2所示,本发明实施例的步骤S2具体包括以下步骤:As shown in FIG. 2, step S2 in the embodiment of the present invention specifically includes the following steps:
S21:将所有待分割的正常器官当作为一个目标,对步骤S1所得到的预处理后的病人图像的各个维度进行2 n倍降采样,基于卷积神经网络模型在2 n倍降采样后的图像上进行目标区域识别,得到所有目标正常器官的粗略位置,再根据目标区域的中心坐标和目标正常器官大小的先验信息对步骤S1中所得到的预处理后的图像进行裁剪,去除图像中大部分的背景区域; S21: Regard all normal organs to be segmented as a target, perform 2 n times downsampling on each dimension of the preprocessed patient image obtained in step S1, based on the convolutional neural network model after 2 n times downsampling Recognize the target area on the image to obtain the rough positions of all target normal organs, and then crop the preprocessed image obtained in step S1 according to the prior information of the center coordinates of the target area and the size of the target normal organ to remove the image Most of the background area;
S22:将同一分区的正常器官当作为一个目标,对步骤S21所得到的裁剪后的图像的各个维度进行2 n-1倍降采样,基于卷积神经网络模型在2 n-1倍降采样后的图像上进行正常器官分区的识别,根据不同的正常器官分区识别结果对步骤S1中所得到的预处理后的图像进行区域裁剪,得到各个正常器官分区的图像; After normal organs when the same partition as a target, various dimensions of the cropped image obtained in step S21 is 2 n-1 times down-sampling, a convolutional neural network model based on the 2 n-1 times downsampling: S22 Perform normal organ partition recognition on the image of, and perform region cropping on the preprocessed image obtained in step S1 according to different normal organ partition recognition results to obtain images of each normal organ partition;
S23:逐级迭代,直到定位出所有正常器官子分区的位置,并裁剪出各个正常器官子分区对应的图像。S23: Iterate step by step until the positions of all normal organ sub-divisions are located, and the images corresponding to each normal organ sub-division are cut out.
步骤S3:根据步骤S2所确定的正常器官子分区内的各个正常器官的分割难度进行分级(如,I级:简单,II级:一般,III级:困难)。在步骤S2所确定的正常器官子分区对应的图像上,采用如图8所示的迭代约束式正常器官分割模型对目标正常器官轮廓线的进行自动勾画,直至所有正常器官子分区内的所有正常器官分割完毕。Step S3: Perform classification according to the division difficulty of each normal organ in the normal organ sub-division determined in step S2 (for example, level I: easy, level II: general, and level III: difficult). On the image corresponding to the normal organ sub-division determined in step S2, the iterative constrained normal organ segmentation model as shown in Fig. 8 is used to automatically delineate the contour line of the target normal organ until all normal organs in all normal organ sub-divisions are The organ segmentation is complete.
如图3所示,步骤S3具体包括以下步骤:As shown in Fig. 3, step S3 specifically includes the following steps:
S31:将步骤S2所确定的正常器官子分区对应的图像作为输入,基于卷积神经网络模型,对I级(第一级)的正常器官进行分割,得到I级(第一级)正常器官的分割结果;S31: Taking the image corresponding to the normal organ sub-region determined in step S2 as input, and segmenting the normal organs of level I (level 1) based on the convolutional neural network model to obtain normal organs of level I (level 1) Segmentation result
S32:将步骤S31得到的I级(第一级)正常器官的分割结果和步骤S2中所确定的正常器官子分区对应的图像作为输入,对II级(第二级)正常器官的分割进行约束,基于卷积神经网络模型,对II级(第二级)的正常器官进行分割,得到II级(第二级)正常器官的分割结果;S32: The segmentation result of the normal organ of level I (level 1) obtained in step S31 and the image corresponding to the normal organ sub-region determined in step S2 are used as input, and the segmentation of the normal organ of level II (level 2) is constrained , Based on the convolutional neural network model, segment the normal organs of level II (level 2), and obtain the segmentation results of normal organs of level II (level 2);
S33:逐级迭代,将所有已分割级别的正常器官的分割结果和步骤S2中所确定的正常器官子分区对应的图像作为输入,对当前级正常器官的分割进行约束,基于卷积神经网络模型,对当前分割级的正常器官进行分割,得到当前级别正常器官的分割结果,直到分割出所有正常器官。S33: Iterate step by step, taking the segmentation results of all normal organs at the segmented level and the images corresponding to the normal organ sub-regions determined in step S2 as input, and constraining the segmentation of normal organs at the current level, based on the convolutional neural network model , To segment the normal organs at the current segmentation level to obtain the segmentation results of the normal organs at the current level until all normal organs are segmented.
其中图7示出了迭代分割框架图,步骤S2和步骤S3中所采用的卷积神经网络模型均是其采用监督学习的方式,根据预先采集的病人影像数据、由经验丰富的医生勾画好的正常器官轮廓线数据和已知的其他正常器官的分割结果(如果存在)进行训练,得到稳定的正常器官检测模型、正常器官子分区检测模型和对应子分区的正常器官分割模型,如图7中虚线部分所示。如图4所示,卷积神经网络模型的具体包括三个步骤:Figure 7 shows the frame diagram of iterative segmentation. The convolutional neural network model used in step S2 and step S3 adopts a supervised learning method, based on pre-collected patient image data and sketched by experienced doctors. The normal organ contour data and the known segmentation results of other normal organs (if any) are trained to obtain a stable normal organ detection model, normal organ sub-division detection model, and normal organ segmentation model corresponding to the sub-division, as shown in Figure 7. The dashed part is shown. As shown in Figure 4, the convolutional neural network model specifically includes three steps:
(A)建立卷积神经网络模型,该卷积神经网络模型以病人图像和已知的其他正常器官的分割结果(如果存在)作为输入,以分割结果作为输出;(A) Establish a convolutional neural network model. The convolutional neural network model takes the patient image and the segmentation results of other known normal organs (if any) as input, and the segmentation results as output;
(B)收集采集的病人影像(CT,MR或PET),和由经验丰富的医生勾画好的正常器官轮廓线。并对收集的病人图像重采样和图像灰度归一化的预处理,再将医生勾画的每一个正常器官的轮廓线转化为目标区域为1,背景区域为0的二进制掩模图像;(B) Collect collected patient images (CT, MR or PET), and contour lines of normal organs drawn by experienced doctors. And pre-process the collected patient image resampling and image gray normalization, and then convert the contour line of each normal organ drawn by the doctor into a binary mask image with a target area of 1 and a background area of 0;
(C)将步骤(B)中预处理后的病人图像作为卷积神经网络模型的输入,根据卷积神经网络模型的当前输出和将步骤(B)中收集的医生勾画的对应正 常器官的掩模图像,计算当前分割模型的损失函数,采用反向传播方法对卷积神经网络模型的参数进行更新。反复迭代,当达到预设的模型训练迭代次数或损失函数达到预设阈值,卷积神经网络模型训练完成,保存模型参数。(C) The patient image preprocessed in step (B) is used as the input of the convolutional neural network model, based on the current output of the convolutional neural network model and the masks of the normal organs drawn by the doctors collected in step (B) Model image, calculate the loss function of the current segmentation model, and use the back propagation method to update the parameters of the convolutional neural network model. Iterate repeatedly. When the preset number of model training iterations is reached or the loss function reaches the preset threshold, the convolutional neural network model training is completed and the model parameters are saved.
其中,如图5所示,步骤S3中对目标正常器官轮廓线的自动勾画包括以下步骤:Wherein, as shown in FIG. 5, the automatic drawing of the contour line of the target normal organ in step S3 includes the following steps:
(A)导入对应的已经训练好卷积神经网络模型;(A) Import the corresponding trained convolutional neural network model;
(B)将对应的图像和已知的其他正常器官的分割结果(如果存在),输入训练好的卷积神经网络模型,得到正常器官的二进制掩模图像(即目标区域为1,背景区域为0);(B) Input the corresponding image and the segmentation results of other known normal organs (if they exist) into the trained convolutional neural network model to obtain the binary mask image of the normal organs (that is, the target area is 1, the background area is 0);
(C)根据步骤(B)得到的正常器官的掩模图像转化为轮廓线。(C) According to step (B), the mask image of the normal organ is converted into contour lines.
基于上述任一实施例,图6为本发明实施例提供的一种医学影像中正常器官的轮廓线自动勾画系统的结构示意图,该系统包括:Based on any of the foregoing embodiments, FIG. 6 is a schematic structural diagram of a system for automatically delineating the contours of normal organs in medical imaging according to an embodiment of the present invention, and the system includes:
病人影像预处理模块:用于获取医学影像前采集的病人影像,并对其进行预处理;Patient image preprocessing module: used to obtain and preprocess patient images collected before medical images;
正常器官分组及定位目标正常器官子分区模块:用于将所有待分割的正常器官逐级分组,并采用迭代式方法逐步定位目标正常器官子分区;Normal organ grouping and target normal organ sub-region module: used to group all normal organs to be segmented step by step, and use an iterative method to gradually locate the target normal organ sub-region;
正常器官分割模块:用于根据正常器官子分区内的各个正常器官的分割难度进行分级;并在正常器官子分区对应的图像上采用迭代约束式正常器官分割模型对目标正常器官轮廓线的进行自动勾画,直至所有正常器官子分区内的所有正常器官分割完毕。Normal organ segmentation module: used to classify the segmentation difficulty of each normal organ in the normal organ sub-division; and use the iterative constrained normal organ segmentation model on the image corresponding to the normal organ sub-division to automatically perform the contour line of the target normal organ Delineate until all normal organs in all normal organ subdivisions are segmented.
综上所述,本发明实施例提供的医学影像中正常器官的轮廓线自动勾画方法及系统针对大型三维图像下的分割对硬件水平要求较高的问题,采用迭代的方式,逐步减少背景区域,减少基于卷积网络的分割模型的计算复杂度,使得其对于硬件设备的要求大大降低。此外,针对图像对比度较低,体积较小的正常器官的分割精度低的问题,在迭代分割框架中,对正常器官实施由易到难的分割,并利用前次迭代的正常器官的分割结果约束下一次迭代的正常器官的分割,提高分割的准确度。In summary, the method and system for automatically delineating the contours of normal organs in medical images provided by the embodiments of the present invention addresses the problem of high hardware requirements for segmentation under large three-dimensional images, and adopts an iterative method to gradually reduce the background area. Reduce the computational complexity of the segmentation model based on the convolutional network, so that its requirements for hardware devices are greatly reduced. In addition, for the problem of low image contrast and low segmentation accuracy of normal organs with small volumes, in the iterative segmentation framework, normal organs are segmented from easy to difficult, and the normal organ segmentation results of the previous iteration are used to constrain The segmentation of normal organs in the next iteration improves the accuracy of segmentation.
图9为本发明实施例提供的一种电子设备的实体结构示意图,如图9所示,该电子设备可以包括:处理器(processor)301、通信接口(Communications Interface)302、存储器(memory)303和通信总线304,其中,处理器301,通信接口302,存储器303通过通信总线304完成相互间的通信。处理器301可以调用存储在存储器303上并可在处理器301上运行的计算机程序,以执行上述各实施例提供的方法,例如包括:FIG. 9 is a schematic diagram of the physical structure of an electronic device provided by an embodiment of the present invention. As shown in FIG. 9, the electronic device may include: a processor 301, a communications interface 302, and a memory 303 And the communication bus 304, wherein the processor 301, the communication interface 302, and the memory 303 communicate with each other through the communication bus 304. The processor 301 can call a computer program stored in the memory 303 and running on the processor 301 to execute the methods provided in the foregoing embodiments, for example, including:
获取医学影像前采集的病人影像,并对其进行预处理;Acquire patient images collected before medical imaging and preprocess them;
将所有待分割的正常器官逐级分组,并采用迭代式方法逐步定位目标正常器官子分区;All normal organs to be segmented are grouped step by step, and an iterative method is used to gradually locate the target normal organ sub-regions;
根据正常器官子分区内的各个正常器官的分割难度进行分级;并在正常器官子分区对应的图像上采用迭代约束式正常器官分割模型对目标正常器官轮廓线的进行自动勾画,直至所有正常器官子分区内的所有正常器官分割完毕。The classification is based on the difficulty of segmentation of each normal organ in the normal organ sub-division; and the iterative constrained normal organ segmentation model is used on the image corresponding to the normal organ sub-division to automatically delineate the contour line of the target normal organ until all normal organs are sub-division. All normal organs in the sub-area have been segmented.
此外,上述的存储器303中的逻辑指令可以通过软件功能单元的形式实现并作为独立的产品销售或使用时,可以存储在一个计算机可读取存储介质中。基于这样的理解,本发明实施例的技术方案本质上或者说对现有技术做出贡献的部分或者该技术方案的部分可以以软件产品的形式体现出来,该计算机软件产品存储在一个存储介质中,包括若干指令用以使得一台计算机设备(可以是个人计算机,服务器,或者网络设备等)执行本发明各个实施例所述方法的全部或部分步骤。而前述的存储介质包括:U盘、移动硬盘、只读存储器(ROM,Read-Only Memory)、随机存取存储器(RAM,Random Access Memory)、磁碟或者光盘等各种可以存储程序代码的介质。In addition, the above-mentioned logical instructions in the memory 303 can be implemented in the form of a software functional unit and when sold or used as an independent product, they can be stored in a computer readable storage medium. Based on this understanding, the technical solutions of the embodiments of the present invention can be embodied in the form of software products in essence or parts that contribute to the prior art or parts of the technical solutions, and the computer software products are stored in a storage medium. , Including several instructions to make a computer device (which can be a personal computer, a server, or a network device, etc.) execute all or part of the steps of the method described in each embodiment of the present invention. The aforementioned storage media include: U disk, mobile hard disk, read-only memory (ROM, Read-Only Memory), random access memory (RAM, Random Access Memory), magnetic disks or optical disks and other media that can store program codes. .
本发明实施例还提供一种非暂态计算机可读存储介质,其上存储有计算机程序,该计算机程序被处理器执行时实现以执行上述各实施例提供的方法,例如包括:The embodiment of the present invention also provides a non-transitory computer-readable storage medium on which a computer program is stored. The computer program is implemented when executed by a processor to perform the methods provided in the foregoing embodiments, for example, including:
获取采集的病人影像,并对其进行预处理;Obtain collected patient images and preprocess them;
将所有待分割的正常器官逐级分组,并采用迭代式方法逐步定位目标正常器官子分区;All normal organs to be segmented are grouped step by step, and an iterative method is used to gradually locate the target normal organ sub-regions;
根据正常器官子分区内的各个正常器官的分割难度进行分级;并在正常器官子分区对应的图像上采用迭代约束式正常器官分割模型对目标正常器官轮廓线的进行自动勾画,直至所有正常器官子分区内的所有正常器官分割完毕。The classification is based on the difficulty of segmentation of each normal organ in the normal organ sub-division; and the iterative constrained normal organ segmentation model is used on the image corresponding to the normal organ sub-division to automatically delineate the contour line of the target normal organ until all normal organs are sub-division. All normal organs in the sub-area have been segmented.
以上所描述的装置实施例仅仅是示意性的,其中所述作为分离部件说明的单元可以是或者也可以不是物理上分开的,作为单元显示的部件可以是或者也可以不是物理单元,即可以位于一个地方,或者也可以分布到多个网络单元上。可以根据实际的需要选择其中的部分或者全部模块来实现本实施例方案的目的。本领域普通技术人员在不付出创造性的劳动的情况下,即可以理解并实施。The device embodiments described above are merely illustrative. The units described as separate components may or may not be physically separated, and the components displayed as units may or may not be physical units, that is, they may be located in One place, or it can be distributed to multiple network units. Some or all of the modules can be selected according to actual needs to achieve the objectives of the solutions of the embodiments. Those of ordinary skill in the art can understand and implement it without creative work.
通过以上的实施方式的描述,本领域的技术人员可以清楚地了解到各实施方式可借助软件加必需的通用硬件平台的方式来实现,当然也可以通过硬件。基于这样的理解,上述技术方案本质上或者说对现有技术做出贡献的部分可以以软件产品的形式体现出来,该计算机软件产品可以存储在计算机可读存储介质中,如ROM/RAM、磁碟、光盘等,包括若干指令用以使得一台计算机设备(可以是个人计算机,服务器,或者网络设备等)执行各个实施例或者实施例的某些部分所述的方法。Through the description of the above implementation manners, those skilled in the art can clearly understand that each implementation manner can be implemented by means of software plus a necessary general hardware platform, and of course, it can also be implemented by hardware. Based on this understanding, the above technical solution essentially or the part that contributes to the existing technology can be embodied in the form of a software product, and the computer software product can be stored in a computer-readable storage medium, such as ROM/RAM, magnetic A disc, an optical disc, etc., include several instructions to make a computer device (which may be a personal computer, a server, or a network device, etc.) execute the methods described in each embodiment or some parts of the embodiment.
最后应说明的是:以上实施例仅用以说明本发明的技术方案,而非对其限制;尽管参照前述实施例对本发明进行了详细的说明,本领域的普通技术人员应当理解:其依然可以对前述各实施例所记载的技术方案进行修改,或者对其中部分技术特征进行等同替换;而这些修改或者替换,并不使相应技术方案的本质脱离本发明各实施例技术方案的精神和范围。Finally, it should be noted that the above embodiments are only used to illustrate the technical solutions of the present invention, not to limit them; although the present invention has been described in detail with reference to the foregoing embodiments, those of ordinary skill in the art should understand that: The technical solutions recorded in the foregoing embodiments are modified, or some of the technical features thereof are equivalently replaced; these modifications or replacements do not cause the essence of the corresponding technical solutions to deviate from the spirit and scope of the technical solutions of the embodiments of the present invention.

Claims (8)

  1. 一种医学影像中正常器官的轮廓线自动勾画方法,其特征在于,包括以下步骤:A method for automatically delineating contours of normal organs in medical imaging, which is characterized in that it comprises the following steps:
    步骤S1:获取医学影像采集的病人影像,并对其进行预处理;Step S1: Obtain patient images collected by medical images and preprocess them;
    步骤S2:将所有待分割的正常器官逐级分组,并采用迭代式方法逐步定位目标正常器官子分区;Step S2: Group all the normal organs to be segmented step by step, and use an iterative method to gradually locate the target normal organ sub-regions;
    步骤S3:根据确定的正常器官子分区内的各个正常器官的分割难度进行分级,并在确定的正常器官子分区对应的图像上采用迭代约束式正常器官分割模型对目标正常器官轮廓线的进行自动勾画,直至所有正常器官子分区内的所有正常器官分割完毕;Step S3: Perform classification according to the segmentation difficulty of each normal organ in the determined normal organ sub-region, and use the iterative constrained normal organ segmentation model on the image corresponding to the determined normal organ sub-region to automatically perform the contour line of the target normal organ Delineate until all normal organs in all normal organ subdivisions are segmented;
    所述步骤S3的迭代约束式正常器官分割模型具体包括以下步骤:The iterative constrained normal organ segmentation model in step S3 specifically includes the following steps:
    S31:将所述步骤S2所确定的正常器官子分区对应的图像作为输入,并基于卷积神经网络模型对第一级的正常器官进行分割,得到第一级正常器官的分割结果;S31: Taking the image corresponding to the normal organ sub-division determined in step S2 as input, and segmenting the first-level normal organ based on the convolutional neural network model to obtain the first-level normal organ segmentation result;
    S32:将所述步骤S31得到的第一级正常器官的分割结果和所述步骤S2中所确定的正常器官子分区对应的图像作为输入,对第二级正常器官的分割进行约束,并基于卷积神经网络模型对第二级的正常器官进行分割,得到第二级正常器官的分割结果;S32: Taking the first-level normal organ segmentation result obtained in step S31 and the image corresponding to the normal organ sub-region determined in step S2 as input, and restricting the second-level normal organ segmentation based on the volume The product neural network model segmented the second-level normal organs, and obtained the second-level normal organ segmentation results;
    S33:逐级迭代,将所有已分割级别的正常器官的分割结果和所述步骤S2中所确定的正常器官子分区对应的图像作为输入,对当前级正常器官的分割进行约束,并基于卷积神经网络模型对当前分割级的正常器官进行分割,得到当前级别正常器官的分割结果,直到分割出所有正常器官。S33: Iterate step by step, taking the segmentation results of all normal organs at the segmented level and the images corresponding to the normal organ sub-regions determined in step S2 as input, and constrain the segmentation of normal organs at the current level, and based on convolution The neural network model segments the normal organs at the current segmentation level, and obtains the segmentation results of the normal organs at the current level until all normal organs are segmented.
  2. 根据权利要求1所述的医学影像中正常器官的轮廓线自动勾画方法,其特征在于,所述病人影像的预处理包括:重采样和图像灰度归一化。The method for automatically delineating contour lines of normal organs in medical images according to claim 1, wherein the preprocessing of the patient images includes: resampling and image gray normalization.
  3. 根据权利要求1所述的医学影像中正常器官的轮廓线自动勾画方法,其特征在于,所述步骤S2具体包括以下步骤:The method for automatically delineating contour lines of normal organs in medical images according to claim 1, wherein the step S2 specifically includes the following steps:
    S21:将所有待分割的正常器官当作为一个目标,对所述步骤S1所得到的预处理后的病人图像的各个维度进行2 n(n≥1)倍降采样,基于卷积神经网络模型在2 n倍降采样后的图像上进行目标区域识别,得到所有目标正常器官的粗略位置,再根据目标区域的中心坐标和目标正常器官大小的先验信息对所述步骤S1中所得到的预处理后的图像进行裁剪,去除图像中大部分的背景区域; S21: Take all normal organs to be segmented as a target, and perform 2 n (n≥1) downsampling on each dimension of the preprocessed patient image obtained in step S1, based on the convolutional neural network model. Perform target region recognition on the down-sampled image by 2n times to obtain the rough positions of all target normal organs, and then perform the preprocessing obtained in step S1 according to the prior information of the center coordinates of the target region and the size of the target normal organs After the image is cropped, most of the background area in the image is removed;
    S22:将同一分区的正常器官当作为一个目标,对所述步骤S21所得到的裁剪后的图像的各个维度进行2 n-1倍降采样,基于卷积神经网络模型在2 n-1倍降采样后的图像上进行正常器官分区的识别,根据不同的正常器官分区识别结果对所述步骤S1中所得到的预处理后的图像进行区域裁剪,得到各个正常器官分区的图像; S22: The same partition when the normal organs as a target, the respective dimensions of the trimmed image obtained in step S21 is 2 n-1 times down-sampling, a convolutional neural network model based on 2 n-1 times the drop Perform normal organ partition recognition on the sampled image, and perform region cropping on the preprocessed image obtained in step S1 according to different normal organ partition recognition results to obtain images of each normal organ partition;
    S23:逐级迭代,直到定位出所有正常器官子分区的位置,并裁剪出各个正常器官子分区对应的图像。S23: Iterate step by step until the positions of all normal organ sub-divisions are located, and the images corresponding to each normal organ sub-division are cut out.
  4. 根据权利要求1所述的医学影像中正常器官的轮廓线自动勾画方法,其特征在于,所述卷积神经网络模型的具体包括以下步骤:The method for automatically delineating contours of normal organs in medical images according to claim 1, wherein the convolutional neural network model specifically includes the following steps:
    建立卷积神经网络模型,该卷积神经网络模型以病人图像和已知的其他正常器官的分割结果作为输入,以分割结果作为输出;Establish a convolutional neural network model. The convolutional neural network model takes the segmentation results of patient images and other known normal organs as input, and the segmentation results as output;
    收集医学影像前采集的病人影像和由经验丰富的医生勾画好的正常器官轮廓线;并对收集的病人图像进行预处理,再将医生勾画的每一个正常器官的轮廓线转化为掩模图像;Collect patient images collected before medical imaging and outlines of normal organs drawn by experienced doctors; preprocess the collected patient images, and then convert the outlines of each normal organ drawn by doctors into mask images;
    将预处理后的病人图像作为卷积神经网络模型的输入,根据卷积神经网络模型的当前输出和收集的医生勾画的对应正常器官的掩模图像计算当前分割模型的损失函数,采用反向传播方法对卷积神经网络模型的参数进行更新;反复迭代,当达到预设的模型训练迭代次数或损失函数达到预设阈值,卷积神经网络模型训练完成,保存模型参数。The preprocessed patient image is used as the input of the convolutional neural network model, and the loss function of the current segmentation model is calculated according to the current output of the convolutional neural network model and the collected mask images of the normal organs outlined by the doctor, using back propagation The method updates the parameters of the convolutional neural network model; iterates repeatedly, and when the preset number of model training iterations is reached or the loss function reaches the preset threshold, the convolutional neural network model training is completed and the model parameters are saved.
  5. 根据权利要求4所述的医学影像中正常器官的轮廓线自动勾画方法,其特征在于,所述步骤S3中对目标正常器官轮廓线的自动勾画包括以下步骤:The method for automatically delineating the contour line of a normal organ in medical images according to claim 4, wherein the automatic delineation of the contour line of the target normal organ in the step S3 comprises the following steps:
    导入对应的已经训练好卷积神经网络模型;Import the corresponding trained convolutional neural network model;
    将对应的图像和已知的其他正常器官的分割结果输入训练好的卷积神经网络模型,得到正常器官的掩模图像;Input the corresponding image and the segmentation results of other known normal organs into the trained convolutional neural network model to obtain the mask image of the normal organ;
    根据得到的正常器官的掩模图像转化为轮廓线。According to the obtained mask image of normal organs, it is transformed into contour lines.
  6. 根据权利要求4或5所述的医学影像中正常器官的轮廓线自动勾画方法,其特征在于,所述掩模图像为二进制掩模图像。The method for automatically delineating contour lines of normal organs in medical images according to claim 4 or 5, wherein the mask image is a binary mask image.
  7. 一种电子设备,包括存储器、处理器及存储在存储器上并可在处理器上运行的计算机程序,其特征在于,所述处理器执行所述程序时实现如权利要求1至6任一项所述的医学影像中正常器官的轮廓线自动勾画方法的步骤。An electronic device, comprising a memory, a processor, and a computer program stored on the memory and running on the processor, wherein the processor executes the program as described in any one of claims 1 to 6 The steps of the method for automatically delineating the contour lines of normal organs in medical images are described.
  8. 一种非暂态计算机可读存储介质,其上存储有计算机程序,其特征在于,该计算机程序被处理器执行时实现如权利要求1至6任一项所述的医学影像中正常器官的轮廓线自动勾画方法的步骤。A non-transitory computer-readable storage medium with a computer program stored thereon, wherein the computer program is characterized in that, when the computer program is executed by a processor, the contour of a normal organ in a medical image according to any one of claims 1 to 6 is realized The steps of the automatic line drawing method.
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