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WO2024119323A1 - Tissue segmentation method for sample image, system, device and medium - Google Patents

Tissue segmentation method for sample image, system, device and medium Download PDF

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Publication number
WO2024119323A1
WO2024119323A1 PCT/CN2022/136664 CN2022136664W WO2024119323A1 WO 2024119323 A1 WO2024119323 A1 WO 2024119323A1 CN 2022136664 W CN2022136664 W CN 2022136664W WO 2024119323 A1 WO2024119323 A1 WO 2024119323A1
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image data
image
gene expression
pixel
tissue segmentation
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French (fr)
Chinese (zh)
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姜琪琛
李敏
李美
黎宇翔
张勇
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BGI Shenzhen Co Ltd
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BGI Shenzhen Co Ltd
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Priority to CN202280102092.7A priority Critical patent/CN120303691A/en
Priority to PCT/CN2022/136664 priority patent/WO2024119323A1/en
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    • GPHYSICS
    • G06COMPUTING OR CALCULATING; COUNTING
    • G06TIMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T7/00Image analysis

Definitions

  • the present invention relates to the field of image processing, and in particular to a tissue segmentation method, system, device and medium for sample images.
  • Medical image tissue segmentation is one of the core links in medical image processing, involving digital image processing, pattern recognition, computer vision, biomedicine and other background disciplines. It is a multidisciplinary technology. This technology can highlight the tissue area of interest to the user, while simplifying the computational complexity of post-processing, bringing convenience to subsequent analysis.
  • the target tissue needs to be photographed by a high-quality microscope for the tissue with a small image.
  • the image quality is poor, the segmentation effect of the target tissue in the image is poor.
  • the technical problem to be solved by the present invention is to overcome the defect in the prior art that when the image quality is poor, the segmentation effect of the target tissue in the image is poor, and to provide a tissue segmentation method, system, device and medium for a sample image.
  • tissue segmentation method for a sample image, the tissue segmentation method comprising:
  • the connected areas of the image data are marked according to the foreground pixels to obtain a target tissue segmentation image.
  • determining the image data by assigning the gene expression amount at each pixel position in the gene expression matrix to the corresponding pixel position in the sample image includes:
  • the gene expression amount at each pixel position in the gene expression matrix is assigned to the corresponding pixel position in the image matrix and all pixel positions are normalized to obtain image data of the sample image.
  • the determining the foreground pixel points of the image data by performing image processing on the image data includes:
  • the foreground pixels of the image data are determined according to the target threshold value and the pixel values of the foreground pixels are unified.
  • the tissue segmentation method further comprises:
  • the background pixels of the image data are determined according to the target threshold value and the pixel values of the background pixels are unified.
  • the tissue segmentation method further comprises:
  • the determining the foreground pixel points of the image data by performing image processing on the image data includes:
  • the foreground pixel points of the image data are determined by image processing on the image data after convolution.
  • the step of marking the connected areas of the image data according to the foreground pixels to obtain the target tissue segmentation image includes:
  • Holes are filled in the image data for which connected area marking is performed.
  • the step of marking the connected areas of the image data according to the foreground pixels to obtain the target tissue segmentation image includes:
  • the foreground pixels with an adjacency relationship are determined as the pixels of the same connected region.
  • the method further comprises:
  • the connected region is discarded.
  • the method further comprises:
  • the method includes:
  • the target tissue segmentation image is upsampled.
  • tissue segmentation system for a sample image, wherein the tissue segmentation system comprises:
  • An acquisition module used to acquire the gene expression amount of the target tissue to be segmented in the sample image and determine the gene expression matrix of the sample image, wherein the gene expression matrix arranges the gene expression amounts according to pixel positions;
  • An image data determination module used to determine image data by assigning the gene expression amount at each pixel position in the gene expression matrix to the corresponding pixel position in the sample image;
  • a foreground pixel point determination module configured to determine the foreground pixel points of the image data by performing image processing on the image data
  • the segmented image determination module is used to mark the connected areas of the image data according to the foreground pixels to obtain a target tissue segmentation image.
  • an electronic device comprising a memory, a processor, and a computer program stored in the memory and executable on the processor, wherein the processor implements the tissue segmentation method of the sample image according to the first aspect when executing the computer program.
  • a computer-readable storage medium on which a computer program is stored, wherein when the computer program is executed by a processor, the method for tissue segmentation of a sample image according to the first aspect is implemented.
  • the present invention generates a gene expression matrix by obtaining the gene expression amount of each pixel position, and converts the gene expression matrix into image data, thereby reducing the use of a microscope to shoot and correct tissue images and improving segmentation efficiency; the image data obtained by the gene expression amount is more accurate.
  • the connected area is determined by determining the foreground pixel points to reduce the interference of the pixel values of the background pixel points in the spatial information on the segmentation result, making the segmentation result more complete and reducing artifacts.
  • FIG1 is a first flow chart of a tissue segmentation method of a sample image provided by an exemplary embodiment of the present invention
  • FIG2 is a flow chart of determining image data of a method for tissue segmentation of a sample image provided by an exemplary embodiment of the present invention
  • FIG3 is a schematic diagram of image data of a tissue segmentation method of a sample image provided by an exemplary embodiment of the present invention.
  • FIG4 is a schematic diagram of a 2D convolution of a tissue segmentation method for a sample image provided by an exemplary embodiment of the present invention
  • FIG5 is a schematic diagram of low-level features of a tissue segmentation method for a sample image provided by an exemplary embodiment of the present invention.
  • FIG6 is a schematic diagram of binarization of a tissue segmentation method of a sample image provided by an exemplary embodiment of the present invention.
  • FIG7 is a schematic diagram of a morphological closing operation of a tissue segmentation method for a sample image provided by an exemplary embodiment of the present invention.
  • FIG8 is a schematic diagram of a morphological opening operation of a tissue segmentation method for a sample image provided by an exemplary embodiment of the present invention.
  • FIG9 is a schematic diagram of connected regions of a tissue segmentation method for a sample image provided by an exemplary embodiment of the present invention.
  • FIG10 is a schematic diagram of hole filling in a tissue segmentation method of a sample image provided by an exemplary embodiment of the present invention.
  • FIG11 is a module diagram of a tissue segmentation system for a sample image provided by an exemplary embodiment of the present invention.
  • FIG. 12 is a structural diagram of an electronic device provided by an exemplary embodiment of the present invention.
  • the embodiment of the present invention provides a tissue segmentation method for a sample image, and the tissue segmentation method includes the following types: a region-based segmentation method, a threshold-based segmentation method, a clustering-based segmentation method, and a manual segmentation method.
  • the region-based segmentation method relies on the intensity uniformity of the image to detect the target boundary of the object region, and this method is likely to cause over-segmentation of the image; the threshold-based segmentation method compares the intensity value with one or more thresholds to segment the object region, and this method is likely to cause more artifacts in the segmentation of the object region, and the threshold needs to be determined through multiple experiments; the clustering-based segmentation method divides pixels into groups or clusters by using similarity metrics such as distance, connectivity, and intensity. This method does not consider spatial information and is sensitive to noise and grayscale unevenness.
  • FIG1 is a tissue segmentation method of a sample image provided by an exemplary embodiment of the present invention.
  • the tissue segmentation method includes:
  • the sample image may preferably be a medical image, which is not specifically limited in this embodiment and may be selected according to actual application scenarios.
  • target tissue may include but is not limited to any one or more of sample tissue, biological tissue, muscle tissue, bone tissue, and cell tissue.
  • Gene expression matrix characterizes the expression of genes in different positions (row and column positions of corresponding gene expression matrix).
  • the data composition of each gene expression amount includes gene identifier, gene coordinates and gene expression amount, characterizing the expression amount of genes in a position.
  • the gene expression amount of cell tissue can be determined by carrying out transcription processing to the DNA of cell tissue.
  • gene expression amount is generally in utf-8 format.
  • the gene expression amount at each pixel position in the sample image is obtained, and the gene expression amount is arranged according to the row coordinates and column coordinates of the pixel position to obtain a gene expression matrix.
  • the gene expression matrix is consistent with the size of the sample image. When the gene expression amount at each pixel position is 0, it indicates that there is no gene of the target tissue at the pixel position.
  • the gene expression amount at each pixel position in the gene expression matrix can represent the gene expression amount of one or more genes. If the size of the gene expression matrix is inconsistent with that of the sample image, the two images or one of the images can be scaled.
  • step S102 specifically includes:
  • the gene expression amount of each pixel position in the gene expression matrix is assigned to the corresponding pixel position in the image matrix and all pixel positions are normalized to obtain image data of the sample image.
  • the gene expression amount at each pixel position in the gene expression matrix is stored in the dictionary with the row coordinates and column coordinates of each pixel position as the key and the gene expression amount as the value.
  • the image matrix after assignment is normalized so that the pixel value of each pixel position is within the interval [0,255], and image data that is more accurate relative to the sample image is obtained, and the impact on subsequent tissue segmentation images is reduced.
  • the image data is preferably in TIFF format, and can also be in JPG format, etc. It is not limited to a specific form of expression and can be selected according to actual conditions.
  • a gene expression matrix is generated by obtaining the gene expression amount at each pixel position, and the gene expression matrix is converted into image data, thereby reducing the process of repeatedly photographing and correcting tissue images through the original microscope, improving the segmentation efficiency, and making the image data more accurate in displaying the target tissue compared to the initial sample image, which can improve the accuracy of subsequent determination of the target tissue, thereby improving the accuracy of target tissue segmentation.
  • the tissue segmentation method before step S103, the tissue segmentation method further includes:
  • the image data is convolved to extract low-level features of the image data.
  • the convolution method preferably uses 2D convolution, and convolution methods such as dilated convolution and depthwise separable convolution can also be used to improve the computation accuracy and expand the perception field of view.
  • the image data after convolution is shown in FIG5 .
  • the foreground pixels of the image data are determined by image processing on the convolved image data.
  • step S103 specifically includes:
  • Each pixel value is used as a pixel threshold to divide the foreground pixel and the background pixel from the image data.
  • the pixel value is in the interval [0, 255]. Taking the pixel value T 0 as an example, the pixel with a pixel value less than T 0 is the foreground pixel, and the pixel with a pixel value greater than T 0 is the background pixel.
  • the variance between the foreground pixel and the background pixel under each pixel threshold condition is determined according to the foreground average pixel value and the background average pixel value.
  • the foreground pixels of the image data are determined according to the target threshold and the pixel values of the foreground pixels are unified to 255, and the pixel values of the background pixels are unified to 0, so as to obtain the binarized image data, as shown in FIG6 .
  • foreground pixels and background pixels may be converted to each other by image inversion.
  • the connected region refers to an image region composed of foreground pixels having the same pixel value and adjacent positions in the image data, that is, a segmented region of the target tissue.
  • step S104 specifically includes:
  • the foreground pixels with an adjacency relationship are determined as the pixels of the same connected region.
  • connected region analysis methods such as the two-pass method and the seed-filling method can be used.
  • a two-pass method is preferably used. Specifically, during the first scanning process, all pixel points of the image data are traversed from left to right and from top to bottom starting from the first pixel point in the upper left corner of the image data, and a label is assigned to each foreground pixel point. If the pixel point adjacent to the upper or left side of the foreground pixel point currently being scanned is 0, the label value of the foreground pixel point currently being scanned is increased by one.
  • the label value of the foreground pixel point adjacent to the upper or left side is assigned to the foreground pixel point currently being scanned. Since the foreground pixels located in the same connected area may have one or more labels with different values during the first scanning process, it is necessary to merge the labels with different values. During the second scanning process, the label values of the foreground pixels with an adjacent relationship are unified, that is, assigned the same label, where the label is the minimum value of the label in the same connected area.
  • the starting position of the scan in the two-pass method is not limited to a specific position.
  • the upper left position in this embodiment is only used for example.
  • the positions of adjacent pixels are also determined according to the scanning direction, and are not specifically limited to the top or left.
  • the connected region is discarded.
  • the pixel values of all connected areas are set to 255 to obtain the image data after the connected areas are marked.
  • step S104 specifically includes:
  • a morphological opening operation is performed on the image data for connected region marking, that is, the pixel points of all connected regions are traversed through the structural element, the pixel points of the connected regions are expanded, and then the expanded connected regions are eroded to smooth the edges of the connected regions of the image data;
  • the image data for connected region labeling is subjected to morphological closing operation, that is, all pixels of the connected regions are traversed through the structural element, the pixels of the connected regions are corroded, and then the corroded connected regions are expanded to eliminate small holes in the connected regions of the image data.
  • morphological closing operation that is, all pixels of the connected regions are traversed through the structural element, the pixels of the connected regions are corroded, and then the corroded connected regions are expanded to eliminate small holes in the connected regions of the image data.
  • step S104 specifically includes:
  • Holes are filled in the image data for connected area marking. Specifically, the image data is copied, and the edges of the connected areas of the copied image data are expanded to prevent incomplete hole filling.
  • the flood filling algorithm is used for filling. The principle is to fill from the first pixel point of the connected area until all the pixels in the connected area are filled with the same pixel value.
  • the copied image data and the image data before copying are image ORed to obtain the image data after hole filling, as shown in Figure 10.
  • the tissue segmentation method further includes: downsampling the image data and upsampling the target tissue segmentation image.
  • the downsampling step is performed after step S102, and an interpolation algorithm can be used, preferably a nearest neighbor interpolation method, in order to reduce the feature dimension of the image data, facilitate subsequent operations, and reduce computing power.
  • Upsampling is performed after step S104, and the interpolation algorithm of upsampling corresponds to the interpolation algorithm of downsampling, in order to restore the target tissue segmentation image to the same size as the gene expression matrix.
  • tissue segmentation system for a sample image.
  • the tissue segmentation system includes:
  • An acquisition module 21 is used to acquire a gene expression matrix of a target tissue, wherein the gene expression matrix includes gene expression amounts of the target tissue arranged according to pixel positions;
  • An image data determination module 22 determines image data by assigning the gene expression amount at each pixel position in the gene expression matrix to the corresponding pixel position in the sample image;
  • a foreground pixel point determination module 23 configured to determine foreground pixel points of the image data by performing image processing on the image data;
  • the segmented image determination module 24 is used to mark the connected areas of the image data according to the foreground pixels to obtain the target tissue segmentation image.
  • the relevant parts can refer to the partial description of the method embodiment.
  • the system embodiment described above is only schematic, in which 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 they may be distributed on multiple network units. Some or all of the modules can be selected according to actual needs to achieve the purpose of the scheme of the present invention. Ordinary technicians in this field can understand and implement it without paying creative work.
  • FIG12 shows a block diagram of an exemplary electronic device 30 suitable for implementing the embodiment of the present invention.
  • the electronic device 30 shown in FIG12 is only an example and should not limit the functions and scope of use of the embodiment of the present invention.
  • the electronic device 30 may be in the form of a general-purpose computing device, for example, it may be a server device.
  • the components of the electronic device 30 may include, but are not limited to: at least one processor 31, at least one memory 32, and a bus 33 connecting different system components (including the memory 32 and the processor 31).
  • the bus 33 includes a data bus, an address bus, and a control bus.
  • the memory 32 may include a volatile memory, such as a random access memory (RAM) 321 and/or a cache memory 322 , and may further include a read-only memory (ROM) 323 .
  • RAM random access memory
  • ROM read-only memory
  • the memory 32 may also include a program tool 325 (or utility) having a set (at least one) of program modules 324, such program modules 324 including but not limited to: an operating system, one or more application programs, other program modules and program data, each of which or some combination may include an implementation of a network environment.
  • program tool 325 or utility
  • program modules 324 including but not limited to: an operating system, one or more application programs, other program modules and program data, each of which or some combination may include an implementation of a network environment.
  • the processor 31 executes various functional applications and data processing by running the computer program stored in the memory 32, such as the method provided in any of the above embodiments.
  • the electronic device 30 may also communicate with one or more external devices 34. Such communication may be performed via an input/output (I/O) interface 35.
  • the model-generated electronic device 30 may also communicate with one or more networks (e.g., a local area network (LAN), a wide area network (WAN), and/or a public network, such as the Internet) via a network adapter 37. As shown, the network adapter 37 communicates with other modules of the model-generated electronic device 30 via a bus 33.
  • networks e.g., a local area network (LAN), a wide area network (WAN), and/or a public network, such as the Internet
  • model-generated electronic device 30 may be used in conjunction with the model-generated electronic device 30, including but not limited to: microcode, device drivers, redundant processors, external disk drive arrays, RAID (disk array) systems, tape drives, and data backup storage systems, etc.
  • An embodiment of the present invention further provides a computer-readable storage medium on which a computer program is stored.
  • the program is executed by a processor, the method provided by any of the above embodiments is implemented.
  • the readable storage medium may include but is not limited to: a portable disk, a hard disk, a random access memory, a read-only memory, an erasable programmable read-only memory, an optical storage device, a magnetic storage device or any suitable combination of the above.
  • the embodiment of the present invention may also be implemented in the form of a program product, which includes program code.
  • program product When the program product is run on a terminal device, the program code is used to enable the terminal device to execute a method for implementing any of the above embodiments.
  • the program code for executing the present invention can be written in any combination of one or more programming languages, and the program code can be executed completely on the user device, partially on the user device, as an independent software package, partially on the user device and partially on a remote device, or completely on the remote device.

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Abstract

Disclosed in the present invention are a tissue segmentation method for a sample image, a system, a device and a medium. The tissue segmentation method comprises: acquiring the gene expression level of a target tissue to be segmented in a sample image, and determining a gene expression matrix of the sample image, the gene expression matrix arranging the gene expression level according to pixel positions; assigning the gene expression level of each pixel position in the gene expression matrix to the corresponding pixel position in the sample image so as to determine image data; performing image processing on the image data to determine foreground pixel points of the image data; and, according to the foreground pixel points, marking the connected region of the image data so as to obtain a target tissue segmented image. By determining foreground pixel points to determine the connected region, the interference of the pixel values of background pixel points on a segmentation result is reduced, thereby enabling the segmentation result to be more complete and reducing artifacts.

Description

样本图像的组织分割方法、系统、设备及介质Method, system, device and medium for tissue segmentation of sample images 技术领域Technical Field

本发明涉及图像处理领域,尤其涉及一种样本图像的组织分割方法、系统、设备及介质。The present invention relates to the field of image processing, and in particular to a tissue segmentation method, system, device and medium for sample images.

背景技术Background technique

医学图像的组织分割是医学图像处理中的核心环节之一,涉及到数字图像处理、模式识别、计算机视觉、生物医学等背景学科,是一项多学科交叉的技术。该项技术能够突出用户感兴趣的组织区域,同时简化后期处理的运算复杂度,为后续分析带来便利。Medical image tissue segmentation is one of the core links in medical image processing, involving digital image processing, pattern recognition, computer vision, biomedicine and other background disciplines. It is a multidisciplinary technology. This technology can highlight the tissue area of interest to the user, while simplifying the computational complexity of post-processing, bringing convenience to subsequent analysis.

现有技术中的组织分割方法对于目标组织进行分割时,对于成像较小的组织需要通过高质量显微镜对目标组织进行拍摄。而当图像的质量较差时,对于图像中目标组织的分割效果较差。When the tissue segmentation method in the prior art segments the target tissue, the target tissue needs to be photographed by a high-quality microscope for the tissue with a small image. When the image quality is poor, the segmentation effect of the target tissue in the image is poor.

发明内容Summary of the invention

本发明要解决的技术问题是为了克服现有技术中当图像的质量较差时,对于图像中目标组织的分割效果较差的缺陷,提供一种样本图像的组织分割方法、系统、设备及介质。The technical problem to be solved by the present invention is to overcome the defect in the prior art that when the image quality is poor, the segmentation effect of the target tissue in the image is poor, and to provide a tissue segmentation method, system, device and medium for a sample image.

本发明是通过下述技术方案来解决上述技术问题:The present invention solves the above technical problems through the following technical solutions:

第一方面,提供一种样本图像的组织分割方法,所述组织分割方法包括:In a first aspect, a tissue segmentation method for a sample image is provided, the tissue segmentation method comprising:

获取样本图像中待分割的目标组织的基因表达量并确定所述样本图像的基因表达矩阵,所述基因表达矩阵按照像素位置对所述基因表达量进行排列;Acquiring gene expression amounts of a target tissue to be segmented in a sample image and determining a gene expression matrix of the sample image, wherein the gene expression matrix arranges the gene expression amounts according to pixel positions;

通过将所述基因表达矩阵中每一像素位置的基因表达量赋值于样本图像中对应的像素位置确定图像数据;Determine image data by assigning the gene expression amount at each pixel position in the gene expression matrix to the corresponding pixel position in the sample image;

通过对所述图像数据进行图像处理以确定所述图像数据的前景像素点;Determine foreground pixels of the image data by performing image processing on the image data;

根据所述前景像素点对所述图像数据的连通区域进行标记得到目标组织分割图像。The connected areas of the image data are marked according to the foreground pixels to obtain a target tissue segmentation image.

可选地,所述通过将所述基因表达矩阵中每一像素位置的基因表达量赋值于样本图像中对应的像素位置确定图像数据,包括:Optionally, determining the image data by assigning the gene expression amount at each pixel position in the gene expression matrix to the corresponding pixel position in the sample image includes:

确定与所述基因表达矩阵相同大小的图像矩阵;Determining an image matrix of the same size as the gene expression matrix;

将所述基因表达矩阵中每一像素位置的基因表达量赋值于图像矩阵中对应的像素位置并对所有像素位置进行归一化处理得到样本图像的图像数 据。The gene expression amount at each pixel position in the gene expression matrix is assigned to the corresponding pixel position in the image matrix and all pixel positions are normalized to obtain image data of the sample image.

可选地,所述通过对所述图像数据进行图像处理以确定所述图像数据的前景像素点,包括:Optionally, the determining the foreground pixel points of the image data by performing image processing on the image data includes:

依次将每一像素值作为像素阈值从所述图像数据中划分出前景像素点和背景像素点;Sequentially using each pixel value as a pixel threshold to divide foreground pixels and background pixels from the image data;

计算每一所述像素阈值条件下所述前景像素点的前景平均像素值及所述背景像素点的背景平均像素值,并根据所述前景平均像素值及所述背景平均像素值确定每一所述像素阈条件下所述前景像素点与背景像素点的方差;Calculating the foreground average pixel value of the foreground pixel point and the background average pixel value of the background pixel point under each of the pixel threshold conditions, and determining the variance of the foreground pixel point and the background pixel point under each of the pixel threshold conditions according to the foreground average pixel value and the background average pixel value;

遍历所有像素阈值,将所述方差为最大时对应的像素阈值确定为目标阈值;Traversing all pixel thresholds, and determining the pixel threshold corresponding to the maximum variance as the target threshold;

根据所述目标阈值确定所述图像数据的前景像素点并对所述前景像素点的像素值进行统一。The foreground pixels of the image data are determined according to the target threshold value and the pixel values of the foreground pixels are unified.

可选地,所述组织分割方法还包括:Optionally, the tissue segmentation method further comprises:

根据所述目标阈值确定所述图像数据的背景像素点并对所述背景像素点的像素值进行统一。The background pixels of the image data are determined according to the target threshold value and the pixel values of the background pixels are unified.

可选地,所述组织分割方法还包括:Optionally, the tissue segmentation method further comprises:

对所述图像数据进行卷积,以提取所述图像数据的低级特征;Performing convolution on the image data to extract low-level features of the image data;

所述通过对所述图像数据进行图像处理以确定所述图像数据的前景像素点,包括:The determining the foreground pixel points of the image data by performing image processing on the image data includes:

通过对进行卷积后的所述图像数据图像处理以确定所述图像数据的前景像素点。The foreground pixel points of the image data are determined by image processing on the image data after convolution.

可选地,所述根据所述前景像素点对所述图像数据的连通区域进行标记得到目标组织分割图像,包括:Optionally, the step of marking the connected areas of the image data according to the foreground pixels to obtain the target tissue segmentation image includes:

对进行连通区域标记的所述图像数据进行形态学开运算,以平滑所述图像数据的连通区域的边缘;Performing a morphological opening operation on the image data for connected region marking to smooth the edges of the connected regions of the image data;

和/或,and / or,

对进行连通区域标记的所述图像数据进行形态学闭运算,以消除所述图像数据的连通区域内的细小孔洞;Performing a morphological closing operation on the image data for connected region marking to eliminate small holes in the connected regions of the image data;

和/或,and / or,

对进行连通区域标记的所述图像数据进行孔洞填充。Holes are filled in the image data for which connected area marking is performed.

可选地,所述根据所述前景像素点对所述图像数据的连通区域进行标记得到目标组织分割图像,包括:Optionally, the step of marking the connected areas of the image data according to the foreground pixels to obtain the target tissue segmentation image includes:

将具有邻接关系的前景像素点确定为同一个连通区域的像素点。The foreground pixels with an adjacency relationship are determined as the pixels of the same connected region.

可选地,所述将具有邻接关系的前景像素点确定为同一个连通区域的像 素点之后,包括:Optionally, after determining the foreground pixels having an adjacency relationship as pixels of the same connected region, the method further comprises:

分别计算每一个所述连通区域的面积,并计算所有所述连通区域的标准差及均值;Calculate the area of each connected region respectively, and calculate the standard deviation and mean of all connected regions;

判断每一所述连通区域的面积是否位于标准差及均值之间;Determine whether the area of each of the connected regions is between the standard deviation and the mean;

若是,则保留所述连通区域;If so, retain the connected area;

若否,则舍弃所述连通区域。If not, the connected region is discarded.

可选地,所述通过将所述基因表达矩阵中每一像素位置的基因表达量赋值于样本图像中对应的像素位置确定图像数据之后,包括:Optionally, after determining the image data by assigning the gene expression amount at each pixel position in the gene expression matrix to the corresponding pixel position in the sample image, the method further comprises:

对所述图像数据进行下采样;downsampling the image data;

所述根据所述前景像素点对所述图像数据的连通区域进行标记得到目标组织分割图像之后,包括:After the connected areas of the image data are marked according to the foreground pixels to obtain the target tissue segmentation image, the method includes:

对所述目标组织分割图像进行上采样。The target tissue segmentation image is upsampled.

第二方面,提供一种样本图像的组织分割系统,其特征在于,所述组织分割系统包括:In a second aspect, a tissue segmentation system for a sample image is provided, wherein the tissue segmentation system comprises:

获取模块,用于获取样本图像中待分割的目标组织的基因表达量并确定所述样本图像的基因表达矩阵,所述基因表达矩阵按照像素位置对所述基因表达量进行排列;An acquisition module, used to acquire the gene expression amount of the target tissue to be segmented in the sample image and determine the gene expression matrix of the sample image, wherein the gene expression matrix arranges the gene expression amounts according to pixel positions;

图像数据确定模块,用于通过将所述基因表达矩阵中每一像素位置的基因表达量赋值于样本图像中对应的像素位置确定图像数据;An image data determination module, used to determine image data by assigning the gene expression amount at each pixel position in the gene expression matrix to the corresponding pixel position in the sample image;

前景像素点确定模块,用于通过对所述图像数据进行图像处理以确定所述图像数据的前景像素点;a foreground pixel point determination module, configured to determine the foreground pixel points of the image data by performing image processing on the image data;

分割图像确定模块,用于根据所述前景像素点对所述图像数据的连通区域进行标记得到目标组织分割图像。The segmented image determination module is used to mark the connected areas of the image data according to the foreground pixels to obtain a target tissue segmentation image.

第三方面,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,其特征在于,所述处理器执行所述计算机程序时实现第一方面所述的样本图像的组织分割方法。According to a third aspect, an electronic device is provided, comprising a memory, a processor, and a computer program stored in the memory and executable on the processor, wherein the processor implements the tissue segmentation method of the sample image according to the first aspect when executing the computer program.

第四方面,提供一种计算机可读存储介质,其上存储有计算机程序,其特征在于,所述计算机程序被处理器执行时实现第一方面所述的样本图像的组织分割方法。According to a fourth aspect, a computer-readable storage medium is provided, on which a computer program is stored, wherein when the computer program is executed by a processor, the method for tissue segmentation of a sample image according to the first aspect is implemented.

本发明通过获取确定每一像素位置的基因表达量生成基因表达矩阵,并将基因表达矩阵转换为图像数据,减少采用显微镜对组织图像进行拍摄和校正,提高分割效率;通过基因表达量所得到的图像数据更为准确。通过确定前景像素点来确定连通区域,以减少空间信息中背景像素点的像素值对分割结果的干扰,使分割结果更为完整,减少伪影。The present invention generates a gene expression matrix by obtaining the gene expression amount of each pixel position, and converts the gene expression matrix into image data, thereby reducing the use of a microscope to shoot and correct tissue images and improving segmentation efficiency; the image data obtained by the gene expression amount is more accurate. The connected area is determined by determining the foreground pixel points to reduce the interference of the pixel values of the background pixel points in the spatial information on the segmentation result, making the segmentation result more complete and reducing artifacts.

附图说明BRIEF DESCRIPTION OF THE DRAWINGS

图1为本发明一示例性实施例提供的一种样本图像的组织分割方法的第一流程图;FIG1 is a first flow chart of a tissue segmentation method of a sample image provided by an exemplary embodiment of the present invention;

图2为本发明一示例性实施例提供的一种样本图像的组织分割方法的确定图像数据的流程图;FIG2 is a flow chart of determining image data of a method for tissue segmentation of a sample image provided by an exemplary embodiment of the present invention;

图3为本发明一示例性实施例提供的一种样本图像的组织分割方法的图像数据示意图;FIG3 is a schematic diagram of image data of a tissue segmentation method of a sample image provided by an exemplary embodiment of the present invention;

图4为本发明一示例性实施例提供的一种样本图像的组织分割方法的2d卷积示意图;FIG4 is a schematic diagram of a 2D convolution of a tissue segmentation method for a sample image provided by an exemplary embodiment of the present invention;

图5为本发明一示例性实施例提供的一种样本图像的组织分割方法的低级特征示意图;FIG5 is a schematic diagram of low-level features of a tissue segmentation method for a sample image provided by an exemplary embodiment of the present invention;

图6为本发明一示例性实施例提供的一种样本图像的组织分割方法的二值化示意图;FIG6 is a schematic diagram of binarization of a tissue segmentation method of a sample image provided by an exemplary embodiment of the present invention;

图7为本发明一示例性实施例提供的一种样本图像的组织分割方法的形态学闭运算示意图;FIG7 is a schematic diagram of a morphological closing operation of a tissue segmentation method for a sample image provided by an exemplary embodiment of the present invention;

图8为本发明一示例性实施例提供的一种样本图像的组织分割方法的形态学开运算示意图;FIG8 is a schematic diagram of a morphological opening operation of a tissue segmentation method for a sample image provided by an exemplary embodiment of the present invention;

图9为本发明一示例性实施例提供的一种样本图像的组织分割方法的连通区域示意图;FIG9 is a schematic diagram of connected regions of a tissue segmentation method for a sample image provided by an exemplary embodiment of the present invention;

图10为本发明一示例性实施例提供的一种样本图像的组织分割方法的孔洞填充示意图;FIG10 is a schematic diagram of hole filling in a tissue segmentation method of a sample image provided by an exemplary embodiment of the present invention;

图11为本发明一示例性实施例提供的一种样本图像的组织分割系统的模块图;FIG11 is a module diagram of a tissue segmentation system for a sample image provided by an exemplary embodiment of the present invention;

图12为本发明一示例性实施例提供的一种电子设备的结构图。FIG. 12 is a structural diagram of an electronic device provided by an exemplary embodiment of the present invention.

具体实施方式Detailed ways

下面通过示例性实施例的方式进一步说明本发明,但并不因此将本发明限制在的实施例范围之中。The present invention is further described below by way of exemplary embodiments, but the present invention is not limited to the scope of the embodiments.

本发明实施例提供一种样本图像的组织分割方法,组织分割方法包括以下几种类型:基于区域的分割方法、基于阈值的分割方法、基于聚类的分割方法、人工分割方法。基于区域的分割方法依赖于图像的强度均匀性来检测对象区域的目标边界,该方法容易造成图像的过度分割;基于阈值的分割方法通过将强度值与一个或多个阈值进行比对从而将对象区域进行分割,该方 法容易使得对象区域的分割存在较多伪影,且阈值需要通过多次实验进行确定;基于聚类的分割方法通过将距离、连通性、强度等相似性度量将像素分成组或簇,该方法没有考虑空间信息,对噪声和灰度不均匀敏感。The embodiment of the present invention provides a tissue segmentation method for a sample image, and the tissue segmentation method includes the following types: a region-based segmentation method, a threshold-based segmentation method, a clustering-based segmentation method, and a manual segmentation method. The region-based segmentation method relies on the intensity uniformity of the image to detect the target boundary of the object region, and this method is likely to cause over-segmentation of the image; the threshold-based segmentation method compares the intensity value with one or more thresholds to segment the object region, and this method is likely to cause more artifacts in the segmentation of the object region, and the threshold needs to be determined through multiple experiments; the clustering-based segmentation method divides pixels into groups or clusters by using similarity metrics such as distance, connectivity, and intensity. This method does not consider spatial information and is sensitive to noise and grayscale unevenness.

图1为本发明一示例性实施例提供的一种样本图像的组织分割方法,参见图1,组织分割方法包括:FIG1 is a tissue segmentation method of a sample image provided by an exemplary embodiment of the present invention. Referring to FIG1 , the tissue segmentation method includes:

S101、获取样本图像中待分割的目标组织的基因表达量并确定样本图像的基因表达矩阵,基因表达矩阵按照像素位置对基因表达量进行排列。S101, obtaining the gene expression amount of the target tissue to be segmented in the sample image and determining the gene expression matrix of the sample image, wherein the gene expression matrix arranges the gene expression amounts according to pixel positions.

在一个实施例中,样本图像优选可以为医学图像,本实施例中不做具体限制,可根据实际应用场景进行选择。In one embodiment, the sample image may preferably be a medical image, which is not specifically limited in this embodiment and may be selected according to actual application scenarios.

在一个实施例中,目标组织可以包括但不限于样本组织、生物组织、肌肉组织、骨骼组织、细胞组织中任一项或多项。基因表达矩阵表征基因在不同位置(对应基因表达矩阵的行列位置)的表达。每一条基因表达量的数据组成包括基因标识符、基因坐标和基因表达量,表征基因在一个位置的表达量。以细胞组织为例,可以通过对细胞组织的DNA进行转录处理以确定细胞组织的基因表达量。此外,基因表达量通常为utf-8格式。In one embodiment, target tissue may include but is not limited to any one or more of sample tissue, biological tissue, muscle tissue, bone tissue, and cell tissue. Gene expression matrix characterizes the expression of genes in different positions (row and column positions of corresponding gene expression matrix). The data composition of each gene expression amount includes gene identifier, gene coordinates and gene expression amount, characterizing the expression amount of genes in a position. Taking cell tissue as an example, the gene expression amount of cell tissue can be determined by carrying out transcription processing to the DNA of cell tissue. In addition, gene expression amount is generally in utf-8 format.

本实施中,通过获取样本图像中每一个像素位置的基因表达量,并按照像素位置的行坐标、列坐标对基因表达量进行排列以得到基因表达矩阵,基因表达矩阵与样本图像的大小一致,当每个像素位置的基因表达量为0时表征在该像素位置不存在目标组织的基因。基因表达矩阵中每个像素位置的基因表达量可以表征一个或多个基因的基因表达量。若基因表达矩阵与样本图像的大小不一致,可以对两个图像或其中的一个图像进行缩放。In this embodiment, the gene expression amount at each pixel position in the sample image is obtained, and the gene expression amount is arranged according to the row coordinates and column coordinates of the pixel position to obtain a gene expression matrix. The gene expression matrix is consistent with the size of the sample image. When the gene expression amount at each pixel position is 0, it indicates that there is no gene of the target tissue at the pixel position. The gene expression amount at each pixel position in the gene expression matrix can represent the gene expression amount of one or more genes. If the size of the gene expression matrix is inconsistent with that of the sample image, the two images or one of the images can be scaled.

S102、通过将所述基因表达矩阵中每一像素位置的基因表达量赋值于样本图像中对应的像素位置确定图像数据。S102, determining image data by assigning the gene expression amount at each pixel position in the gene expression matrix to the corresponding pixel position in the sample image.

在一个实施例中,步骤S102具体包括:In one embodiment, step S102 specifically includes:

确定与所述基因表达矩阵相同大小的图像矩阵;Determining an image matrix of the same size as the gene expression matrix;

将所述基因表达矩阵中每一像素位置的基因表达量赋值于图像矩阵中对应的像素位置并对所有像素位置进行归一化处理得到样本图像的图像数据。The gene expression amount of each pixel position in the gene expression matrix is assigned to the corresponding pixel position in the image matrix and all pixel positions are normalized to obtain image data of the sample image.

参见图2,将基因表达矩阵中每一像素位置的基因表达量以每个像素位置的行坐标与列坐标为键、基因表达量为值存储至字典中。创建一个与基因表达矩阵相同大小的全0图像矩阵,并按照字典中存储的基因表达量的行坐标与列坐标的位置赋值于图像矩阵中的相同位置,即图像矩阵中相同像素位置的基因表达量与基因表达矩阵中相同像素位置的基因表达量相同。对赋值后的图像矩阵进行归一化,使每一像素位置的像素值在[0,255]区间内,得到 相对样本图像更为准确的图像数据,并减少对于后续组织分割图像的影响。图像数据参见图3所示,图像数据的格式优选为TIFF格式,也可以为JPG格式等,并不局限于某一具体表现形式,可根据实际情况进行选择。Referring to FIG. 2, the gene expression amount at each pixel position in the gene expression matrix is stored in the dictionary with the row coordinates and column coordinates of each pixel position as the key and the gene expression amount as the value. Create an all-0 image matrix of the same size as the gene expression matrix, and assign the row coordinates and column coordinates of the gene expression amount stored in the dictionary to the same position in the image matrix, that is, the gene expression amount at the same pixel position in the image matrix is the same as the gene expression amount at the same pixel position in the gene expression matrix. The image matrix after assignment is normalized so that the pixel value of each pixel position is within the interval [0,255], and image data that is more accurate relative to the sample image is obtained, and the impact on subsequent tissue segmentation images is reduced. As shown in FIG. 3, the image data is preferably in TIFF format, and can also be in JPG format, etc. It is not limited to a specific form of expression and can be selected according to actual conditions.

在本实施例中,通过获取确定每一像素位置的基因表达量生成基因表达矩阵,并将基因表达矩阵转换为图像数据,减少通过原始显微镜对组织图像进行反复拍摄和校正的过程,提高分割效率,并使得图像数据相较于初始的样本图像对于目标组织的展示更为准确,能够提升后续对于目标组织确定的准确度,进而提升目标组织分割的准确度。In this embodiment, a gene expression matrix is generated by obtaining the gene expression amount at each pixel position, and the gene expression matrix is converted into image data, thereby reducing the process of repeatedly photographing and correcting tissue images through the original microscope, improving the segmentation efficiency, and making the image data more accurate in displaying the target tissue compared to the initial sample image, which can improve the accuracy of subsequent determination of the target tissue, thereby improving the accuracy of target tissue segmentation.

S103、通过对图像数据进行图像处理以确定图像数据的前景像素点;S103, determining foreground pixels of the image data by performing image processing on the image data;

在一个实施例中,步骤S103之前,组织分割方法还包括:In one embodiment, before step S103, the tissue segmentation method further includes:

参见图4,对图像数据进行卷积,以提取图像数据的低级特征。其中,卷积方法优选采用2d卷积,也可以采用空洞卷积、深度可分离卷积等卷积方式来提升计算虚度和扩大感受视野,卷积后的图像数据参见图5所示。Referring to FIG4 , the image data is convolved to extract low-level features of the image data. The convolution method preferably uses 2D convolution, and convolution methods such as dilated convolution and depthwise separable convolution can also be used to improve the computation accuracy and expand the perception field of view. The image data after convolution is shown in FIG5 .

通过对进行卷积后的图像数据图像处理以确定图像数据的前景像素点。The foreground pixels of the image data are determined by image processing on the convolved image data.

在一个实施例中,步骤S103具体包括:In one embodiment, step S103 specifically includes:

依次将每一像素值作为像素阈值从图像数据中划分出前景像素点和背景像素点,像素值为[0,255]区间。以像素值T 0为例,像素值小于T 0的像素点为前景像素点,像素值大于T 0的像素点为背景像素点。 Each pixel value is used as a pixel threshold to divide the foreground pixel and the background pixel from the image data. The pixel value is in the interval [0, 255]. Taking the pixel value T 0 as an example, the pixel with a pixel value less than T 0 is the foreground pixel, and the pixel with a pixel value greater than T 0 is the background pixel.

计算每一像素阈值条件下前景像素点的前景平均像素值及背景像素点的背景平均像素值。Calculate the foreground average pixel value of the foreground pixels and the background average pixel value of the background pixels under each pixel threshold condition.

根据前景平均像素值及背景平均像素值确定每一像素阈值条件下前景像素点与背景像素点的方差。The variance between the foreground pixel and the background pixel under each pixel threshold condition is determined according to the foreground average pixel value and the background average pixel value.

遍历所有像素阈值,将方差为最大时对应的像素阈值确定为目标阈值;Traverse all pixel thresholds and determine the pixel threshold corresponding to the maximum variance as the target threshold;

根据目标阈值确定图像数据的前景像素点并对前景像素点的像素值统一为255,将背景像素点的像素值进行统一为0,得到二值化后的图像数据,参见图6所示。The foreground pixels of the image data are determined according to the target threshold and the pixel values of the foreground pixels are unified to 255, and the pixel values of the background pixels are unified to 0, so as to obtain the binarized image data, as shown in FIG6 .

可选地,前景像素点和背景像素点可以通过图像反转相互转换。Optionally, foreground pixels and background pixels may be converted to each other by image inversion.

S104、根据前景像素点对图像数据的连通区域进行标记得到目标组织分割图像。S104, marking the connected areas of the image data according to the foreground pixels to obtain a target tissue segmentation image.

在一个实施例中,连通区域指图像数据中具有相同像素值且位置相邻的前景像素点组成的图像区域,即目标组织的分割区域。In one embodiment, the connected region refers to an image region composed of foreground pixels having the same pixel value and adjacent positions in the image data, that is, a segmented region of the target tissue.

在一个实施例中,步骤S104具体包括:In one embodiment, step S104 specifically includes:

将具有邻接关系的前景像素点确定为同一个连通区域的像素点。The foreground pixels with an adjacency relationship are determined as the pixels of the same connected region.

其中,可以采用two-pass(两遍扫描)法、seed-filling(种子填色)法等 连通区域分析法。Among them, connected region analysis methods such as the two-pass method and the seed-filling method can be used.

本实施例中优选采用two-pass法,具体地,第一次扫描过程中,从图像数据的左上方的第一个像素点开始从左向右、从上到下遍历图像数据的所有像素点,为每一个前景像素点赋予一个label(标签),若当前扫描的前景像素点的上方或者左方所邻接的像素点为0,则当前扫描的前景像素点的label值加一,若当前扫描的前景像素点的上方或者左方所邻接的像素点不为0,即存在前景像素点与当前扫描的前景像素点邻接,则将上方或左方所邻接的前景像素点的label值赋值于当前扫描的前景像素点;由于在第一次扫描过程中可能会将位于统一连通区域的前景像素点具有一个或多个不同值的label,因此需要将不同值的label进行合并,第二次扫描过程中,将具有邻接关系的前景像素点的label值进行统一,即赋予一个相同的label,其中label为同一连通区域内label的最小值。需要说明的是,two-pass法中扫描的起始位置并不限制为某一具体位置,本实施例中的左上方仅用于示例说明,另在为前景像素点赋予label值的过程中也根据扫描的行进方向确定邻接的像素点的位置,并不具体限制为上方或左方。In this embodiment, a two-pass method is preferably used. Specifically, during the first scanning process, all pixel points of the image data are traversed from left to right and from top to bottom starting from the first pixel point in the upper left corner of the image data, and a label is assigned to each foreground pixel point. If the pixel point adjacent to the upper or left side of the foreground pixel point currently being scanned is 0, the label value of the foreground pixel point currently being scanned is increased by one. If the pixel point adjacent to the upper or left side of the foreground pixel point currently being scanned is not 0, that is, there is a foreground pixel point adjacent to the foreground pixel point currently being scanned, then the label value of the foreground pixel point adjacent to the upper or left side is assigned to the foreground pixel point currently being scanned. Since the foreground pixels located in the same connected area may have one or more labels with different values during the first scanning process, it is necessary to merge the labels with different values. During the second scanning process, the label values of the foreground pixels with an adjacent relationship are unified, that is, assigned the same label, where the label is the minimum value of the label in the same connected area. It should be noted that the starting position of the scan in the two-pass method is not limited to a specific position. The upper left position in this embodiment is only used for example. In the process of assigning label values to foreground pixels, the positions of adjacent pixels are also determined according to the scanning direction, and are not specifically limited to the top or left.

分别计算每一个连通区域的面积,并计算所有连通区域的标准差及均值;Calculate the area of each connected region separately, and calculate the standard deviation and mean of all connected regions;

判断每一连通区域的面积是否位于标准差及均值之间;Determine whether the area of each connected region is between the standard deviation and the mean;

若是,则保留连通区域;If so, keep the connected region;

若否,则舍弃连通区域。If not, the connected region is discarded.

对于保留的连通区域,将所有连通区域的像素值设置为255,得到连通区域标记后的图像数据。For the retained connected areas, the pixel values of all connected areas are set to 255 to obtain the image data after the connected areas are marked.

在一个实施例中,步骤S104具体包括:In one embodiment, step S104 specifically includes:

参见图7,对进行连通区域标记的图像数据进行形态学开运算,即通过结构元素遍历所有连通区域的像素点,对连通区域的像素点膨胀处理后再对膨胀处理后的连通区域进行腐蚀操作,以平滑图像数据的连通区域的边缘;Referring to FIG. 7 , a morphological opening operation is performed on the image data for connected region marking, that is, the pixel points of all connected regions are traversed through the structural element, the pixel points of the connected regions are expanded, and then the expanded connected regions are eroded to smooth the edges of the connected regions of the image data;

参见图8,对进行连通区域标记的图像数据进行形态学闭运算,即通过结构元素遍历所有连通区域的像素点,对连通区域的像素点进行腐蚀处理后再对腐蚀处理后的连通区域进行膨胀操作,以消除图像数据的连通区域内的细小孔洞。对图像数进行形态学开运算及形态学闭运算后的图像数据参见图9。Referring to FIG8 , the image data for connected region labeling is subjected to morphological closing operation, that is, all pixels of the connected regions are traversed through the structural element, the pixels of the connected regions are corroded, and then the corroded connected regions are expanded to eliminate small holes in the connected regions of the image data. The image data after morphological opening and morphological closing operations are shown in FIG9 .

在一个实施例中,步骤S104具体包括:In one embodiment, step S104 specifically includes:

对进行连通区域标记的图像数据进行孔洞填充,具体地,对图像数据进行复制,对复制后的图像数据连通区域进行边缘扩充,以防止孔洞填充不完全,并采用泛洪填充算法进行填充,其原理为从连通区域的第一个像素点进 行填充直至连通区域内所有的像素点填充为相同的像素值,对复制后的图像数据和复制前的图像数据进行图像或运算,得到孔洞填充后的图像数据,参见图10所示。Holes are filled in the image data for connected area marking. Specifically, the image data is copied, and the edges of the connected areas of the copied image data are expanded to prevent incomplete hole filling. The flood filling algorithm is used for filling. The principle is to fill from the first pixel point of the connected area until all the pixels in the connected area are filled with the same pixel value. The copied image data and the image data before copying are image ORed to obtain the image data after hole filling, as shown in Figure 10.

在一个实施例中,组织分割方法还包括:对图像数据进行下采样和对目标组织分割图像进行上采样。下采样的步骤在对步骤S102之后执行,可以采用插值算法,优选采用最近邻插值法,目的在于降低图像数据的特征维度,便于后续的运算,减少算力。上采样在步骤S104之后执行,上采样的插值算法与下采样的插值算法对应,目的在于将目标组织分割图像恢复至与基因表达矩阵的相同大小。In one embodiment, the tissue segmentation method further includes: downsampling the image data and upsampling the target tissue segmentation image. The downsampling step is performed after step S102, and an interpolation algorithm can be used, preferably a nearest neighbor interpolation method, in order to reduce the feature dimension of the image data, facilitate subsequent operations, and reduce computing power. Upsampling is performed after step S104, and the interpolation algorithm of upsampling corresponds to the interpolation algorithm of downsampling, in order to restore the target tissue segmentation image to the same size as the gene expression matrix.

本发明一示例性实施例提供一种样本图像的组织分割系统,参见图11,组织分割系统包括:An exemplary embodiment of the present invention provides a tissue segmentation system for a sample image. Referring to FIG. 11 , the tissue segmentation system includes:

获取模块21,用于获取目标组织的基因表达矩阵,基因表达矩阵中包括按照像素位置进行排列的目标组织的基因表达量;An acquisition module 21 is used to acquire a gene expression matrix of a target tissue, wherein the gene expression matrix includes gene expression amounts of the target tissue arranged according to pixel positions;

图像数据确定模块22,通过将所述基因表达矩阵中每一像素位置的基因表达量赋值于样本图像中对应的像素位置确定图像数据;An image data determination module 22 determines image data by assigning the gene expression amount at each pixel position in the gene expression matrix to the corresponding pixel position in the sample image;

前景像素点确定模块23,用于通过对图像数据进行图像处理以确定图像数据的前景像素点;A foreground pixel point determination module 23, configured to determine foreground pixel points of the image data by performing image processing on the image data;

分割图像确定模块24,用于根据前景像素点对图像数据的连通区域进行标记得到目标组织分割图像。The segmented image determination module 24 is used to mark the connected areas of the image data according to the foreground pixels to obtain the target tissue segmentation image.

对于系统实施例而言,由于其基本对应于方法实施例,所以相关之处参见方法实施例的部分说明即可。以上所描述的系统实施例仅仅是示意性的,其中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发明方案的目的。本领域普通技术人员在不付出创造性劳动的情况下,即可以理解并实施。As for the system embodiment, since it basically corresponds to the method embodiment, the relevant parts can refer to the partial description of the method embodiment. The system embodiment described above is only schematic, in which 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 they may be distributed on multiple network units. Some or all of the modules can be selected according to actual needs to achieve the purpose of the scheme of the present invention. Ordinary technicians in this field can understand and implement it without paying creative work.

本发明一示例实施例示出的一种电子设备,参见图12所示,示出了适于用来实现本发明实施方式的示例性电子设备30的框图。图12显示的电子设备30仅仅是一个示例,不应对本发明实施例的功能和使用范围带来任何限制。An electronic device according to an exemplary embodiment of the present invention is shown in FIG12 , which shows a block diagram of an exemplary electronic device 30 suitable for implementing the embodiment of the present invention. The electronic device 30 shown in FIG12 is only an example and should not limit the functions and scope of use of the embodiment of the present invention.

如图3所示,电子设备30可以以通用计算设备的形式表现,例如其可以为服务器设备。电子设备30的组件可以包括但不限于:上述至少一个处理器31、上述至少一个存储器32、连接不同系统组件(包括存储器32和处理器31)的总线33。As shown in Fig. 3, the electronic device 30 may be in the form of a general-purpose computing device, for example, it may be a server device. The components of the electronic device 30 may include, but are not limited to: at least one processor 31, at least one memory 32, and a bus 33 connecting different system components (including the memory 32 and the processor 31).

总线33包括数据总线、地址总线和控制总线。The bus 33 includes a data bus, an address bus, and a control bus.

存储器32可以包括易失性存储器,例如随机存取存储器(RAM)321和/或高速缓存存储器322,还可以进一步包括只读存储器(ROM)323。The memory 32 may include a volatile memory, such as a random access memory (RAM) 321 and/or a cache memory 322 , and may further include a read-only memory (ROM) 323 .

存储器32还可以包括具有一组(至少一个)程序模块324的程序工具325(或实用工具),这样的程序模块324包括但不限于:操作系统、一个或者多个应用程序、其它程序模块以及程序数据,这些示例中的每一个或某种组合中可能包括网络环境的实现。The memory 32 may also include a program tool 325 (or utility) having a set (at least one) of program modules 324, such program modules 324 including but not limited to: an operating system, one or more application programs, other program modules and program data, each of which or some combination may include an implementation of a network environment.

处理器31通过运行存储在存储器32中的计算机程序,从而执行各种功能应用以及数据处理,例如上述任一实施例所提供的方法。The processor 31 executes various functional applications and data processing by running the computer program stored in the memory 32, such as the method provided in any of the above embodiments.

电子设备30也可以与一个或多个外部设备34通信。这种通信可以通过输入/输出(I/O)接口35进行。并且,模型生成的电子设备30还可以通过网络适配器37与一个或者多个网络(例如局域网(LAN),广域网(WAN)和/或公共网络,例如因特网)通信。如图所示,网络适配器37通过总线33与模型生成的电子设备30的其它模块通信。应当明白,尽管图中未示出,可以结合模型生成的电子设备30使用其它硬件和/或软件模块,包括但不限于:微代码、设备驱动器、冗余处理器、外部磁盘驱动阵列、RAID(磁盘阵列)系统、磁带驱动器以及数据备份存储系统等。The electronic device 30 may also communicate with one or more external devices 34. Such communication may be performed via an input/output (I/O) interface 35. Furthermore, the model-generated electronic device 30 may also communicate with one or more networks (e.g., a local area network (LAN), a wide area network (WAN), and/or a public network, such as the Internet) via a network adapter 37. As shown, the network adapter 37 communicates with other modules of the model-generated electronic device 30 via a bus 33. It should be understood that, although not shown in the figure, other hardware and/or software modules may be used in conjunction with the model-generated electronic device 30, including but not limited to: microcode, device drivers, redundant processors, external disk drive arrays, RAID (disk array) systems, tape drives, and data backup storage systems, etc.

应当注意,尽管在上文详细描述中提及了电子设备的若干单元/模块或子单元/模块,但是这种划分仅仅是示例性的并非强制性的。实际上,根据本发明的实施方式,上文描述的两个或更多单元/模块的特征和功能可以在一个单元/模块中具体化。反之,上文描述的一个单元/模块的特征和功能可以进一步划分为由多个单元/模块来具体化。It should be noted that although several units/modules or sub-units/modules of the electronic device are mentioned in the above detailed description, this division is merely exemplary and not mandatory. In fact, according to an embodiment of the present invention, the features and functions of two or more units/modules described above can be embodied in one unit/module. Conversely, the features and functions of one unit/module described above can be further divided into multiple units/modules to be embodied.

本发明实施例还提供一种计算机可读存储介质,其上存储有计算机程序,程序被处理器执行时实现上述任一实施例所提供的方法。An embodiment of the present invention further provides a computer-readable storage medium on which a computer program is stored. When the program is executed by a processor, the method provided by any of the above embodiments is implemented.

其中,可读存储介质可以采用的更具体可以包括但不限于:便携式盘、硬盘、随机存取存储器、只读存储器、可擦拭可编程只读存储器、光存储器件、磁存储器件或上述的任意合适的组合。The readable storage medium may include but is not limited to: a portable disk, a hard disk, a random access memory, a read-only memory, an erasable programmable read-only memory, an optical storage device, a magnetic storage device or any suitable combination of the above.

在可能的实施方式中,本发明实施例还可以实现为一种程序产品的形式,其包括程序代码,当程序产品在终端设备上运行时,程序代码用于使终端设备执行实现上述任一实施例的方法。In a possible implementation manner, the embodiment of the present invention may also be implemented in the form of a program product, which includes program code. When the program product is run on a terminal device, the program code is used to enable the terminal device to execute a method for implementing any of the above embodiments.

其中,可以以一种或多种程序设计语言的任意组合来编写用于执行本发明的程序代码,程序代码可以完全地在用户设备上执行、部分地在用户设备上执行、作为一个独立的软件包执行、部分在用户设备上部分在远程设备上执行或完全在远程设备上执行。Among them, the program code for executing the present invention can be written in any combination of one or more programming languages, and the program code can be executed completely on the user device, partially on the user device, as an independent software package, partially on the user device and partially on a remote device, or completely on the remote device.

虽然以上描述了本发明的具体实施方式,但是本领域的技术人员应当理解,这仅是举例说明,本发明的保护范围是由所附权利要求书限定的。本领域的技术人员在不背离本发明的原理和实质的前提下,可以对这些实施方式做出多种变更或修改,但这些变更和修改均落入本发明的保护范围。Although the specific embodiments of the present invention are described above, it should be understood by those skilled in the art that this is only for illustration and the protection scope of the present invention is defined by the appended claims. Those skilled in the art may make various changes or modifications to these embodiments without departing from the principles and essence of the present invention, but these changes and modifications all fall within the protection scope of the present invention.

Claims (12)

一种样本图像的组织分割方法,其特征在于,所述组织分割方法包括:A tissue segmentation method for a sample image, characterized in that the tissue segmentation method comprises: 获取样本图像中待分割的目标组织的基因表达量并确定所述样本图像的基因表达矩阵,所述基因表达矩阵按照像素位置对所述基因表达量进行排列;Acquiring gene expression amounts of a target tissue to be segmented in a sample image and determining a gene expression matrix of the sample image, wherein the gene expression matrix arranges the gene expression amounts according to pixel positions; 通过将所述基因表达矩阵中每一像素位置的基因表达量赋值于样本图像中对应的像素位置确定图像数据;Determine image data by assigning the gene expression amount at each pixel position in the gene expression matrix to the corresponding pixel position in the sample image; 通过对所述图像数据进行图像处理以确定所述图像数据的前景像素点;Determine foreground pixels of the image data by performing image processing on the image data; 根据所述前景像素点对所述图像数据的连通区域进行标记得到目标组织分割图像。The connected areas of the image data are marked according to the foreground pixels to obtain a target tissue segmentation image. 如权利要求1所述的组织分割方法,其特征在于,所述通过将所述基因表达矩阵中每一像素位置的基因表达量赋值于样本图像中对应的像素位置确定图像数据,包括:The tissue segmentation method according to claim 1, characterized in that the determining of image data by assigning the gene expression amount at each pixel position in the gene expression matrix to the corresponding pixel position in the sample image comprises: 确定与所述基因表达矩阵相同大小的图像矩阵;Determining an image matrix of the same size as the gene expression matrix; 将所述基因表达矩阵中每一像素位置的基因表达量赋值于图像矩阵中对应的像素位置并对所有像素位置进行归一化处理得到样本图像的图像数据。The gene expression amount of each pixel position in the gene expression matrix is assigned to the corresponding pixel position in the image matrix and all pixel positions are normalized to obtain image data of the sample image. 如权利要求1所述的组织分割方法,其特征在于,所述通过对所述图像数据进行图像处理以确定所述图像数据的前景像素点,包括:The tissue segmentation method according to claim 1, characterized in that the step of performing image processing on the image data to determine the foreground pixels of the image data comprises: 依次将每一像素值作为像素阈值从所述图像数据中划分出前景像素点和背景像素点;Sequentially using each pixel value as a pixel threshold to divide foreground pixels and background pixels from the image data; 计算每一所述像素阈值条件下所述前景像素点的前景平均像素值及所述背景像素点的背景平均像素值,并根据所述前景平均像素值及所述背景平均像素值确定每一所述像素阈条件下所述前景像素点与背景像素点的方差;Calculating the foreground average pixel value of the foreground pixel and the background average pixel value of the background pixel under each pixel threshold condition, and determining the variance of the foreground pixel and the background pixel under each pixel threshold condition according to the foreground average pixel value and the background average pixel value; 遍历所有像素阈值,将所述方差为最大时对应的像素阈值确定为目标阈值;Traversing all pixel thresholds, and determining the pixel threshold corresponding to the maximum variance as the target threshold; 根据所述目标阈值确定所述图像数据的前景像素点并对所述前景像素点的像素值进行统一。The foreground pixels of the image data are determined according to the target threshold and the pixel values of the foreground pixels are unified. 如权利要求3所述的组织分割方法,其特征在于,所述组织分割方法还包括:The tissue segmentation method according to claim 3, characterized in that the tissue segmentation method further comprises: 根据所述目标阈值确定所述图像数据的背景像素点并对所述背景像素点的像素值进行统一。The background pixels of the image data are determined according to the target threshold value and the pixel values of the background pixels are unified. 如权利要求1所述的组织分割方法,其特征在于,所述组织分割方法 还包括:The tissue segmentation method according to claim 1, characterized in that the tissue segmentation method further comprises: 对所述图像数据进行卷积,以提取所述图像数据的低级特征;Performing convolution on the image data to extract low-level features of the image data; 所述通过对所述图像数据进行图像处理以确定所述图像数据的前景像素点,包括:The determining the foreground pixel points of the image data by performing image processing on the image data includes: 通过对进行卷积后的所述图像数据图像处理以确定所述图像数据的前景像素点。The foreground pixel points of the image data are determined by image processing on the image data after convolution. 如权利要求1所述的组织分割方法,其特征在于,所述根据所述前景像素点对所述图像数据的连通区域进行标记得到目标组织分割图像,包括:The tissue segmentation method according to claim 1, characterized in that the step of marking the connected areas of the image data according to the foreground pixels to obtain the target tissue segmentation image comprises: 对进行连通区域标记的所述图像数据进行形态学开运算,以平滑所述图像数据的连通区域的边缘;Performing a morphological opening operation on the image data for connected region marking to smooth the edges of the connected regions of the image data; 和/或,and / or, 对进行连通区域标记的所述图像数据进行形态学闭运算,以消除所述图像数据的连通区域内的细小孔洞;Performing a morphological closing operation on the image data for connected region marking to eliminate small holes in the connected regions of the image data; 和/或,and / or, 对进行连通区域标记的所述图像数据进行孔洞填充。Holes are filled in the image data for which connected area marking is performed. 如权利要求1所述的组织分割方法,其特征在于,所述根据所述前景像素点对所述图像数据的连通区域进行标记得到目标组织分割图像,包括:The tissue segmentation method according to claim 1, characterized in that the step of marking the connected areas of the image data according to the foreground pixels to obtain the target tissue segmentation image comprises: 将具有邻接关系的前景像素点确定为同一个连通区域的像素点。The foreground pixels with an adjacency relationship are determined as the pixels of the same connected region. 如权利要求7所述的组织分割方法,其特征在于,所述将具有邻接关系的前景像素点确定为同一个连通区域的像素点之后,包括:The tissue segmentation method according to claim 7, characterized in that after determining the foreground pixels having an adjacency relationship as pixels of the same connected region, the method further comprises: 分别计算每一个所述连通区域的面积,并计算所有所述连通区域的标准差及均值;Calculate the area of each connected region respectively, and calculate the standard deviation and mean of all connected regions; 判断每一所述连通区域的面积是否位于标准差及均值之间;Determine whether the area of each of the connected regions is between the standard deviation and the mean; 若是,则保留所述连通区域;If yes, retain the connected area; 若否,则舍弃所述连通区域。If not, the connected region is discarded. 如权利要求1所述的组织分割方法,其特征在于,所述通过将所述基因表达矩阵中每一像素位置的基因表达量赋值于样本图像中对应的像素位置确定图像数据之后,包括:The tissue segmentation method according to claim 1, characterized in that after determining the image data by assigning the gene expression amount at each pixel position in the gene expression matrix to the corresponding pixel position in the sample image, the method further comprises: 对所述图像数据进行下采样;downsampling the image data; 所述根据所述前景像素点对所述图像数据的连通区域进行标记得到目标组织分割图像之后,包括:After the connected areas of the image data are marked according to the foreground pixels to obtain the target tissue segmentation image, the method includes: 对所述目标组织分割图像进行上采样。The target tissue segmentation image is upsampled. 一种样本图像的组织分割系统,其特征在于,所述组织分割系统包括:A tissue segmentation system for a sample image, characterized in that the tissue segmentation system comprises: 获取模块,用于获取样本图像中待分割的目标组织的基因表达量并确定 所述样本图像的基因表达矩阵,所述基因表达矩阵按照像素位置对所述基因表达量进行排列;an acquisition module, used to acquire the gene expression amount of the target tissue to be segmented in the sample image and determine the gene expression matrix of the sample image, wherein the gene expression matrix arranges the gene expression amounts according to pixel positions; 图像数据确定模块,用于通过将所述基因表达矩阵中每一像素位置的基因表达量赋值于样本图像中对应的像素位置确定图像数据;An image data determination module, used to determine image data by assigning the gene expression amount at each pixel position in the gene expression matrix to the corresponding pixel position in the sample image; 前景像素点确定模块,用于通过对所述图像数据进行图像处理以确定所述图像数据的前景像素点;a foreground pixel point determination module, configured to determine the foreground pixel points of the image data by performing image processing on the image data; 分割图像确定模块,用于根据所述前景像素点对所述图像数据的连通区域进行标记得到目标组织分割图像。The segmented image determination module is used to mark the connected areas of the image data according to the foreground pixels to obtain a target tissue segmentation image. 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计算机程序时实现权利要求1-9中任一项所述的样本图像的组织分割方法。An electronic device comprises a memory, a processor and a computer program stored in the memory and executable on the processor, wherein the processor implements the tissue segmentation method of a sample image according to any one of claims 1 to 9 when executing the computer program. 一种计算机可读存储介质,其上存储有计算机程序,其特征在于,所述计算机程序被处理器执行时实现权利要求1-9中任一项所述的样本图像的组织分割方法。A computer-readable storage medium having a computer program stored thereon, wherein when the computer program is executed by a processor, the method for tissue segmentation of a sample image according to any one of claims 1 to 9 is implemented.
PCT/CN2022/136664 2022-12-05 2022-12-05 Tissue segmentation method for sample image, system, device and medium Ceased WO2024119323A1 (en)

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