Pathological whole slide image cell positioning and coordinate mapping method, device and equipment based on openslide and storage medium
Patent Information
- Authority / Receiving Office
- CN · China
- Patent Type
- Applications(China)
- Current Assignee / Owner
- THE THIRD AFFILIATED HOSPITAL OF SUN YAT SEN UNIV
- Filing Date
- 2026-03-31
- Publication Date
- 2026-06-26
Smart Images
Figure CN122289288A_ABST
Abstract
Description
Technical Field
[0001] This disclosure relates to the field of data processing technology. Specifically, it relates to a method, apparatus, device, and storage medium for cell localization and coordinate mapping of whole-slice pathological images based on OpenSlide. Background Technology
[0002] When processing nasal polyp pathology slides, they are typically segmented into multiple sub-images, and cell identification is performed on each sub-image. However, current technologies lack a comprehensive coordinate indexing system for each sub-image, hindering the tracing and integration of cells across the entire slide. Existing technologies mostly focus on sub-image-level detection results when processing sub-images, failing to establish a unified spatial coordinate indexing system between sub-images and the entire pathology slide image. This makes it difficult to accurately map cell detection results within sub-images back to their spatial locations within the entire slide image, hindering subsequent analyses such as spatial distribution analysis of cells across the entire slide. Therefore, establishing a comprehensive coordinate indexing system for each sub-image of a nasal polyp pathology slide to achieve accurate mapping of sub-detection results to the spatial coordinates of the entire slide is a technical problem to be solved in this field. Summary of the Invention
[0003] This disclosure provides a method, apparatus, device, and storage medium for cell localization and coordinate mapping of whole-slice pathological images based on OpenSlide.
[0004] According to one aspect of this disclosure, a method for cell localization and coordinate mapping of whole-slice pathological images based on OpenSlide is provided, including: The nasal polyp pathology slide is cut into multiple sub-images according to the preset sub-image size and step size; Based on the coordinate information of each sub-image on the nasal polyp pathological slide and the size of each sub-image, each sub-image is named respectively; Positive cells are located in each of the sub-graphs to obtain the sub-graph coordinates of each positive cell in each of the sub-graphs; Based on the coordinate information in the names of each subgraph and the subgraph coordinates of each positive cell in each subgraph, the full-graph coordinates of each positive cell in each subgraph are determined. Based on the full-map coordinates of each positive cell in each of the sub-maps, the coordinate information of each positive cell is identified in the nasal polyp pathological slide.
[0005] According to one aspect of this disclosure, a device for cell localization and coordinate mapping of whole-slice pathological images based on OpenSlide is provided, comprising: The pathology slide cutting module is used to cut nasal polyp pathology slides into multiple sub-images according to preset sub-image sizes and step sizes. The sub-image naming module is used to name each sub-image based on its coordinate information on the nasal polyp pathological slide and its size. The cell localization module is used to locate positive cells in each of the sub-graphs and obtain the sub-graph coordinates of each positive cell in each of the sub-graphs; The coordinate transformation module is used to determine the full-map coordinates of each positive cell in each sub-map based on the coordinate information in the naming of each sub-map and the sub-map coordinates of each positive cell in each sub-map. The coordinate identification module is used to identify the coordinate information of each positive cell in the nasal polyp pathological slide based on the full-map coordinates of each positive cell in each of the sub-maps.
[0006] According to another aspect of this disclosure, an electronic device is provided, comprising: At least one processor; and The memory is communicatively connected to the at least one processor; wherein, The memory stores instructions that can be executed by the at least one processor to enable the at least one processor to perform any of the OpenSlide-based methods for cell localization and coordinate mapping of whole-slice pathological images in the embodiments of this disclosure.
[0007] According to another aspect of this disclosure, a non-transitory computer-readable storage medium is provided storing computer instructions, wherein the computer instructions are used to cause the computer to perform any of the OpenSlide-based methods for cell localization and coordinate mapping of whole-slice pathological images according to any embodiment of this disclosure.
[0008] According to the technology disclosed herein, a nasal polyp pathology slide is divided into multiple sub-images according to a preset sub-image size and step size. Each sub-image is named based on its coordinates on the nasal polyp pathology slide and its size. Positive cells are located in each sub-image to obtain the sub-image coordinates of each positive cell. Based on the coordinates in the names of each sub-image and the sub-image coordinates of each positive cell, the global coordinates of each positive cell in each sub-image are determined. Based on the global coordinates of each positive cell in each sub-image, the coordinate information of each positive cell is identified in the nasal polyp pathology slide. This facilitates spatial tracing of the segmented sub-images and quantitative statistical analysis of positive cells. For example, users can find the global coordinate information of each positive cell in the nasal polyp pathology slide, and for each sub-image, users can obtain the global coordinate and size information of the sub-image simply by its name.
[0009] It should be understood that the description in this section is not intended to identify key or essential features of the embodiments of this disclosure, nor is it intended to limit the scope of this disclosure. Other features of this disclosure will become readily apparent from the following description. Attached Figure Description
[0010] The accompanying drawings are provided to better understand this solution and do not constitute a limitation of this disclosure. Wherein: Figure 1 This is a flowchart of a method for cell localization and coordinate mapping of whole-slice pathological images based on OpenSlide, according to an embodiment of this disclosure; Figure 2 This is a schematic diagram of various sub-images of a nasal polyp pathological slide according to an embodiment of this disclosure; Figure 3 This is a schematic diagram illustrating the identification of each positive cell in a nasal polyp pathological slide according to an embodiment of this disclosure; Figure 4 This is a flowchart of another embodiment of the OpenSlide-based method for cell localization and coordinate mapping of whole-slice pathological images; Figure 5 This is a structural block diagram of a pathological whole-slice image cell localization and coordinate mapping device based on OpenSlide according to an embodiment of the present disclosure; Figure 6 This is a block diagram of an electronic device according to an embodiment of the present disclosure. Detailed Implementation
[0011] The exemplary embodiments of this disclosure are described below with reference to the accompanying drawings, including various details of the embodiments to aid understanding, and should be considered merely exemplary. Therefore, those skilled in the art will recognize that various changes and modifications can be made to the embodiments described herein without departing from the scope of this disclosure. Similarly, for clarity and brevity, descriptions of well-known functions and structures are omitted in the following description.
[0012] Figure 1 This is a flowchart of a method for cell localization and coordinate mapping of whole-slice pathological images based on OpenSlide, according to an embodiment of this disclosure.
[0013] like Figure 1 As shown, this OpenSlide-based method for cell localization and coordinate mapping in whole-slice pathological images can include: S110, according to the preset sub-image size and step size, cut the nasal polyp pathology slide into multiple sub-images; S120. Based on the coordinate information of each sub-image on the nasal polyp pathological slide and the size of the sub-image, each sub-image is named respectively. S130, locate positive cells in each sub-map to obtain the sub-map coordinates of each positive cell in each sub-map; S140, Based on the coordinate information in the naming of each subplot and the subplot coordinates of each positive cell in each subplot, determine the full-plot coordinates of each positive cell in each subplot. S150 identifies the coordinate information of each positive cell in the nasal polyp pathology slide based on the full-map coordinates of each positive cell in each sub-map.
[0014] like Figure 2 As shown, it illustrates the naming of the various sub-images in a nasal polyp pathology slide. For example... Figure 3 As shown, it displays the coordinate information of each positive cell in the pathological slide of nasal polyps.
[0015] In one embodiment, naming each sub-image based on its coordinate information on the nasal polyp pathological slide and its size includes: concatenating the coordinates of the upper left corner of the sub-image on the nasal polyp pathological slide with its size to obtain the name of the sub-image.
[0016] In one embodiment, the step of cutting the nasal polyp pathological slide into multiple sub-images according to a preset sub-image size and step size includes: scaling the nasal polyp pathological slide based on a preset scaling ratio; denoising the scaled nasal polyp pathological slide; enlarging the scaled and denoised nasal polyp pathological slide based on the magnification ratio corresponding to the scaling ratio; and cutting the nasal polyp pathological slide, which has been successively scaled, denoised, and enlarged, into multiple sub-images.
[0017] In one embodiment, the step of magnifying the scaled and denoised nasal polyp pathological slide based on the magnification ratio corresponding to the scaling ratio includes: identifying pathological tissue in the scaled and denoised nasal polyp pathological slide to determine the pathological tissue region in the nasal polyp pathological slide; performing an integral operation on the pathological tissue region; and, if the integral result of the pathological tissue region meets a preset integral condition, magnifying the scaled and denoised nasal polyp pathological slide based on the magnification ratio corresponding to the scaling ratio.
[0018] like Figure 4 As shown, it illustrates the sub-image segmentation process of a nasal polyp pathology slide and the process of identifying positive cells in the sub-image.
[0019] In one embodiment, the step of performing integration on the pathological tissue region includes: dividing the pathological tissue region into a grid and binarizing it; and performing integration on the gridded and binarized pathological tissue region.
[0020] Figure 5 This is a structural block diagram of a pathological whole-slice image cell localization and coordinate mapping device based on OpenSlide according to an embodiment of the present disclosure.
[0021] like Figure 5 As shown, this OpenSlide-based device for cell localization and coordinate mapping of whole-slice pathological images includes: The pathology slide cutting module 510 is used to cut nasal polyp pathology slides into multiple sub-images according to preset sub-image sizes and step sizes. The sub-image naming module 520 is used to name each sub-image based on the coordinate information of each sub-image on the nasal polyp pathological slide and the size of the sub-image. The cell localization module 530 is used to locate positive cells in each of the sub-graphs and obtain the sub-graph coordinates of each positive cell in each of the sub-graphs; The coordinate transformation module 540 is used to determine the full-map coordinates of each positive cell in each sub-map based on the coordinate information in the naming of each sub-map and the sub-map coordinates of each positive cell in each sub-map. The coordinate identification module 550 is used to identify the coordinate information of each positive cell in the nasal polyp pathological slide based on the full-map coordinates of each positive cell in each of the sub-maps.
[0022] In one implementation, the subgraph naming module is specifically used for: The sub-image is named by concatenating the coordinates of the upper left corner of the nasal polyp pathology slide with the sub-image size.
[0023] In one embodiment, the pathological slide cutting module includes: A scaling unit is used to scale the nasal polyp pathological slide based on a preset scaling ratio. A noise reduction unit is used to denoise the scaled-up nasal polyp pathological slide; The magnification unit is used to magnify the scaled and denoised nasal polyp pathological slide based on the magnification ratio corresponding to the scaling ratio. The cutting unit is used to cut the nasal polyp pathological slide, which has been successively scaled, denoised, and magnified, into multiple sub-images.
[0024] In one embodiment, the amplification unit is specifically used for: The pathological tissue in the scaled and denoised nasal polyp pathological slide is identified to determine the pathological tissue region in the nasal polyp pathological slide. Perform an integral operation on the pathological tissue region; If the integration result of the pathological tissue area meets the preset integration conditions, the scaled and denoised nasal polyp pathological slide is magnified based on the magnification ratio corresponding to the scaling ratio.
[0025] In one embodiment, the integral operation on the pathological tissue region includes: The pathological tissue area is meshed and binarized; Integral calculations are performed on the meshed and binarized pathological tissue regions.
[0026] The specific functions and examples of each module and submodule of the apparatus in this disclosure can be found in the relevant descriptions of the corresponding steps in the above method embodiments, and will not be repeated here.
[0027] The acquisition, storage, and application of user personal information involved in the technical solution disclosed herein comply with the provisions of relevant laws and regulations and do not violate public order and good morals.
[0028] According to embodiments of this disclosure, this disclosure also provides an electronic device, a readable storage medium, and a computer program product.
[0029] Figure 6 This is a structural block diagram of an electronic device according to an embodiment of the present disclosure. Figure 6 As shown, the electronic device includes a memory 410 and a processor 420. The memory 410 stores a computer program that can run on the processor 420. There can be one or more memories 410 and processors 420. The memory 410 can store one or more computer programs, which, when executed by the electronic device, cause the electronic device to perform the methods provided in the above-described method embodiments. The electronic device may also include a communication interface 430 for communicating with external devices and performing data exchange and transmission.
[0030] If the memory 410, processor 420, and communication interface 430 are implemented independently, they can be interconnected via a bus to communicate with each other. This bus can be an Industry Standard Architecture (ISA) bus, a Peripheral Component Interconnect (PCI) bus, or an Extended Industry Standard Architecture (EISA) bus, etc. This bus can be divided into address bus, data bus, control bus, etc. For ease of representation, Figure 6The bus is represented by a single thick line, but this does not mean that there is only one bus or one type of bus.
[0031] Optionally, in a specific implementation, if the memory 410, processor 420 and communication interface 430 are integrated on a single chip, the memory 410, processor 420 and communication interface 430 can communicate with each other through an internal interface.
[0032] It should be understood that the aforementioned processor can be a Central Processing Unit (CPU), or other general-purpose processors, Digital Signal Processors (DSPs), Application Specific Integrated Circuits (ASICs), Field-Programmable Gate Arrays (FPGAs), or other programmable logic devices, discrete gate or transistor logic devices, discrete hardware components, etc. General-purpose processors can be microprocessors or any conventional processor. It is worth noting that the processor can be a processor supporting Advanced Reduced Instruction Set Machines (ARM) architecture.
[0033] Further, optionally, the aforementioned memory may include read-only memory and random access memory, and may also include non-volatile random access memory. The memory may be volatile or non-volatile, or may include both. Non-volatile memory may include read-only memory (ROM), programmable read-only memory (PROM), erasable programmable read-only memory (EPROM), electrically erasable programmable read-only memory (EEPROM), or flash memory. Volatile memory may include random access memory (RAM), which serves as an external cache. Many forms of RAM are available by way of example, but not limitation. Examples include Static Random Access Memory (SRAM), Dynamic Random Access Memory (DRAM), Synchronous DRAM (SDRAM), Double Data SDRAM (DDR SDRAM), Enhanced Synchronous DRAM (ESDRAM), Synchlink DRAM (SLDRAM), and Direct RAMBUS RAM (DR RAM).
[0034] In the above embodiments, implementation can be achieved, in whole or in part, through software, hardware, firmware, or any combination thereof. When implemented in software, it can be implemented, in whole or in part, as a computer program product. The computer program product includes one or more computer instructions. When the computer instructions are loaded and executed on a computer, all or part of the processes or functions described in the embodiments of this disclosure are generated. The computer can be a general-purpose computer, a special-purpose computer, a computer network, or other programmable device. The computer instructions can be stored in a computer-readable storage medium or transmitted from one computer-readable storage medium to another. For example, the computer instructions can be transmitted from one website, computer, server, or data center to another via wired (e.g., coaxial cable, fiber optic, Digital Subscriber Line, DSL) or wireless (e.g., infrared, Bluetooth, microwave, etc.) means. The computer-readable storage medium can be any available medium accessible to a computer, or a data storage device such as a server or data center that integrates one or more available media. The available media may be magnetic media (e.g., floppy disks, hard disks, magnetic tapes), optical media (e.g., Digital Versatile Discs (DVDs)), or semiconductor media (e.g., Solid State Disks (SSDs)). It is worth noting that the computer-readable storage media mentioned in this disclosure may be non-volatile storage media; in other words, they may be non-transient storage media.
[0035] Those skilled in the art will understand that all or part of the steps of the above embodiments can be implemented by hardware or by a program instructing related hardware. The program can be stored in a computer-readable storage medium, such as a read-only memory, a disk, or an optical disk.
[0036] In the description of the embodiments of this disclosure, references to terms such as "one embodiment," "some embodiments," "example," "specific example," or "some examples," etc., indicate that a specific feature, structure, material, or characteristic described in connection with that embodiment or example is included in at least one embodiment or example of this disclosure. Furthermore, the specific features, structures, materials, or characteristics described may be combined in any suitable manner in one or more embodiments or examples. Moreover, without contradiction, those skilled in the art can combine and integrate the different embodiments or examples described in this specification, as well as the features of those different embodiments or examples.
[0037] In the description of the embodiments disclosed herein, unless otherwise stated, " / " means "or". For example, A / B can mean A or B. The "and / or" in this document is merely a description of the relationship between related objects, indicating that three relationships can exist. For example, A and / or B can represent: A existing alone, A and B existing simultaneously, and B existing alone.
[0038] In the description of embodiments of this disclosure, the terms "first" and "second" are used for descriptive purposes only and should not be construed as indicating or implying relative importance or implicitly specifying the number of indicated technical features. Therefore, a feature defined as "first" or "second" may explicitly or implicitly include one or more of that feature. In the description of embodiments of this disclosure, unless otherwise stated, "a plurality of" means two or more.
[0039] The above description is merely an exemplary embodiment of this disclosure and is not intended to limit this disclosure. Any modifications, equivalent substitutions, improvements, etc., made within the spirit and principles of this disclosure should be included within the protection scope of this disclosure.
Claims
1. A method for cell localization and coordinate mapping in whole-slice pathological images based on OpenSlide, characterized in that, include: The nasal polyp pathology slide is cut into multiple sub-images according to the preset sub-image size and step size; Based on the coordinate information of each sub-image on the nasal polyp pathological slide and the size of each sub-image, each sub-image is named respectively; Positive cells are located in each of the sub-graphs to obtain the sub-graph coordinates of each positive cell in each of the sub-graphs; Based on the coordinate information in the names of each subgraph and the subgraph coordinates of each positive cell in each subgraph, the full-graph coordinates of each positive cell in each subgraph are determined. Based on the full-map coordinates of each positive cell in each of the sub-maps, the coordinate information of each positive cell is identified in the nasal polyp pathological slide.
2. The method according to claim 1, characterized in that, The process of naming each sub-image based on its coordinate information on the nasal polyp pathological slide and its size includes: The sub-image is named by concatenating the coordinates of the upper left corner of the nasal polyp pathology slide with the sub-image size.
3. The method according to claim 1, characterized in that, The process of cutting nasal polyp pathological slides into multiple sub-images according to preset sub-image sizes and step sizes includes: The nasal polyp pathological slide is scaled based on a preset scaling ratio. The scaled-up nasal polyp pathology slides were denoised. Based on the magnification ratio corresponding to the scaling ratio, the scaled and denoised nasal polyp pathological slide is magnified; The nasal polyp pathological slide, after being scaled, denoised, and magnified in sequence, is cut into multiple sub-images.
4. The method according to claim 1, characterized in that, The process of magnifying the scaled and denoised nasal polyp pathological slide based on the magnification ratio corresponding to the scaling ratio includes: The pathological tissue in the scaled and denoised nasal polyp pathological slide is identified to determine the pathological tissue region in the nasal polyp pathological slide. Perform an integral operation on the pathological tissue region; If the integration result of the pathological tissue area meets the preset integration conditions, the scaled and denoised nasal polyp pathological slide is magnified based on the magnification ratio corresponding to the scaling ratio.
5. The method according to claim 1, characterized in that, The integral operation on the pathological tissue region includes: The pathological tissue area is meshed and binarized; Integral calculations are performed on the meshed and binarized pathological tissue regions.
6. A device for cell localization and coordinate mapping of whole-slice pathological images based on OpenSlide, characterized in that, include: The pathology slide cutting module is used to cut nasal polyp pathology slides into multiple sub-images according to preset sub-image sizes and step sizes. The sub-image naming module is used to name each sub-image based on its coordinate information on the nasal polyp pathological slide and its size. The cell localization module is used to locate positive cells in each of the sub-graphs and obtain the sub-graph coordinates of each positive cell in each of the sub-graphs; The coordinate transformation module is used to determine the full-map coordinates of each positive cell in each sub-map based on the coordinate information in the naming of each sub-map and the sub-map coordinates of each positive cell in each sub-map. The coordinate identification module is used to identify the coordinate information of each positive cell in the nasal polyp pathological slide based on the full-map coordinates of each positive cell in each of the sub-maps.
7. The apparatus according to claim 6, characterized in that, The subgraph naming module is specifically used for: The sub-image is named by concatenating the coordinates of the upper left corner of the nasal polyp pathology slide with the sub-image size.
8. The apparatus according to claim 7, characterized in that, The pathological slide cutting module includes: A scaling unit is used to scale the nasal polyp pathological slide based on a preset scaling ratio. A noise reduction unit is used to denoise the scaled-up nasal polyp pathological slide; The magnification unit is used to magnify the scaled and denoised nasal polyp pathological slide based on the magnification ratio corresponding to the scaling ratio. The cutting unit is used to cut the nasal polyp pathological slide, which has been successively scaled, denoised, and magnified, into multiple sub-images.
9. An electronic device, characterized in that, include: At least one processor; as well as A memory communicatively connected to the at least one processor; wherein, The memory stores instructions that can be executed by the at least one processor to enable the at least one processor to perform the method of any one of claims 1-5.
10. A non-transitory computer-readable storage medium storing computer instructions, characterized in that, The computer instructions are used to cause the computer to perform the method according to any one of claims 1-5.