CN105574148A - Digital slide storage system and digital slide browsing method - Google Patents
Digital slide storage system and digital slide browsing method Download PDFInfo
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- CN105574148A CN105574148A CN201510939657.9A CN201510939657A CN105574148A CN 105574148 A CN105574148 A CN 105574148A CN 201510939657 A CN201510939657 A CN 201510939657A CN 105574148 A CN105574148 A CN 105574148A
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- G06F16/10—File systems; File servers
- G06F16/16—File or folder operations, e.g. details of user interfaces specifically adapted to file systems
- G06F16/164—File meta data generation
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- G06—COMPUTING; CALCULATING OR COUNTING
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- G06F16/00—Information retrieval; Database structures therefor; File system structures therefor
- G06F16/10—File systems; File servers
- G06F16/13—File access structures, e.g. distributed indices
- G06F16/134—Distributed indices
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- G06—COMPUTING; CALCULATING OR COUNTING
- G06F—ELECTRIC DIGITAL DATA PROCESSING
- G06F16/00—Information retrieval; Database structures therefor; File system structures therefor
- G06F16/50—Information retrieval; Database structures therefor; File system structures therefor of still image data
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Abstract
The invention discloses a digital slide storage system. The digital slide storage system comprises a metadata storage module used for storing metadata, and providing writing and reading interfaces of the metadata; an image storage module used for storing slide image data; a slide reconstruction module connected with the image storage module and used for cutting image layers under various magnifications into a plurality of small slide images in a specific patch size; a transmission module connected with the image storage module and the metadata storage module and used for reading slide metadata and image data of different manufacturers, and transmitting the slide metadata and image data to corresponding storage modules; and a browsing module connected with the image storage module and the metadata storage module and used for acquiring and displaying the slide images. The invention further comprises a digital slide browsing method based on the digital slide storage system. The digital slide storage system and the digital slide browsing method provided by the invention can efficiently store digital slides, and can realize instant browsing of the digital slides.
Description
Technical field
The present invention relates to digital slices field of storage, particularly a kind of digital slices storage system and digital slices browsing method.
Background technology
In today of large data age, increasing information is digitized so that by computer search, browse, analyze.Microscopic section is digitized too, and it is primarily of binary picture data and metadata composition.Wherein view data comprises the binary data under multiple resolution.Metadata comprises the contents such as section scanning information, storage format, patient-relevant informa.The storage of conventional digital section is in units of section, view data is stored with image pyramid layering (structure as shown in Figure 1), 101 be wherein bottom sectioning image in Fig. 1,102 is high-resolution bottom layer image, 103 for checking image-region, 104 is the middle multiplying power image of intermediate resolution, and 105 is middle multiplying power sectioning image, and 106 is the thumbnail of low resolution.Because digital slices stock size is all more than tens00000000 pixels, need the hundreds of million even memory capacity of gigabytes; Metadata is then stored in file in the mode such as key-value pair, XML, JSON.Finally be packaged into single large files or some files, be directly stored on file system.This storage mode also exists following problem:
1) when query filter section metadata, after needing to open respectively and often opening section file, just can read metadata, inefficiency, simultaneously easily occur mistake when Concurrency Access;
2) when many people browse same section, can access same file, hot spot data is too concentrated, easily causes performance bottleneck simultaneously;
3) there is Single Point of Faliure, if file part damages, then usually cause whole section content all cannot read;
4) need to solve data backup problem, with antimagnetic disc or file corruption, cause loss of data;
5) owing to storing in units of section, before file transfer is complete, cannot use;
6) the section form of different vendor is different, can only store respectively, cannot unified interface use;
7) concurrent, highly reliable, the extendible facility of the height that novel object storage system cannot be adopted to bring.
Summary of the invention
For above-mentioned technical matters, object of the present invention is just to provide a kind of efficient digital slices storage system and the digital slices browsing method based on this digital slices storage system, for efficient storage digital slices, the object of the instantaneously browsing of digital slices can be realized simultaneously.
In order to realize above-mentioned object, this invention takes following solution: a kind of digital slices storage system, is characterized in that, comprising:
Metadata store module: for the storage of metadata, and write and fetch interface that metadata is provided;
Image storage module: be made up of distributed objects storage system, adopts prolongable system architecture, for the storage of slice image data;
Module is rebuild in section: be connected with image storage module, for the image layer under each multiplying power is cut into some little paster images with the patch size of specifying;
Transport module: with image storage module and metadata store model calling, for section metadata and the view data of responsible reading different vendor, and is transferred to corresponding memory module;
Browse module: with image storage module and metadata store model calling, for obtaining and showing sectioning image.
Preferably, described distributed objects storage system is Ali's cloud OSS, AzureBlob or AWSS3 of the OpenStackSwift increased income, publicly-owned cloud.
The present invention also comprises a kind of digital slices browsing method based on above-mentioned digital slices storage system, specifically comprises the steps:
Step 1: transport module reads metadata, and transfers to metadata store module;
Step 2: after metadata store module receives metadata, by its write into Databasce;
Step 3: transport module reads slice image pyramid structure view data, and the image information be cut to after some little paster images transfers to image storage module;
Step 4: after image storage module receives view data, by it stored in distributed objects storage system;
Step 5: according to slice transmission situation, after the corresponding lower image of upper layer images completes image, can generate upper layer images by lower image;
Step 6: browser obtains section metadata from metadata store module;
Step 7: browser obtains required sectioning image according to browsing area, convergent-divergent multiple from image storage module:
Step 8: image storage module returns view data by distributed objects storage system;
Step 9: browse module and obtain paster image and show.。
Preferably, the metadata described in step 1 comprises section scanning information, storage format, patient-relevant informa's content.Such as: physical size, section scanning multiple, cutting bak stay size etc. that overall unique section id, section size, the every pixel of sectioning image are corresponding.
Preferably, the image information described in step 3 comprises the binary picture data, layer index, cutting coordinate information etc. of cutting bak stay.
Adopt technique scheme, digital slices storage system of the present invention and digital slices browsing method; Separated by will cut into slices metadata and binary picture data and store; Usage data stores metadata can obtain metadata by fast fetching, and effectively manages and statistical study; After super large Iamge Segmentation being become some little pasters, use distributed objects storage system to store respectively simultaneously, can high concurrent acquisition data, and carry out the storage of high reliability; Store digital slices in this way, have that retrieval is convenient, data-interface simple consistent, process local data is convenient, the features such as extendability is good, can reach the requirement such as High Availabitity, high concurrent, high persistence simultaneously.
Accompanying drawing explanation
Fig. 1 is sectioning image pyramid storage organization;
Fig. 2 is digital slices storage system logic relation schematic diagram of the present invention.
Embodiment
Below provide a specific embodiment to describe detailed step of the present invention in detail, but the interest field be not intended to limit the present invention.
As shown in Figure 2, digital slices storage system of the present invention comprises a kind of digital slices storage system, it is characterized in that, comprising:
Metadata store module: can be made up of some databases, efficiently, reliably stores support by high availability scheme for section metadata provides, provides write and the fetch interface of metadata;
View data memory module: for the storage of sectioning image; Be made up of distributed objects storage system, adopt extendible system architecture, utilize multiple stage storage server to share memory load, utilize location server to locate storage information, not only increase the reliability of system, availability and access efficiency, be also easy to expansion; According to availability, concurrent and persistent request, configuration object storage system, automatic multi redundancy backup to store child node, to reach indices.Distributed objects storage system can for the OpenStackSwift increased income, Ali's cloud OSS, AzureBlob, AWSS3 of publicly-owned cloud;
Module is rebuild in section: be connected with image storage module, for the image layer under each multiplying power is cut into some little paster images with the patch size of specifying;
Transport module: with image storage module and metadata store model calling, for section metadata and the view data of responsible reading different vendor, and is transferred to corresponding memory module;
Browse module: with image storage module and metadata store model calling, for obtaining and showing sectioning image.
In addition, the present invention also comprises a kind of digital slices browsing method based on above-mentioned digital slices storage system, and it comprises the steps (distributed objects storage system is for AzureBlob):
Step 1: transport module reads section metadata according to each section Vendor Interface, and transmits it to metadata store module, metadata comprises the contents such as section scanning information, storage format, patient-relevant informa; Such as: physical size, section scanning multiple, cutting bak stay size etc. that overall unique section id, section size, the every pixel of sectioning image are corresponding;
Step 2: metadata store module receive section metadata after by its write into Databasce, and according to section Id carry out index, to accelerate follow-up metadata query;
Step 3: transport module reads sectioning image pyramid structure view data, then the image layer under each multiplying power is cut into some little paster images with the patch size of specifying (as every block 256 × 256 pixel); Finally be made up of the unique identification/Id/layerIndex_x_y.jpg of request resource the section Id of paster, layer index (layerIndex), coordinate (x, y), binary picture data transferred to image storage module simultaneously; Wherein, layer index is with bottom for 0, and every convergent-divergent one deck adds 1; Coordinate removes pinup picture size gained with paster upper left corner relative image layer pixel coordinate;
Step 4: after image storage module receives data, to cut into slices, Id creates Container, under the pinup picture of same section is deposited in same Container with layerIndex_x_y.jpg filename, AzureBlob is according to Container, filename and current server loading condition, select best storage node to store, on different memory nodes, have the redundant storage of three parts, to reach the requirement to the index such as availability, persistence simultaneously;
Step 5: according to slice transmission situation, due to image pyramid structure, upper layer images reduces generation by lower image, so after the corresponding lower image of upper layer images completes transmission, can generate upper layer images according to lower image; If bottom layer image is 40 times, with 0.5 multiplying power convergent-divergent, then the 1st layer is 20 times of images, point (X on it, Y) corresponding bottom coordinate is (2*X, 2*Y), and namely the 1st layer of coordinate is that the paster of (0,0) is by the 0th layer (0,0), (1,0), (0,1), (1,1) four pieces of pasters reduce gained; In conjunction with native system storage scheme and above process of reconstruction, volume of transmitted data can be reduced;
Step 6: browse module according to the Id browsing section, from metadata store module, quick obtaining section metadata, understands the information such as sectioning image pyramid structure, size;
Step 7: according to the current browsing area of section, convergent-divergent multiple, calculated the paster image formed needed for current viewport by metadata store module, the unique identification/Id/layerIndex_x_y.jpg of composition pinup picture resource, and obtain from image storage module with this;
Step 8: after image storage module receives request, by distributed objects storage system from three nodes having required paster image, selects optimum node and returns view data;
Step 9: browse module and obtain paster image and show.
Although specifically show in conjunction with preferred embodiment and describe the present invention; but those skilled in the art should be understood that; not departing from the spirit and scope of the present invention that appended claims limits; in the form and details the present invention is made a variety of changes, be protection scope of the present invention.
Claims (5)
1. a digital slices storage system, is characterized in that, comprising:
Metadata store module: for the storage of metadata, and write and fetch interface that metadata is provided;
Image storage module: be made up of distributed objects storage system, adopts prolongable system architecture, for the storage of slice image data;
Module is rebuild in section: be connected with image storage module, for the image layer under each multiplying power is cut into some little paster images with the patch size of specifying;
Transport module: with image storage module and metadata store model calling, for section metadata and the view data of responsible reading different vendor, and is transferred to corresponding memory module;
Browse module: with image storage module and metadata store model calling, for obtaining and showing sectioning image.
2. a kind of digital slices storage system according to claim 1, is characterized in that, described distributed objects storage system is Ali's cloud OSS, AzureBlob or AWSS3 of the OpenStackSwift increased income, publicly-owned cloud.
3. a digital slices browsing method, is characterized in that: adopt the digital slices storage system described in claim 1 or 2, and comprise the steps:
Step 1: transport module reads metadata, and transfers to metadata store module;
Step 2: after metadata store module receives metadata, by its write into Databasce;
Step 3: transport module reads slice image pyramid structure view data, and the image information be cut to after some little paster images transfers to image storage module;
Step 4: after image storage module receives view data, by it stored in distributed objects storage system;
Step 5: according to slice transmission situation, after the corresponding lower image of upper layer images completes image, can generate upper layer images by lower image;
Step 6: browser obtains section metadata from metadata store module;
Step 7: browser obtains required sectioning image according to browsing area, convergent-divergent multiple from image storage module:
Step 8: image storage module returns view data by distributed objects storage system;
Step 9: browse module and obtain paster image and show.
4. digital slices browsing method according to claim 3, is characterized in that: the metadata described in step 1 comprises section scanning information, storage format, patient-relevant informa's content.
5. digital slices browsing method according to claim 3, is characterized in that: the image information described in step 3 comprises binary picture data, layer index, the cutting coordinate information of cutting bak stay.
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Cited By (6)
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| CN106599529A (en) * | 2016-10-20 | 2017-04-26 | 宁波江丰生物信息技术有限公司 | Digital slice processing system |
| CN106845122A (en) * | 2017-01-24 | 2017-06-13 | 宁波江丰生物信息技术有限公司 | A kind of encrypted transmission method of digital slices |
| CN108172277A (en) * | 2017-12-19 | 2018-06-15 | 浙江大学 | A kind of more multiplying power digital slices image storages and the method and system of browsing |
| CN110572569A (en) * | 2019-10-21 | 2019-12-13 | 麦克奥迪（厦门）医疗诊断系统有限公司 | Panoramic image generation method and file storage format and browsing method thereof |
| CN110910302A (en) * | 2019-11-29 | 2020-03-24 | 西安交通大学 | Method for storing, reading and writing extra-large image |
| CN112259223A (en) * | 2020-10-22 | 2021-01-22 | 河北工业大学 | Patient-level tumor intelligent diagnosis method based on full-field digital section |
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| CN110910302A (en) * | 2019-11-29 | 2020-03-24 | 西安交通大学 | Method for storing, reading and writing extra-large image |
| CN112259223A (en) * | 2020-10-22 | 2021-01-22 | 河北工业大学 | Patient-level tumor intelligent diagnosis method based on full-field digital section |
| CN112259223B (en) * | 2020-10-22 | 2022-08-30 | 河北工业大学 | Patient-level tumor intelligent diagnosis method based on full-field digital section |
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Application publication date: 20160511 |