WO2020062841A1 - 一种提高数字切片扫描仪建模速度的方法 - Google Patents

一种提高数字切片扫描仪建模速度的方法 Download PDF

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WO2020062841A1
WO2020062841A1 PCT/CN2019/082784 CN2019082784W WO2020062841A1 WO 2020062841 A1 WO2020062841 A1 WO 2020062841A1 CN 2019082784 W CN2019082784 W CN 2019082784W WO 2020062841 A1 WO2020062841 A1 WO 2020062841A1
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line
modeling
scanning
improving
model
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PCT/CN2019/082784
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French (fr)
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康军
贾守礼
陈木旺
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麦克奥迪实业集团有限公司
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Priority to US16/981,709 priority Critical patent/US11373366B2/en
Priority to JP2020542005A priority patent/JP7037262B2/ja
Priority to DE112019000345.3T priority patent/DE112019000345T5/de
Publication of WO2020062841A1 publication Critical patent/WO2020062841A1/zh

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    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06T—IMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T17/00—Three dimensional [3D] modelling, e.g. data description of 3D objects
    • G06T17/05—Geographic models
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06T—IMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T17/00—Three dimensional [3D] modelling, e.g. data description of 3D objects
    • G—PHYSICS
    • G02—OPTICS
    • G02B—OPTICAL ELEMENTS, SYSTEMS OR APPARATUS
    • G02B21/00—Microscopes
    • G02B21/0004—Microscopes specially adapted for specific applications
    • G02B21/002—Scanning microscopes
    • G02B21/0024—Confocal scanning microscopes (CSOMs) or confocal "macroscopes"; Accessories which are not restricted to use with CSOMs, e.g. sample holders
    • G02B21/008—Details of detection or image processing, including general computer control
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06T—IMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T3/00—Geometric image transformation in the plane of the image
    • G06T3/40—Scaling the whole image or part thereof
    • G06T3/4038—Scaling the whole image or part thereof for image mosaicing, i.e. plane images composed of plane sub-images

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  • the invention belongs to the field of microscopy technology, in particular to a method for improving the modeling speed and accuracy of a digital slice scanner.
  • Digital slice scanner is a precision instrument that integrates optical, mechanical, electronic, computer and other multi-disciplinary technologies. By controlling the microscopic imaging system and the slice to move with a certain regularity, it collects multiple continuous high-resolution microscopic images. , And then stitching to generate a high-resolution full-slice image (WSI, also known as virtual slice). After turning a traditional slice into a high-resolution digital picture, users can browse the slice on a computer or mobile device anytime and anywhere without the microscope. At the same time, it will never fade, easy to save, manage, share, and view the entire field of view. Shrinking and other advantages. It has been widely used in the fields of pathological diagnosis, teaching training, drug research and scientific research.
  • Patent 201310549353.2 adopts single-frame image focus optimization. By analyzing the current image Z-focus data of the same field of view in the field of view and the Z-level focus data of different images collected in the same field of view, a high-quality scanned image can be obtained. Speed performance is again affected.
  • the focal plane position is such that when scanning, there is no need to move the Z axis to collect multiple images to calculate the defocus amount, and only the Z axis needs to be driven according to the modeled focal plane position, which significantly increases the speed.
  • the above technical solutions have the following shortcomings.
  • the image quality depends on the number of model points. The more the number, the closer the focal plane model is to the actual focal plane, and the better the image quality.
  • the speed of modeling will also be reduced. Slower.
  • the modeling speed is a major factor that affects the modeling scan time.
  • the focal plane model has been calculated before scanning, if there is an error in the stage during scanning, such as the model point is not the same as the focal plane position during modeling and scanning imaging, it will also lead to image quality Falling, that is, the accuracy of the repeated motion of the stage is high.
  • the purpose of the present invention is to provide a method for improving the modeling speed of a digital slice scanner. Modeling and scanning imaging are performed in units of scanning line strips, and modeling and scanning are performed on the current line strip. After that, modeling and scanning imaging of the next line strip are performed. The time it takes to wrap a line at the end of a line and return to the beginning of the next line, and complete the modeling during this time. In this way, the modeling time is paralleled with the scanning and wrapping process, which effectively reduces the equivalent modeling time.
  • the scanning area is divided into multiple scanning line strips during scanning, and each scanning line strip is scanned and imaged in turn, and then seamlessly stitched into a complete digital slice.
  • the beginning of the stripe is moved toward the end of the line. After each line is scanned, it returns to the beginning of the next line to be scanned. During this period, the focal plane position of the model point on the line to be scanned is obtained and constructed. Mode, and then use this model to image from the beginning of the line to the end of the line.
  • the scanning camera is a line scan camera or an area scan camera. Specifically, when working, first go to the end of the first scanning line strip, and select a few points as model points on the first line strip. During the return to the beginning of the line, obtain the focal plane positions of these model points and perform modeling After reaching the beginning of the line and completing the modeling, imaging of the first line is started.
  • the line After scanning the line, the line is directly wrapped to the end of the second line, and after returning to the line of the second line During the first process, the second line band is modeled (including selecting model points to obtain the focal point position of the model point), and the second line band is imaged after reaching the beginning of the second line band, and so on. Subsequent line bands are modeled and scanned for imaging until all line bands for the scanning area are imaged.
  • the position and number of model points used in line strip modeling can be flexibly determined, and some line strips are not allowed to have model points. It is preferable to select at least one position as a model point for each strip.
  • model points on the line band Preferably, if there are model points on the line band, only the model points on the line band may be used in the line band modeling, and the modeling method may adopt piecewise linear fitting, polynomial fitting, and the like. It can also be combined with existing model points, such as the model points on the scanned strips, or the model points that have been obtained in advance.
  • the modeling method can use the triangular patch method, nonlinear polynomial method, and so on.
  • model points on the line strip that have been scanned can also include model points obtained in advance.
  • the modeling method can use the triangular patch method. , Non-linear polynomial method, etc.
  • the present invention has the following advantages: first, without reducing the scanning speed, adding model points and improving the quality of scanned images; and second, performing modeling and scanning imaging in units of line bands without cumulative errors.
  • the requirements on the stage are low.
  • FIG. 1 is a schematic diagram of a method for improving modeling speed of a digital slice scanner based on line band modeling and imaging;
  • FIG. 2 is a schematic diagram of modeling using piecewise linear fitting and polynomial fitting for a method for improving the modeling speed of a digital slice scanner according to the present invention
  • FIG. 3 is a schematic diagram of modeling using a triangular patch method and a non-linear polynomial method to improve the modeling speed of a digital slice scanner according to the present invention
  • FIG. 4 is a schematic diagram of a unidirectional imaging method for improving the modeling speed of a digital slice scanner according to the present invention.
  • a method for improving the modeling speed of a digital slice scanner adopts unidirectional scanning imaging, and uses scanning line bands as a unit for modeling and scanning imaging. And return to the beginning of the next scanning line with the period to obtain the focal point position of the model point on the next line and model.
  • the equipment assembly includes a stage for placing the sliced sample and driving the sliced sample to move along the X-axis direction and move along the Y-axis direction.
  • the X and Y-axis directions are perpendicular to each other and form a horizontal plane; the lighting device, The illumination device is used for partially or totally illuminating the sliced sample; the objective lens is used to observe the sliced sample against the bright part; the Z-axis controller controls the objective lens to move in the Z-axis direction to The objective lens is focused to obtain a clear image of the sliced sample.
  • the Z axis direction is along the imaging optical axis direction of the automatic scanning system of the microsection, which is perpendicular to the X and Y axes, respectively.
  • the X, Y, and Z axes form an orthogonal coordinate system. ;
  • the sample may not necessarily be placed on the xy stage. It only needs to ensure that the imaging system and the sample can move orthogonally, that is, only the x axis drives the sample movement, and the y axis drives the imaging system to move in the orthogonal direction.
  • Step 2 Prepare a sample, place the sliced sample on a stage, and use a lighting device to illuminate part or all of the sliced sample;
  • Step three the focal plane is modeled, the objective lens is used to obtain the focal plane position of each area on the sliced sample, and the focal plane model of the sliced sample is established by the scanning camera, and then the field of view size is obtained, and then the computing device is used to obtain the field of view size Decide the width and number of scanning strip lines;
  • Step 4 One-way imaging, modeling and scanning imaging in units of scanning line bands, using the period of line feed and returning to the beginning of the next scanning line band to obtain the focal point position of the model point on the next line band and modeling .
  • the model points on the line strip are selected when the line strip is modeled.
  • the modeling method uses piecewise linear fitting or polynomial fitting.
  • the model points on the row band and the obtained model points on the previous row band are combined when the row band is modeled.
  • the obtained model points on the previous row of bands are the model points on the already scanned band.
  • the model points obtained on the previous line may also be model points obtained in advance.
  • the modeling method uses triangular patch method or nonlinear polynomial method.
  • the modeling method can adopt piecewise linear fitting, polynomial fitting, etc. It can also be combined with existing model points, such as the model points on the scanned strips, or the model points that have been obtained in advance.
  • the modeling method can use the triangular patch method, nonlinear polynomial method, and so on.
  • the scanning camera divides the scanning area into multiple scanning line strips during scanning, scans and scans each scanning line strip in turn, and then seamlessly stitches it into a complete digital slice.
  • scanning the line strip uses a single direction, that is, imaging
  • imaging The time is from the beginning of the scanning strip to the end of the line. After each scanning of a line strip, it returns to the beginning of the next line strip to be scanned. During this period, the focus of the model point on the line to be scanned is obtained. Face position and modeling, and then follow this model to image from the beginning of the line to the end of the line.
  • Scanning cameras are line scan cameras or area scan cameras.
  • the position and number of model points used in the line strip modeling may allow some line strips to have no model points. For those line strips without model points, existing model points may be combined, such as
  • the model points on the scanned line strips may also include model points obtained in advance.
  • the modeling method may use a triangular patch method, a nonlinear polynomial method, and the like. By scanning the camera, the scanning area is divided into multiple scanning line strips during scanning, and each scanning line strip is scanned and imaged in turn, and then seamlessly stitched into a complete digital slice. When scanning the line strips in a single direction, that is, imaging The time is from the beginning of the scanning strip to the end of the line.
  • Scanning cameras are line scan cameras or area scan cameras.
  • the difference between the first embodiment and the second embodiment is that in the first embodiment, piecewise linear fitting, polynomial fitting, or triangular patch method, non-linear polynomial method, etc. are used to complete the line band modeling with model points on the line band. .
  • the second embodiment adopts the triangular patch method and the non-linear polynomial method to complete the line band modeling without the model points on the line band.
  • the method for improving the modeling speed of the digital slice scanner provided by the present invention has been described in detail above.

Abstract

本发明公开了一种提高数字切片扫描仪建模速度的方法，属于显微技术领域，用于改进目前采用的焦面建模方法的速度和质量，一方面，由于图像质量的要求，导致建模的速度缓慢；另一方面，由于模型点在建模时和扫描成像时的焦面位置不一样，会导致图像的质量下降，即对载物台的运动重复精度较高的问题。本发明以扫描行带为单位进行建模和扫描成像，在当前行带建模并扫描结束后再进行下一个行带的建模和扫描成像，其中下一个行带的建模利用从当前行带行尾换行并返回到下一个行带行首的时间，在此期间完成建模，这样将建模时间与扫描换行过程并行，有效减少等效的建模时间。

Description

一种提高数字切片扫描仪建模速度的方法 技术领域
本发明属于显微技术领域，具体来说，是一种提高数字切片扫描仪建模速度和准确度的方法。
背景技术
数字切片扫描仪是一种集光学、机械、电子、计算机等多学科技术为一体的精密仪器，通过控制显微成像系统和切片以一定的规则运动，采集多张连续的高分辨率显微图像，再拼接生成一张高分辨率的全切片图像(WSI，也称为虚拟切片)。将传统切片变成一张高分辨率的数字图片后，用户可以脱离显微镜随时随地在计算机或移动设备上浏览切片，同时具有永不褪色，易于保存、管理、分享、全视场查看可随意放大缩小等优点。已经广泛应用于病理诊断、教学培训、药物研究和科学研究等领域。
随着应用的推广，对扫描仪的性能越来越高，特别是扫描质量与速度，要获得比较好的图像质量，要求每个视野对焦准确，而通常数字化一张切片需要拍摄成千上万个视野的图像，所以对焦方式会影响扫描速度。传统的每个视野都对焦，虽然可以获得较好的图像质量，但速度成为瓶颈。
专利201310549353.2采用单帧图像的聚焦优化，通过对视场中同一个视野图像的当前图像Z聚焦数据和同一个视野已采集的不同图像Z层面聚焦数据进行分析可以得到高质量的扫描图像，但扫描速度性能又受到影响。
目前更多的是采用焦面建模的方法，如专利201110283732.2，即先选取切片的若干视场计算出焦面位置作为模型点，根据这几个模型点通过算法估算出切片中每个视场的焦面位置，这样在扫描时，不需要再移动Z轴采集多张图像计算离焦量，只需根据建模的焦面位置驱动Z轴即可，显著提高速度。但是上述技术方案存在以下不足，第一，图像质量则取决于模型点的数量，数量越多，其焦面模型越接近实际的焦面，图像质量越好，但会导致建模的速度也就越慢。所以建模速度是影响建模扫描法时间的一种主要因素。第二，由于焦面模型在扫描之前己经计算完成，如果在扫描过程中载物台出现误差，如模型点在建模时和扫描成像时的焦面位置不一样，也会导致图像的质量下降，即对载物台的运动重复精度较高。
发明内容
本发明目的是旨在提供了一种提高数字切片扫描仪建模速度的方法。采用以扫描行带为单位进行建模和扫描成像，在当前行带建模并扫描，结束后再进行下一个行带的建模和扫描成像，其中下一个行带的建模利用了从当前行带行尾换行并返回到下一个行带行首的时间，在此期间完成建模，这样将建模时间与扫描换行过程并行，有效减少等效的建模时间。
为实现上述技术目的，本发明采用的技术方案如下：
通过扫描相机在扫描时会将扫描区域分割成多个扫描行带，依次对每个扫描行带扫描成像，然再无缝拼接成一张完整的数字切片，扫描行带时采用单方向，即成像时都是从扫描
条带的行首往行尾方向进行，每扫描完一个行带时都要返回至下一个待扫描行带的行首，在此期间获得待扫描行带上模型点的焦面位置并进行建模，然后依照此模型从行首开始往行尾方向成像。其中，所述扫描相机采用线扫相机或面阵相机。具体为工作时先走到第一个扫描行带的行尾，并在第一个行带上选取若干点作为模型点，在返回至行首期间获得这些模型点的焦面位置并进行建模，到达行首并完成建模后开始对第一个行带进行成像，该行带 扫描成像后，直接换行到第二个扫描行带的行尾，在返回至第二个扫描行带的行首过程中，对第二个行带进行建模(包括选取模型点，获得模型点的焦面位置)，到达第二个行带行首后开始对第二行带进行成像，依此类推对后续的行带进行建模和扫描成像，直至完成扫描区域所有行带的成像。
在进行行带建模时所用模型点的位置及数量都可灵活确定，允许部分行带没有模型点，优选的为每个条带上至少选择1个位置作为模型点。
优选的，对于行带上有模型点的，在进行行带建模时可以仅用该行带上的模型点，建模方法可以采用分段线性拟合、多项式拟合等。也可以结合已有的模型点，如已完成扫描的行带上模型点，也可以包括事先已获得的模型点，建模方法可以采用三角面片法，非线性多项式法等。
优选的，对于行带上没有模型点的，可以结合已有的模型点，如已完成扫描的行带上模型点，也可以包括事先已获得的模型点，建模方法可以采用三角面片法，非线性多项式法等。
本发明相比现有技术，其一，在没有降低扫描速度的情况下，增加了模型点，提高了扫描图像质量，其二，以行带为单位进行建模和扫描成像，没有累积误差，对载物台的要求低。
附图说明
本发明可以通过附图给出的非限定性实施例进一步说明；
图1为本发明一种提高数字切片扫描仪建模速度的方法的基于行带建模及成像的方法示意图；
图2为本发明一种提高数字切片扫描仪建模速度的方法采用分段线性拟合、多项式拟合建模示意图；
图3为本发明一种提高数字切片扫描仪建模速度的方法采用三角面片法，非线性多项式法建模示意图；
图4为本发明一种提高数字切片扫描仪建模速度的方法单向成像示意图。
具体实施方式
为了使本领域的技术人员可以更好地理解本发明，下面结合附图和实施例对本发明技术方案进一步说明。
如图1，图2，图3，图4所示，一种提高数字切片扫描仪建模速度的方法，采用单方向扫描成像，以扫描行带为单位进行建模和扫描成像，利用在换行并返回下一个扫描行带行首的期间内获得下一个行带上模型点的焦面位置并建模。
具体包括以下步骤，
步骤一，设备组装，包括载物台，该载物台用于放置切片样品并带动切片样品沿X轴方向运动、沿Y轴方向移动，X、Y轴方向彼此垂直并构成水平面；照明装置，该照明装置用于对切片样品的局部或全部照亮；物镜，该物镜用于对照亮部分的切片样品进行观察；Z轴控制器，该Z轴控制器控制物镜沿Z轴方向移动，以使物镜调焦获得切片样品清晰的图像，Z轴方向沿该显微切片的全自动扫描系统的成像光轴方向，与X、Y轴分别垂直，X，Y、Z三轴构成正交坐标系；当然需要指出的是，样品未必放在xy载物台上。只要保证成像系统和样品可以正交运动即可，即：仅x轴带动样品运动，y轴带动成像系统在正交方向运动。
步骤二，准备样品，将切片样品放置在载物台上，采用照明装置照亮切片样品的局部或全部区域；
步骤三，焦面建模，采用物镜获取切片样品上各区域的焦面位置，并通过扫描相机建立切片样品的焦面模型，进而获取视场大小，再利用计算设备，通过获取的视场大小决定扫描条带行带的宽度和个数；
步骤四，单向成像，以扫描行带为单位进行建模和扫描成像，利用在换行并返回下一个扫描行带行首的期间内获得下一个行带上模型点的焦面位置并建模。
优选的，在行带建模时仅选用该行带上的模型点。建模方法采用分段线性拟合或多项式拟合等。
优选的，在行带建模时结合该行带上的模型点以及前一行带上的已获得的模型点。前一行带上的已获得的模型点是已经扫描完的条带上的模型点。当然，前一行带上的已获得的模型点也可以是事先获得的模型点。建模方法采用三角面片法或非线性多项式法等。
实施例一，
作为优选实施方案一，在进行行带建模时所用模型点的位置及数量，优选的为每个条带上至少选择1个位置作为模型点。对于行带上有模型点的，在进行行带建模时可以仅用该行带上的模型点，建模方法可以采用分段线性拟合、多项式拟合等。也可以结合已有的模型点，如已完成扫描的行带上模型点，也可以包括事先已获得的模型点，建模方法可以采用三角面片法，非线性多项式法等。通过扫描相机在扫描时会将扫描区域分割成多个扫描行带，依次对每个扫描行带扫描成像，然后再无缝拼接成一张完整的数字切片，扫描行带时采用单方向，即成像时都是从扫描条带的行首往行尾方向进行，每扫描完一个行带时都要返回至下一个待扫描行带的行首，在此期间获得待扫描行带上模型点的焦面位置并进行建模，然后依照此模型从行首开始往行尾方向成像。扫描相机采用线扫相机或面阵相机。
实施例二，
作为优选实施方案二，在进行行带建模时所用模型点的位置及数量，允许部分行带上可以没有模型点，对于行带上没有模型点的，可以结合已有的模型点，如已完成扫描的行带上模型点，也可以包括事先已获得的模型点，建模方法可以采用三角面片法，非线性多项式法等。通过扫描相机在扫描时会将扫描区域分割成多个扫描行带，依次对每个扫描行带扫描成像，然再无缝拼接成一张完整的数字切片，扫描行带时采用单方向，即成像时都是从扫描条带的行首往行尾方向进行，每扫描完一个行带时都要返回至下一个待扫描行带的行首，在此期间获得待扫描行带上模型点的焦面位置并进行建模，然后依照此模型从行首开始往行尾方向成像。扫描相机采用线扫相机或面阵相机。
实施例一和实施例二的区别在于，实施例一采用分段线性拟合、多项式拟合，或采用三角面片法，非线性多项式法等，完成行带上有模型点的行带建模。其中，当出现行带上没有模型点的行带，实施例二采用三角面片法，非线性多项式法，完成行带上没有模型点的行带建模。以上对本发明提供的一种提高数字切片扫描仪建模速度的方法进行了详细介绍。
具体实施例的说明只是用于帮助理解本发明的方法及其核心思想。应当指出，对于本技术领域的普通技术人员来说，在不脱离本发明原理的前提下，还可以对本发明进行若干改进和修饰，这些改进和修饰也落入本发明权利要求的保护范围内。

Claims (10)

  1. 一种提高数字切片扫描仪建模速度的方法，采用单方向扫描成像，其特征在于：以扫描行带为单位进行建模和扫描成像，利用换行并返回下一个扫描行带行首的期间内获得下一个行带上模型点的焦面位置并建模。
  2. 根据权利要求1所述的一种提高数字切片扫描仪建模速度的方法，其特征在于：在行带建模时仅选用该行带上的模型点。
  3. 根据权利要求2所述的一种提高数字切片扫描仪建模速度的方法，其特征在于：建模方法采用分段线性拟合或多项式拟合。
  4. 据权利要求1所述的一种提高数字切片扫描仪建模速度的方法，其特征在于：在行带建模时结合该行带上的模型点以及前一行带上的已获得的模型点。
  5. 根据权利要求4所述的一种提高数字切片扫描仪建模速度的方法，其特征在于：前一行带上的已获得的模型点是已经扫描完的行带上的模型点。
  6. 根据权利要求4所述的一种提高数字切片扫描仪建模速度的方法，其特征在于：前一行带上的已获得的模型点是事先获得的模型点。
  7. 根据权利要求5或6所述的一种提高数字切片扫描仪建模速度的方法，其特征在于：建模方法采用三角面片法或非线性多项式法。
  8. 根据权利要求2或4所述的一种提高数字切片扫描仪建模速度的方法，其特征在于：扫描相机在扫描时会将扫描区域分割成多个扫描行带，依次对每个扫描行带扫描成像，然后再无缝拼接成一张完整的数字切片，扫描行带时采用单方向，即成像时都是从扫描条带的行首往行尾方向进行，每扫描完一个行带都要返回至下一个待扫描行带的行首，在此期间获得待扫描行带上模型点的焦面位置并进行建模，然后依照此模型从行首开始往行尾方向扫描成像。
  9. 根据权利要求8所述的一种提高数字切片扫描仪建模速度的方法，其特征在于：所述扫描相机采用线扫相机或面阵相机。
  10. 根据权利要求9所述的一种提高数字切片扫描仪建模速度的方法，其特征在于：在进行行带建模时所用模型点的位置及数量都可灵活确定，且允许部分行带没有模型点，优选的为每个条带上至少选择1个位置作为模型点。
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