CN111292315A - Rapid registration algorithm for pathological section tissue area - Google Patents
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Abstract
The invention discloses a pathological section tissue area rapid registration algorithm, which comprises the following steps: s100, acquiring a thumbnail a1 from the digital slice A1, and acquiring a thumbnail a2 from the digital slice A2; s200, segmenting a tissue region map b1 from a thumbnail a1, and segmenting a tissue region map b2 from a thumbnail a 2; s300, taking the tissue region map b1 as a template, taking mutual information measurement of the tissue region map b1 and the tissue region map b2 as an objective function, and searching an optimal transformation matrix from three dimensions of a rotation angle, scale transformation and turning over to enable the mutual information measurement of the tissue region map b1 and the transformed tissue region map b2 to be maximum, so that a coarse registration result c1 is obtained; s400, the tissue region map b1 is used as a template, the coarse registration result c1 is used as an initialization image, and similarity measurement in the tissue region map b1 and the coarse registration result c1 is optimized, so that the optimal solution can be converged quickly, and a fine registration result is obtained. The invention has better generalization capability of the registration process and higher registration efficiency.
Description
Technical Field
The invention relates to the technical field of image matching, in particular to a rapid registration algorithm for a pathological section tissue region.
Background
Clinically, a plurality of sections are taken from the same tissue by histological immunohistochemical staining of a pathology department, different staining agents are used for staining, and doctors perform registration in the brain and sea when reading the sections. This method is difficult to register effectively in the brain when the sections are too lightly stained, and the physician needs repeated comparisons to overlap the regions in the brain.
The currently available solution is to perform registration directly on the images taken on the digital scan slices, but rotation, flip, displacement and slight deformation conditions are usually present for different slices. The direct registration method is time consuming and cannot guarantee correct registration.
Disclosure of Invention
The invention aims to provide a rapid registration algorithm for a pathological section tissue region, which has better generalization capability of a registration process and higher registration efficiency.
In order to achieve the purpose, the invention is realized by adopting the following technical scheme:
the invention discloses a pathological section tissue area rapid registration algorithm, which comprises the following steps:
s100, acquiring a thumbnail a1 from the digital slice A1, and acquiring a thumbnail a2 from the digital slice A2;
s200, segmenting a tissue region map b1 from a thumbnail a1, and segmenting a tissue region map b2 from a thumbnail a 2;
s300, taking the tissue region map b1 as a template, taking mutual information measurement of the tissue region map b1 and the tissue region map b2 as an objective function, and searching an optimal transformation matrix from three dimensions of a rotation angle, scale transformation and turning over to enable the mutual information measurement of the tissue region map b1 and the transformed tissue region map b2 to be maximum, so that a coarse registration result c1 is obtained;
s400, the tissue region map b1 is used as a template, the coarse registration result c1 is used as an initialization image, and similarity measurement in the tissue region map b1 and the coarse registration result c1 is optimized, so that the optimal solution can be converged quickly, and a fine registration result is obtained.
Preferably, in step S200, the segmentation algorithm includes a threshold segmentation algorithm, a region growing segmentation algorithm, and a segmentation algorithm based on deep learning.
Preferably, in step S300, the method for determining the optimal transformation matrix includes the following steps:
S3111and rotating the tissue region map b2 by the angle p to obtain a tissue region map b 2'1Comparison of tissue region map b 2'1And the tissue region map b1 to obtain a mutual information measure k1;
S3112And a tissue region map b 2'1Rotating the angle p to obtain a tissue region map b 2'2Comparison of tissue region map b 2'2And the tissue region map b1 to obtain a mutual information measure k2;
……
S311iAnd a tissue region map b 2'i-1Rotating the angle p to obtain a tissue region map b 2'iComparison of tissue region map b 2'iAnd the tissue region map b1 to obtain a mutual information measure ki;
……
S311nAnd a tissue region map b 2'n-1Rotating the angle p to obtain a tissue region map b 2'nComparison of tissue region map b 2'nAnd the tissue region map b1 to obtain a mutual information measure kn;
S312, measuring k from mutual information1Mutual information metric knIn the selected maximum mutual information measure kmaxDetermining the corresponding most suitable rotation angle, obtaining a tissue region map b2_1,
wherein 1 < i < n, n p 360 °.
Preferably, in step S300, the method for determining the optimal transformation matrix further includes the following steps:
S3211and converting the tissue region map b2_1 into magnification q to obtain a tissue region map b2_ 1'1Comparison of tissue region map b2_ 1'1And the tissue region map b1 are obtainedMutual information metric x1;
……
S321hAnd a tissue region map b2_ 1'h-1The magnification q was converted to obtain a tissue region map b2_ 1'hComparison of tissue region map b2_ 1'hAnd the tissue region map b1 to obtain a mutual information measure xh;
……
S321mAnd a tissue region map b2_ 1'm-1The magnification q was converted to obtain a tissue region map b2_ 1'mComparison of tissue region map b2_ 1'mAnd the tissue region map b1 to obtain a mutual information measure xm;
S322, measuring x from mutual information1Mutual information metric xmIn the selected maximum mutual information metric xmaxThen, the corresponding optimum conversion magnification is determined, and the tissue region map b2_2 is obtained.
Preferably, in step S300, the method for determining the optimal transformation matrix further includes the following steps:
s331, turning over the tissue region map b2_2 to obtain a tissue region map b2_2 ', comparing the tissue region map b2_ 2' with the tissue region map b1 to obtain a mutual information metric y, and comparing the mutual information metric y with a maximum mutual information metric xmaxAnd a corresponding coarse registration result c1 is obtained.
Preferably, the angle p for each rotation is 1 °.
Preferably, the magnification q per conversion is 0.05 times,
step S3211~S321mIn the tissue region map b2_1, the entire conversion magnification is from 0.8 times to 1.2 times.
Preferably, in step S300, the step of,
mutual information metric calculates the similarity of X and Y images by measuring the distance between the joint distribution p (X, Y) and the completely independent p (X) p (Y) correlation distribution, the calculation formula being:
preferably, in step S400, the similarity measure in the optimized tissue region map b1 and the coarse registration result c1 is an intensity-based image matching method.
Preferably, in step S400, the algorithm for optimizing the similarity measure in the tissue region map b1 and the coarse registration result c1 includes a gradient descent algorithm.
The invention has the beneficial effects that:
1. the invention solves the problem that the regions such as positive contrast and the like which are irrelevant to registration have influence on the result of the registration algorithm;
2. the invention solves the problems of long time consumption and difficult optimization of direct registration;
3. the invention has better generalization capability of the registration process and higher registration efficiency.
Drawings
FIG. 1 is a schematic illustration of a thumbnail a 1;
FIG. 2 is a schematic illustration of thumbnail a 2;
FIG. 3 is a schematic view of tissue region map b 1;
FIG. 4 is a schematic view of tissue region map b 2;
FIG. 5 is a flowchart illustrating the step S300;
fig. 6 is a schematic diagram of the coarse registration result c 1;
fig. 7 is an overlay display effect of the tissue region map b1 and the coarse registration result c 1;
fig. 8 is an overlapping display effect of the tissue region map b1 and the fine registration result in step S400.
Detailed Description
In order to make the objects, technical solutions and advantages of the present invention more apparent, the present invention is further described in detail below with reference to the accompanying drawings.
As shown in fig. 1 to 8, the present invention comprises the following steps:
s100, thumbnail acquisition:
acquiring a thumbnail a1 and a thumbnail a2 from a digital slice WSI to be registered;
s200, effective area segmentation:
dividing the effective regions in the thumbnail by using a division algorithm, wherein the division algorithm comprises traditional division algorithms such as threshold division and region growing and a division algorithm based on deep learning, the division algorithm is not limited to the traditional division algorithm, the division algorithm is used for dividing a tissue region map b1 from the thumbnail a1, and the division algorithm is used for dividing a tissue region map b2 from the thumbnail a 2;
s300, coarse image registration:
and (3) taking the tissue region map b1 as a template, taking the mutual information measurement of the tissue region map b1 and the tissue region map b2 as an objective function, and searching an optimal transformation matrix from three dimensions of rotation angle, scale transformation and whether turning over, so that the mutual information measurement of the tissue region map b1 and the transformed tissue region map b2 is maximum, and a coarse registration result is obtained.
When the method for searching the optimal transformation matrix is adopted, the mutual information quantity between the tissue region graph b2 and the tissue region graph b1 after the tissue region graph b2 is transformed by a rotation angle of 0-359 degrees is calculated, and the angle when the mutual information quantity is the maximum is taken as the rotation angle;
setting the current rotation angle as an initial quantity, calculating the mutual information quantity of each scale transformation between 0.8 and 1.2 by taking 0.05 times as the granularity, and taking the multiplying power when the maximum mutual information quantity is taken as the scale transformation quantity;
and finally comparing the mutual information quantity before and after mirror image turning, taking the maximum state as the optimal state, and calculating a transformation matrix by using the current rotation angle, the scale variation and whether turning is performed or not.
Wherein the mutual information metric calculates the similarity of the X and Y images by measuring the distance between the joint distribution p (X, Y) and the completely independent p (X) p (Y) correlation distribution by the formula:
s400, fine image registration:
by taking the tissue region map b1 as a template, taking the coarse registration result c1 as an initialization image, optimizing similarity measures in the tissue region map b1 and the coarse registration result c1 by using an optimization algorithm such as a gradient descent algorithm and the like, the optimal solution can be converged quickly to obtain a fine registration result,
the method adopted in the step is a classic intensity-based image matching method, details in the process are not in the patent protection range, and the method is only used as a loop in the whole process of the scheme.
The present invention is capable of other embodiments, and various changes and modifications may be made by one skilled in the art without departing from the spirit and scope of the invention.
Claims (10)
1. A pathological section tissue region fast registration algorithm is characterized by comprising the following steps:
s100, acquiring a thumbnail a1 from the digital slice A1, and acquiring a thumbnail a2 from the digital slice A2;
s200, segmenting a tissue region map b1 from a thumbnail a1, and segmenting a tissue region map b2 from a thumbnail a 2;
s300, taking the tissue region map b1 as a template, taking mutual information measurement of the tissue region map b1 and the tissue region map b2 as an objective function, and searching an optimal transformation matrix from three dimensions of a rotation angle, scale transformation and turning over to enable the mutual information measurement of the tissue region map b1 and the transformed tissue region map b2 to be maximum, so that a coarse registration result c1 is obtained;
s400, the tissue region map b1 is used as a template, the coarse registration result c1 is used as an initialization image, and similarity measurement in the tissue region map b1 and the coarse registration result c1 is optimized, so that the optimal solution can be converged quickly, and a fine registration result is obtained.
2. The registration algorithm of claim 1, wherein: in step S200, the segmentation algorithm includes a threshold segmentation algorithm, a region growing segmentation algorithm, and a segmentation algorithm based on deep learning.
3. The registration algorithm of claim 1, wherein: in step S300, the method for determining the optimal transformation matrix includes the following steps:
S3111and rotating the tissue region map b2 by the angle p to obtain a tissue region map b 2'1Is toTissue comparison region map b 2'1And the tissue region map b1 to obtain a mutual information measure k1;
S3112And a tissue region map b 2'1Rotating the angle p to obtain a tissue region map b 2'2Comparison of tissue region map b 2'2And the tissue region map b1 to obtain a mutual information measure k2;
……
S311iAnd a tissue region map b 2'i-1Rotating the angle p to obtain a tissue region map b 2'iComparison of tissue region map b 2'iAnd the tissue region map b1 to obtain a mutual information measure ki;
……
S311nAnd a tissue region map b 2'n-1Rotating the angle p to obtain a tissue region map b 2'nComparison of tissue region map b 2'nAnd the tissue region map b1 to obtain a mutual information measure kn;
S312, measuring k from mutual information1Mutual information metric knIn the selected maximum mutual information measure kmaxDetermining the corresponding most suitable rotation angle, obtaining a tissue region map b2_1,
wherein 1 < i < n, n p 360 °.
4. The registration algorithm of claim 3, wherein: in step S300, the method for determining the optimal transformation matrix further includes the following steps:
S3211and converting the tissue region map b2_1 into magnification q to obtain a tissue region map b2_ 1'1Comparison of tissue region map b2_ 1'1And the tissue region map b1 to obtain a mutual information measure x1;
……
S321hAnd a tissue region map b2_ 1'h-1The magnification q was converted to obtain a tissue region map b2_ 1'hComparison of tissue region map b2_ 1'hAnd the tissue region map b1 to obtain a mutual information measure xh;
……
S321mTissue regionDomain map b2_ 1'm-1The magnification q was converted to obtain a tissue region map b2_ 1'mComparison of tissue region map b2_ 1'mAnd the tissue region map b1 to obtain a mutual information measure xm;
S322, measuring x from mutual information1Mutual information metric xmIn the selected maximum mutual information metric xmaxThen, the corresponding optimum conversion magnification is determined, and the tissue region map b2_2 is obtained.
5. The registration algorithm of claim 1, wherein: in step S300, the method for determining the optimal transformation matrix further includes the following steps:
s331, turning over the tissue region map b2_2 to obtain a tissue region map b2_2 ', comparing the tissue region map b2_ 2' with the tissue region map b1 to obtain a mutual information metric y, and comparing the mutual information metric y with a maximum mutual information metric xmaxAnd a corresponding coarse registration result c1 is obtained.
6. The registration algorithm of claim 3, wherein: the angle p of each rotation is 1 °.
7. The registration algorithm of claim 4, wherein: the multiplying power q of each transformation is 0.05 times,
step S3211~S321mIn the tissue region map b2_1, the entire conversion magnification is from 0.8 times to 1.2 times.
8. The registration algorithm according to any of claims 3-7, wherein: in the step S300, the process is performed,
mutual information metric calculates the similarity of X and Y images by measuring the distance between the joint distribution p (X, Y) and the completely independent p (X) p (Y) correlation distribution, the calculation formula being:
9. the registration algorithm of claim 1, wherein: in step S400, the similarity measure in the optimized tissue region map b1 and the coarse registration result c1 is an intensity-based image matching method.
10. The registration algorithm of claim 9, wherein: in step S400, the algorithm for optimizing the similarity measure in the tissue region map b1 and the coarse registration result c1 includes a gradient descent algorithm.
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