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Research on key algorithms of automatic device for observing the behavior of zebrafish
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摘要:
斑马鱼行为学研究已受到越来越多的关注，其空间坐标计算是斑马鱼行为分析的基础。本文设计了一种基于双目立体视觉技术的斑马鱼行为学自动观测装置。结合p率阈值化和模式阈值化，提出了图像阈值算法。计算斑马鱼图像轮廓像素坐标的平均值，得到单条斑马鱼的水平二维坐标X和Y。当不同斑马鱼的Y坐标差异较大时，对两台摄像机各自得到的斑马鱼的Y坐标分别按大小排序，同一序号即为同一目标；当Y坐标大小较为接近时，应用最小距离法识别同一斑马鱼。根据折射定理和观测装置结构，推导出斑马鱼三维空间坐标计算公式。算法复杂度分析显示本文提出的算法具有较少的运行时间。通过预设多条模型鱼的位置进行测试，计算结果与预设位置接近，验证了本文提出算法的正确性。
Abstract:Studies on the zebrafish behavior have attracted more and more attention. The algorithm of 3D coordinate calculation is the basis of zebrafish behavioral analysis. An automatic device for observing the behavior of zebrafish was designed based on binocular stereo vision technology. According to methods of p-rate threshold and pattern threshold, the image threshold algorithm was proposed. Horizontal X and Y coordinates of single zebrafish were figured out by calculating the average of pixel coordinates of image contour. If the difference of Y coordinate values among different zebrafishes is large, two groups of zebrafishes captured by two cameras will be set up separately according to the Y coordinate values, and the same serial number in two groups means the same target. If the difference of Y coordinate is small, the same target in different cameras was identified by the method of minimum distance. The formula of three-dimensional coordinates was conducted based on the refraction theorem and the structure of the observation device. Algorithm analysis shows that the running time of the algorithm proposed in the paper is saved. Validating testing to a number of fishes is designed and carried out to show that the calculated coordinates are close to the preset locations.
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Overview: Zebrafish, which is highly analogous to humans in terms of physiology and genetics, is widely used in the fields of fertility, genetics, behavioral science and molecular biology. More and more researchers have been attracted by the zebrafish behaviors. An automatic device for observing the behavior of zebrafish was designed based on the binocular stereo vision technology. The zebrafish behavioral characteristics can be calculated and analyzed by the real-time video data that is collected from two digital cameras, and the algorithm of 3D coordinate calculation is the basis of zebrafish behavioral analysis. According to methods of P-rate threshold and pattern threshold, the image threshold algorithm was proposed. Image threshold method was proposed according to the image threshold, and the image segmentation was calculated based on the threshold image. The image contour of zebrafish was calculated based on the image segmentation, and then the horizontal X and Y coordinates of single zebrafish were figured out by calculating the average of pixel coordinates of image contour. If the difference of Y coordinate values among different zebrafishes is large, two groups of zebrafishes will be set up separately according to the Y coordinate values decided by each camera, and the same serial number in two groups means the same target. If the difference of Y coordinate is small, the same target in different cameras was identified by the method of minimum distance. A three-dimensional Cartesian coordinate system was constructed. The straight line of zebrafish was calculated according to refraction principle and the optical path of zebrafish above the surface of the water, which was determined by the right camera. At the same time, the zebrafish was on the plane that was calculated by the optical path of zebrafish above the surface of the water, which was determined by the left camera. The formula of three-dimensional coordinates was conducted based on the straight line and the plane. The behaviors, such as stillness, direction, speed, etc., were calculated based on the change of zebrafish coordinates in unit time, and then the analyses of the behavior characteristics of zebrafish were put forward. Algorithm analysis shows that the running time of the algorithm proposed in the paper is saved. Five stationary model fish were randomly placed in different locations, and the coordinates of each model fish were calculated. The difference between the calculated results and the actual position shows that the maximum error is less than 12 mm and the maximum error rate is about 12%, which could meet the needs of the zebrafish experiment.
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图 1 斑马鱼行为学自动观测装置组成结构
Figure 1. Structure of the automatic device for observing the behavior of zebrafish
表 1 多条模型鱼静止坐标实验数据
Table 1. The static coordinate experimental data of model fishs
设置坐标/mm 计算坐标/mm 计算误差/mm X Y Z X Y Z X Y Z 1号鱼 84 -59 -82 96 -56 -88 12 3 -6 2号鱼 -33 -29 -44 -25 -31 -48 8 -2 -4 3号鱼 -77 64 -111 -77 70 -112 0 6 -1 4号鱼 -29 -96 -28 -31 -96 -33 -2 0 -5 5号鱼 -121 -91 -103 -123 -94 -96 -2 -3 7 
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表 2 单条模型鱼行为分析实验数据
Table 2. Experimental data of behavior analysis in single model fish
开始坐标/mm 结束坐标/mm 方向 距离/mm 速度/(mm·s-1) 行为 X0 Y0 Z0 X1 Y1 Z1 α β 第1次 -4 3 -140 100 0 -145 -2 -2 104 20.7 向右 第2次 9 -1 -155 -90 3 -155 177 0 98 19.7 向左 第3次 5 5 -145 8 101 -140 91 3 97 19.3 向前 第4次 5 -8 147 5 -106 -151 269 -3 98 19.7 向后 第5次 -1 -6 -159 2 -3 -62 51 87 103 20.7 向上
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