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An automatic algorithm for identification and straightening images of curved human chromosomes

机译：识别和矫正弯曲人类染色体图像的自动算法

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摘要

Karyotyping is a standard method for presenting the complete set of the pictures of human chromosomes in a table-like format. It is usually used by a cytogenetic expert to predict the common genetic abnormalities. Producing a Karyotype from microscopic images of human chromosomes is a tedious and time-consuming task, so an automatic Karyotyping system would help the cytogenetic expert in his/her routine work. Automatic Karyotyping algorithms usually suffer the non-rigid nature of the chromosomes, which makes them to have unpredictable shapes and sizes in the images. One such problem that usually needs the operator's interaction is the existence of curved chromosomes within the images. In this paper, an effective algorithm for identification and straightening of curved human chromosomes is presented. This will extend the domain of application of the most of the previously reported algorithms to the curved chromosomes. The proposed algorithm is applied to single chromosomes that are initially modified by means of a Median filter. The medial axis (MA) of the filtered image is then extracted using a thinning procedure, which is carried out on the binary version of the image. By comparing the Euclidean distance of the endpoints and the length of the MA, a curved chromosome is identified. For chromosome straightening, the initially extracted medial axis is then modified by extending it in both ends considering the slope of the MA. Next, the original input image is intensity sampled over many closely located perpendicular lines to the MA along the chromosome which are then mapped into a matrix (as rows) producing a vertically oriented straight chromosome. For evaluation, the algorithm is applied to 54 selected highly curved chromosomes obtained at the pro-metaphase stage, which were provided by the Cytogenetic Laboratory of Cancer Institute, Imam Hospital, Tehran, Iran. The density profile and the centromeric index of the chromosomes which are among the most important and commonly used features for chromosome identification are calculated by the expert both before and after the straightening procedure. The mean squared error and the variance of the difference between the two are then obtained and compared. The results show a good agreement between the two, hence the effectiveness of the proposed method. The proposed algorithm therefore extends the domain of application of the previously reported algorithms to the highly curved chromosomes.
机译：核型分析是一种标准的方法，用于以表格形式显示人类染色体的完整图片。细胞遗传学专家通常使用它来预测常见的遗传异常。从人类染色体的显微图像产生核型是一项繁琐且耗时的工作，因此自动核型分析系统将帮助细胞遗传学专家进行日常工作。自动核型分析算法通常会遭受染色体的非刚性性质，这使它们在图像中具有不可预测的形状和大小。通常需要操作员互动的此类问题之一是图像中存在弯曲的染色体。本文提出了一种有效的识别和矫正弯曲人类染色体的算法。这将把大多数先前报道的算法的应用领域扩展到弯曲染色体。所提出的算法适用于最初通过中值滤波器修改的单个染色体。然后，使用细化过程提取滤波图像的中间轴（MA），该过程在图像的二进制版本上执行。通过比较端点的欧式距离和MA的长度，可以确定弯曲的染色体。对于染色体拉直，然后考虑到MA的斜率，通过在两端延伸来修改最初提取的中间轴。接下来，原始输入图像在沿着染色体的许多靠近MA的垂直线上进行强度采样，然后将其映射到矩阵（成行）中，产生垂直取向的直染色体。为了进行评估，将该算法应用于在前中期阶段获得的54条高度弯曲的染色体，这些染色体是由伊朗德黑兰伊玛目医院癌症研究所的细胞遗传学实验室提供的。在矫直过程之前和之后，专家都会计算出染色体的密度分布图和着丝粒指数，这些是染色体鉴定中最重要和最常用的特征。然后获得均方误差和两者之间差异的方差并进行比较。结果表明两者之间有很好的一致性，因此该方法的有效性。因此，所提出的算法将先前报道的算法的应用范围扩展到高度弯曲的染色体。

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