Abstract
Karyotype analysis based on chromosome banding and microscopic imaging is an important means for the diagnosis of genetic symptoms. Chromosome extraction is one of the key steps in karyotype analysis, but it faces some complex situations i.e. chromosome overlaps and adhesions, which are still a challenge for traditional algorithms. Here, we proposed a method for chromosome extraction based on deep learning. In this method, U-Net was used to segment the original micrographs to remove background noise such as nuclei and other interferences. Then YOLOv3 was used to detect and extract each chromosome. Further, U-Net was used again to extract the single chromosomes precisely. The results show that this method can remove effectively the interferences outside the chromosomes, and accurately extract the overlapping and adhesive chromosomes. The accuracy of extracting chromosomes from the raw G-band chromosome images reaches 99.3%. This method is of great significance for the development of automatic karyotype analysis technology.
Highlights
The karyotype analysis method analyzes the microscopic images of chromosomes in the middle division by means of banding technique, and diagnoses diseases according to the variations in the structure and number of chromosomes
Our main contribution is that we propose an end-to-end method for chromosome extraction based on the optimized combination of YOLOv3 [6] and U-Net [7], which are used for chromosome detection and chromosome segmentation, respectively
Translation and flipping of the original micrographs, the number of the image samples was expanded to 1300, of which 600 samples were used as the training set, 400 samples were used as the validation set, and the rest were used as the test set
Summary
The karyotype analysis method analyzes the microscopic images of chromosomes in the middle division by means of banding technique, and diagnoses diseases according to the variations in the structure and number of chromosomes. A typical micrograph of chromosomes is shown in Fig. (a). The karyotype map obtained by extraction and classification is shown in Fig. (b), which can be used as the basis for disease diagnosis. Accurately extracting each chromosome from the disordered original micrograph is the prerequisite for successful karyotype analysis. Chromosome extraction still mainly depends on trained professionals. Manual operations are time-consuming and laborious, which are not conducive to the analysis of a large number of samples
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