A Clinical Dataset and Various Baselines for Chromosome Instance Segmentation

<italic>Background:</italic> In medicine, chromosome karyotyping analysis plays a crucial role in prenatal diagnosis for diagnosing whether a fetus has severe defects or genetic diseases. However, chromosome instance segmentation is the most critical obstacle to automatic chromosome karyotyping analysis due to the complicated morphological characteristics of chromosome clusters, restricting chromosome karyotyping analysis to highly depend on skilled clinical analysts. <italic>Method:</italic> In this paper, we build a clinical dataset and propose multiple segmentation baselines to tackle the chromosome instance segmentation problem of various overlapping and touching chromosome clusters. First, we construct a clinical dataset for deep learning-based chromosome instance segmentation models by collecting and annotating 1,655 privacy-removal chromosome clusters. After that, we design a chromosome instance labeled dataset augmentation (<italic>CILA</italic>) algorithm for the clinical dataset to improve the generalization performance of deep learning-based models. Last, we propose a chromosome instance segmentation framework and implement multiple baselines for the proposed framework based on various instance segmentation models. <italic>Results and Conclusions:</italic>Experiments evaluated on the clinical dataset show that the best baseline of the proposed framework based on the Mask-RCNN model yields an outstanding result with <inline-formula><tex-math notation="LaTeX">$77\%$</tex-math><alternatives><mml:math><mml:mrow><mml:mn>77</mml:mn><mml:mo>%</mml:mo></mml:mrow></mml:math><inline-graphic xlink:href="lin-ieq1-3089507.gif"/></alternatives></inline-formula> <inline-formula><tex-math notation="LaTeX">$mAP$</tex-math><alternatives><mml:math><mml:mrow><mml:mi>m</mml:mi><mml:mi>A</mml:mi><mml:mi>P</mml:mi></mml:mrow></mml:math><inline-graphic xlink:href="lin-ieq2-3089507.gif"/></alternatives></inline-formula>, <inline-formula><tex-math notation="LaTeX">$97.5\%$</tex-math><alternatives><mml:math><mml:mrow><mml:mn>97</mml:mn><mml:mo>. </mml:mo><mml:mn>5</mml:mn><mml:mo>%</mml:mo></mml:mrow></mml:math><inline-graphic xlink:href="lin-ieq3-3089507.gif"/></alternatives></inline-formula> <inline-formula><tex-math notation="LaTeX">$AP^{50}$</tex-math><alternatives><mml:math><mml:mrow><mml:mi>A</mml:mi><mml:msup><mml:mi>P</mml:mi><mml:mn>50</mml:mn></mml:msup></mml:mrow></mml:math><inline-graphic xlink:href="lin-ieq4-3089507.gif"/></alternatives></inline-formula>, and <inline-formula><tex-math notation="LaTeX">$95.5\%\ AP^{75}$</tex-math><alternatives><mml:math><mml:mrow><mml:mn>95</mml:mn><mml:mo>. </mml:mo><mml:mn>5</mml:mn><mml:mo>%</mml:mo><mml:mspace width="4pt"/><mml:mi>A</mml:mi><mml:msup><mml:mi>P</mml:mi><mml:mn>75</mml:mn></mml:msup></mml:mrow></mml:math><inline-graphic xlink:href="lin-ieq5-3089507.gif"/></alternatives></inline-formula> segmentation <italic>precision</italic>, and <inline-formula><tex-math notation="LaTeX">$95.38\%$</tex-math><alternatives><mml:math><mml:mrow><mml:mn>95</mml:mn><mml:mo>. </mml:mo><mml:mn>38</mml:mn><mml:mo>%</mml:mo></mml:mrow></mml:math><inline-graphic xlink:href="lin-ieq6-3089507.gif"/></alternatives></inline-formula> <italic>accuracy</italic>, which exceeds results reported in current chromosome instance segmentation methods. The quantitative evaluation results demonstrate the effectiveness and advancement of the proposed method for the chromosome instance segmentation problem. The experimental code and privacy-removal clinical dataset can be found at Github.