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In Computer methods and programs in biomedicine

BACKGROUND AND OBJECTIVE : Owing to the variable shapes, large size difference, uneven grayscale and dense distribution among biological cells in an image, it is still a challenging task for the standard Mask R-CNN to accurately detect and segment cells. Especially, the state-of-the-art anchor-based methods fail to generate the anchors of sufficient scales effectively according to the various sizes and shapes of cells, thereby hardly covering all scales of cells.

METHODS : We propose an adaptive approach to learn the anchor shape priors from data samples, and the aspect ratios and the number of anchor boxes can be dynamically adjusted by using ISODATA clustering algorithm instead of human prior knowledge in this work. To solve the identification difficulties for small objects owing to the multiple down-samplings in a deep learning-based method, a densification strategy of candidate anchors is presented to enhance the effects of identifying tinny size cells. Finally, a series of comparative experiments are conducted on various datasets to select appropriate a network structure and verify the effectiveness of the proposed methods.

RESULTS : The results show that the ResNet-50-FPN combining the ISODATA method and densification strategy can obtain better performance than other methods in multiple metrics (including AP, Precision, Recall, Dice and PQ) for various biological cell datasets, such as U373, GoTW1, SIM+ and T24.

CONCLUSIONS : Our adaptive algorithm could effectively learn the anchor shape priors from the various sizes and shapes of cells. It is promising and encouraging for a real-world anchor-based detection and segmentation application of biomedical engineering in the future.

Hu Haigen, Liu Aizhu, Zhou Qianwei, Guan Qiu, Li Xiaoxin, Chen Qi


Anchor densification, Anchor shape, Cell detection and segmentation, ISODATA, Mask R-CNN