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Abstract Background Medical image segmentation is an important processing step in most of medical image analysis. Thus, high accuracy and robustness are required for them. The current deep neural network based medical segmentation methods have good effect on image with balanced foreground and background, but it will loss the characteristics of small targets on image with imbalanced foreground and background after multiple convolutions. Methods In order to retain the features of small targets in the deep network, we proposed a new medical image segmentation model based on the U-Net with squeeze-and-excitation and attention modules which form a spiral closed path,callled as Spiral Squeeze-and-Excitation and Attention NET (SEA-NET) in this paper. The segmentation model used squeeze-and-extraction modules to adjust the channel information to enhance the useful information and used attention modules to adjust the spatial information of the feature map to highlight the target area for small target segmentation when up-sampling. The deep semantic information is integrated into the shallow feature map by the attention model. Therefore, the deep semantic information cannot be scattered by continuous up-sampling. We used cross entropy loss + Tversky loss function for fast convergence and well processing the imbalanced data sets. Our proposed SEA-NET was tested on the brain MRI dataset LPBA40 and peripheral blood smear images. Conclusions On brain MRI data, the average value of the Dice coefficient we obtained reached 98.1 $$\%$$ % . On the peripheral blood smear dataset, our proposed model has a good segmentation effect on adhesion cells. Results The experimental results proved that the proposed SEA-Net performed better than U-Net, U-Net++, etc. in medical image segmentation.