Dense-UNet: a novel multiphoton in vivo cellular image segmentation model based on a convolutional neural network

Abstract

Background: Multiphoton microscopy (MPM) offers a feasible approach for the biopsy in clinical medicine, but it has not been used in clinical applications due to the lack of efficient image processing methods, especially the automatic segmentation technology. Segmentation technology is still one of the most challenging assignments of the MPM imaging technique.

Methods: The MPM imaging segmentation model based on deep learning is one of the most effective methods to address this problem. In this paper, the practicability of using a convolutional neural network (CNN) model to segment the MPM image of skin cells in vivo was explored. A set of MPM in vivo skin cells images with a resolution of 128×128 was successfully segmented under the Python environment with TensorFlow. A novel deep-learning segmentation model named Dense-UNet was proposed. The Dense-UNet, which is based on U-net structure, employed the dense concatenation to deepen the depth of the network architecture and achieve feature reuse. This model included four expansion modules (each module consisted of four down-sampling layers) to extract features.

Results: Sixty training images were taken from the dorsal forearm using a femtosecond Ti:Sa laser running at 735 nm. The resolution of the images is 128×128 pixels. Experimental results confirmed that the accuracy of Dense-UNet (92.54%) was higher than that of U-Net (88.59%), with a significantly lower loss value of 0.1681. The 90.60% Dice coefficient value of Dense-UNet outperformed U-Net by 11.07%. The F1-Score of Dense-UNet, U-Net, and Seg-Net was 93.35%, 90.02%, and 85.04%, respectively.

Conclusions: The deepened down-sampling path improved the ability of the model to capture cellular fined-detailed boundary features, while the symmetrical up-sampling path provided a more accurate location based on the test result. These results were the first time that the segmentation of MPM in vivo images had been adopted by introducing a deep CNN to bridge this gap in Dense-UNet technology. Dense-UNet has reached ultramodern performance for MPM images, especially for in vivo images with low resolution. This implementation supplies an automatic segmentation model based on deep learning for high-precision segmentation of MPM images in vivo.

Keywords: Skin in vivo; U-Net; dense-UNet; image segmentation; multiphoton microscopy (MPM).

Figure 1

Schematic diagram of proposed Dense-UNet architecture.

Figure 2

Flow chart of a dense_block.

Figure 3

Flow chart of Dense-UNet.

Figure 4

MPM images of the dorsal forearm shin in vivo. Excitation wavelength λex =720 nm. FOV = 200×200 µm. Resolution = 256×256 pixels. MPM, multiphoton microscopy.

Figure 5

MPM images of human skin in vivo and segmentation results. The first column shows the MPM image of human skin in vivo. The following three columns display the segmentation results by Dense-UNet, U-Net, and SegNet, respectively. Resolution = 128 × 128 pixels.