DeepQuantify: deep learning and quantification system of white blood cells in light microscopy images of injured skeletal muscles.

White blood cells (WBCs) are the most diverse types of cells observed in the healing process of injured skeletal muscles. In the recovery process, WBCs exhibit a dynamic cellular response and undergo multiple changes of the protein expression. The progress of healing can be analyzed by the number of WBCs or by the number of specific proteins observed in light microscopy images obtained at different time points after injury. We propose a deep learning quantification and analysis system called DeepQuantify to analyze WBCs in light microscopy images of uninjured and injured muscles of female mice. The DeepQuantify system features in segmentation using the localized iterative Otsu's thresholding method, masking postprocessing, and classification of WBCs with a convolutional neural network (CNN) classifier to achieve a high accuracy and a low manpower cost. The proposed two-layer CNN classifier designed based on the optimization hypothesis is evaluated and compared with other CNN classifiers. The DeepQuantify system adopting these CNN classifiers is evaluated for quantifying CD68-positive macrophages and 7/4-positive neutrophils and compared with the state-of-the-art deep learning segmentation architectures. DeepQuantify achieves an accuracy of 90.64% and 89.31% for CD68-positive macrophages and 7/4-positive neutrophils, respectively. The DeepQuantify system employing the proposed two-layer CNN architecture achieves better performance than those deep segmentation architectures. The quantitative analysis of two protein dynamics during muscle recovery is also presented.