Objective In order to analyze the number and morphology of cells in the process of cell culture conveniently.Methods In this paper, we introduce a cell counting method which can directly count cells in culture dish from images of commercial optical microscope by applying deep learning technology.Results In order to implement cell segmentation and counting, labeling and training is carried out on the image of adherent cells and suspension cells by a U-Net structure network. The cell growth curve is plotted and the inhibition rate of inhibitor is calculated by this algorithm, which shows the practicability of the algorithm.Conclusion It is feasible to do cell segmentation in dish by deep learning method.