Clostridioides difficile infection (C. diff) is the most common cause of death due to secondary infection in hospital patients in the United States. Detection of C. diff cells in scanning electron microscopy (SEM) images is an important task to quantify the efficacy of the under-development treatments. However, detecting C. diff cells in SEM images is a challenging problem due to the presence of inhomogeneous illumination and occlusion. An Illumination normalization pre-processing step destroys the texture and adds noise to the image. Furthermore, cells are often clustered together resulting in touching cells and occlusion. In this paper, DETCID, a deep cell detection method using adversarial training, specifically robust to inhomogeneous illumination and occlusion, is proposed. An adversarial network is developed to provide region proposals and pass the proposals to a feature extraction network. Furthermore, a modified IoU metric is developed to allow the detection of touching cells in various orientations. The results indicate that DETCID outperforms the state-of-the-art in detection of touching cells in SEM images by at least 20 percent improvement of mean average precision.