CellCentroidFormer: Combining Self-attention and Convolution for Cell Detection

Cell detection in microscopy images is important to study how cells move and interact with their environment. Most recent deep learning-based methods for cell detection use convolutional neural networks (CNNs). However, inspired by the success in other computer vision applications, vision transformers (ViTs) are also used for this purpose. We propose a novel hybrid CNN-ViT model for cell detection in microscopy images to exploit the advantages of both types of deep learning models. We employ an efficient CNN, that was pre-trained on the ImageNet dataset, to extract image features and utilize transfer learning to reduce the amount of required training data. Extracted image features are further processed by a combination of convolutional and transformer layers, so that the convolutional layers can focus on local information and the transformer layers on global information. Our centroid-based cell detection method represents cells as ellipses and is end-to-end trainable. Furthermore, we show that our proposed model can outperform a fully convolutional baseline model on four different 2D microscopy datasets. Code is available at: https://github.com/roydenwa/cell-centroid-former