MICRA-Net: MICRoscopy Analysis Neural Network to solve detection, classification, and segmentation from a single simple auxiliary task

High throughput quantitative analysis of microscopy images presents a challenge due to the complexity of the image content and the difficulty to retrieve precisely annotated datasets. In this paper we introduce a weakly-supervised MICRoscopy Analysis neural network (MICRA-Net) that can be trained on a simple main classification task using image-level annotations to solve multiple the more complex auxiliary semantic segmentation task and other associated tasks such as detection or enumeration. MICRA-Net relies on the latent information embedded within a trained model to achieve performances similar to state-of-the-art architectures when no precisely annotated dataset is available. This learnt information is extracted from the network using gradient class activation maps, which are combined to generate detailed feature maps of the biological structures of interest. We demonstrate how MICRA-Net significantly alleviates the Expert annotation process on various microscopy datasets and can be used for high-throughput quantitative analysis of microscopy images.