System and method for classifying and segmenting microscopy images with deep multiple instance learning

Abstract

Systems and methods that receive as input microscopy images, extract features, and apply layers of processing units to compute one or more set of cellular phenotype features, corresponding to cellular densities and/or fluorescence measured under different conditions. The system is a neural network architecture having a convolutional neural network followed by a multiple instance learning (MIL) pooling layer. The system does not necessarily require any segmentation steps or per cell labels as the convolutional neural network can be trained and tested directly on raw microscopy images in real-time. The system computes class specific feature maps for every phenotype variable using a fully convolutional neural network and uses multiple instance learning to aggregate across these class specific feature maps. The system produces predictions for one or more reference cellular phenotype variables based on microscopy images with populations of cells.