Reconstructing cell cycle and disease progression using deep learning

We show that deep convolutional neural networks combined with non-linear dimension reduction enable reconstructing biological processes based on raw image data. We demonstrate this by recon-structing the cell cycle of Jurkat cells and disease progression in diabetic retinopathy. In further analysis of Jurkat cells, we detect and separate a subpopulation of dead cells in an unsupervised manner and, in classifying discrete cell cycle stages, we reach a 6-fold reduction in error rate compared to a recent approach based on boosting on image features. In contrast to previous methods, deep learning based predictions are fast enough for on-the-fly analysis in an imaging flow cytometer.