DeepCell Kiosk: Scaling deep learning-enabled cellular image analysis with Kubernetes

Abstract

Deep learning is transforming the analysis of biological images but applying these models to large datasets remains challenging. Here we describe the DeepCell Kiosk, cloud-native software that dynamically scales deep learning workflows to accommodate large imaging datasets. To demonstrate the scalability and affordability of this software, we identified cell nuclei in 106 1-megapixel images in ~5.5 h for ~$250, with a sub-$100 cost achievable depending on cluster configuration. The DeepCell Kiosk can be downloaded at https://github.com/vanvalenlab/kiosk-console; a persistent deployment is available at https://deepcell.org.