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

In Nature methods ; h5-index 152.0

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 ~US$250, with a cost below US$100 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/ .

Bannon Dylan, Moen Erick, Schwartz Morgan, Borba Enrico, Kudo Takamasa, Greenwald Noah, Vijayakumar Vibha, Chang Brian, Pao Edward, Osterman Erik, Graf William, Van Valen David

2021-Jan