Using DeepContact with Amira graphical user interface.

DeepContact is a deep learning software for high-throughput quantification of membrane contact site (MCS) in 2D electron microscopy images. This protocol will guide users through incorporating available DeepContact models in Amira's artificial intelligence module, thereby allowing invoking of DeepContact functions in organelle segmentation and quantifying of MCS with a user-friendly graphical user interface of Amira software. For complete details on the use and execution of this protocol, please refer to Liu et al. (2022).1.