Using DeepContact with Amira graphical user interface

Liqing Liu; Hongjun Wu; Shuxin Yang; Ke Yi; Junjie Hu; Li Xiao; Tao Xu

doi:10.1016/j.xpro.2023.102558

Using DeepContact with Amira graphical user interface

STAR Protoc. 2023 Dec 15;4(4):102558. doi: 10.1016/j.xpro.2023.102558. Epub 2023 Sep 16.

Authors

Liqing Liu¹, Hongjun Wu², Shuxin Yang³, Ke Yi², Junjie Hu⁴, Li Xiao⁵, Tao Xu⁶

Affiliations

¹ Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. Electronic address: liuliqing@ibp.ac.cn.
² School of Artificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China.
³ Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China; School of Computer and Control Engineering, University of Chinese Academy of Sciences, Beijing, China.
⁴ National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. Electronic address: huj@ibp.ac.cn.
⁵ Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China; School of Artificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China; School of Computer and Control Engineering, University of Chinese Academy of Sciences, Beijing, China. Electronic address: andrew.lxiao@gmail.com.
⁶ National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; College of Life Science, University of Chinese Academy of Sciences, Beijing, China; School of Biomedical Engineering, Guangzhou Medical University, Guangzhou, Guangdong, China. Electronic address: xutao@ibp.ac.cn.

Abstract

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.

Keywords: Cell Biology; Computer Sciences; Microscopy.

MeSH terms

Algorithms*
Artificial Intelligence*
Microscopy, Electron
Software