Using DeepContact with Amira graphical user interface

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

STAR Protocols (Dec 2023)

Using DeepContact with Amira graphical user interface

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

Affiliations

Liqing Liu: Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; Corresponding author
Hongjun Wu: School of Artificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China
Shuxin Yang: 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
Ke Yi: School of Artificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China
Junjie Hu: National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; Corresponding author
Li Xiao: 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; Corresponding author
Tao Xu: 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; Corresponding author

Journal volume & issue: Vol. 4, no. 4
p. 102558

Abstract

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Summary: 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 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Published in STAR Protocols

ISSN: 2666-1667 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science: Science (General)
Website: https://star-protocols.cell.com/

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