DeepContact: High-throughput quantification of membrane contact sites based on electron microscopy imaging

Membrane contact site (MCS)-mediated organelle interactions play essential roles in the cell. Quantitative analysis of MCSs reveals vital clues for cellular responses under various physiological and pathological conditions. However, an efficient tool is lacking. Here, we developed DeepContact, a dee...

Full description

Saved in:
Bibliographic Details
Published in:The Journal of cell biology 2022-09, Vol.221 (9), p.1
Main Authors: Liu, Liqing, Yang, Shuxin, Liu, Yang, Li, Xixia, Hu, Junjie, Xiao, Li, Xu, Tao
Format: Article
Language:English
Subjects:
Biophysics
Electron microscopy
Entanglement
Image segmentation
Membranes
Mitochondria
Organelles
Physiology
Sertoli cells
Statistical analysis
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Membrane contact site (MCS)-mediated organelle interactions play essential roles in the cell. Quantitative analysis of MCSs reveals vital clues for cellular responses under various physiological and pathological conditions. However, an efficient tool is lacking. Here, we developed DeepContact, a deep-learning protocol for optimizing organelle segmentation and contact analysis based on label-free EM. DeepContact presents high efficiency and flexibility in interactive visualizations, accommodating new morphologies of organelles and recognizing contacts in versatile width ranges, which enables statistical analysis of various types of MCSs in multiple systems. DeepContact profiled previously unidentified coordinative rearrangements of MCS types in cultured cells with combined nutritional conditions. DeepContact also unveiled a subtle wave of ER–mitochondrial entanglement in Sertoli cells during the seminiferous epithelial cycle, indicating its potential in bridging MCS dynamics to physiological and pathological processes.
ISSN:0021-9525
1540-8140
DOI:10.1083/jcb.202106190