MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography

2024/01/05 by Lorenz Lamm, Simon Zufferey, Hanyi Zhang +12 · 1 voice · 52 citations
Biochemistry, Genetics and Molecular Biology · Earth and Planetary Sciences · Engineering · #Advanced Electron Microscopy Techniques and Applications #Artificial intelligence #Biology #Computer science #Data mining #End-to-end principle #Geophysical and Geoelectrical Methods #Membrane #Microfluidic and Bio-sensing Technologies #Robustness (evolution) #Segmentation

paper · pdf · doi:10.1101/2024.01.05.574336

openalex publication_date 2024/01/05 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05

Abstract

Abstract Cryo-electron tomography (cryo-ET) provides unique insights into macromolecular complexes in their native environments, yet membrane analysis remains a major bottleneck due to low signal-to-noise ratios, missing wedge artifacts, and the complexity of membrane-associated proteins. Existing tools often require extensive manual annotation, struggle with generalization across datasets, and lack integrated solutions for segmentation, protein localization, and quantitative analysis. We introduce MemBrain v2, a deep learning-enabled framework that unifies these tasks into a streamlined pipeline. MemBrain-seg leverages a diverse, collaboratively generated training dataset and specialized model training strategies to achieve generalizable membrane segmentation across variable tomographic conditions. MemBrain-pick enables data-efficient localization of membrane-bound proteins by integrating geometric constraints with deep learning, reducing the need for extensive manual annotation. MemBrain-stats provides quantitative insights into protein distributions, computing spatial metrics to analyze intra-membrane particle organization. MemBrain v2 integrates seamlessly into cryo-ET workflows, providing an accessible and structured approach to membrane analysis. The full package is available at https://github.com/CellArchLab/MemBrain-v2 .

Citations

• A Comprehensive Survey on Transfer Learning

Cited by

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• Advances in cryo-ET data processing: meeting the demands of visual proteomics. [europepmc]
• Ribosomes hibernate on mitochondria during cellular stress. [europepmc]
• CryoVesNet: A dedicated framework for synaptic vesicle segmentation in cryo-electron tomograms. [europepmc]
• Cryo-electron tomography: en route to the molecular anatomy of organisms and tissues. [europepmc]
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• Hemifusomes and interacting proteolipid nanodroplets mediate multi-vesicular body formation. [europepmc]
• A generalizable and targeted molecular biopsy approach for in situ cryogenic electron tomography of vitreous brain tissue. [europepmc]
• Ancestral sequence reconstruction of the Mic60 Mitofilin domain reveals residues supporting respiration in yeast. [europepmc]
• A practical look at cryo-electron tomography image processing: Key considerations for new biological discoveries. [europepmc]
• Endogenous retrovirus-like proteins recruit UBQLN2 to stress granules and shape their functional biology. [europepmc]
• In situ cryo-ET visualization of mitochondrial depolarization and mitophagic engulfment. [europepmc]
• Integrated structural biology of the native malarial translation machinery and its inhibition by an antimalarial drug. [europepmc]
• Membrane contact sites between chloroplasts and the pathogen interface underpin plant focal immune responses. [europepmc]
• Molecular architecture of thylakoid membranes within intact spinach chloroplasts. [europepmc]
• cryoTIGER: deep-learning based tilt interpolation generator for enhanced reconstruction in cryo electron tomography. [europepmc]
• Visualization of lysosomal membrane proteins by cryo electron tomography. [europepmc]
• Visualizing influenza A virus assembly by in situ cryo-electron tomography. [europepmc]
• Systematic membrane thickness variation across cellular organelles revealed by cryo-ET. [europepmc]
• Cryo-electron tomography reveals coupled flavivirus replication, budding and maturation. [europepmc]
• An Asgard archaeon with internal membrane compartments [europepmc]
• Nuclear pores safeguard the integrity of the nuclear envelope [europepmc]
• Charting the molecular landscape of neuronal organisation within the hippocampus using cryo electron tomography [europepmc]

Discussions

• 🦠🧠 MemBrain update! 🧠🦠 We’ve updated our preprint! It now covers the full MemBrain v2 pipeline for end-to-end membrane analysis in #CryoET: segmentation, particle picking, and spatial statistics. [bsky, 80 points, 2 comments]

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