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

Lamm, L.; Zufferey, S.; Righetto, R. D.; Wietrzynski, W.; Yamauchi, K. A.; Burt, A.; Liu, Y.; Zhang, H.; Martinez-Sanchez, A.; Ziegler, S.; Isensee, F.; Schnabel, J. A.; Engel, B. D.; Peng, T.

doi:10.1101/2024.01.05.574336

bioRxiv · 10.1101/2024.01.05.574336

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

Lamm, L.·Zufferey, S.·Righetto, R. D.·Wietrzynski, W.·Yamauchi, K. A.·Burt, A.·Liu, Y.·Zhang, H.·Martinez-Sanchez, A.·Ziegler, S.·Isensee, F.·Schnabel, J. A.·Engel, B. D.·Peng, T.

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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.

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Lamm, L., Zufferey, S., Righetto, R. D., Wietrzynski, W., Yamauchi, K. A., Burt, A., Liu, Y., Zhang, H., Martinez-Sanchez, A., Ziegler, S., Isensee, F., Schnabel, J. A., Engel, B. D., Peng, T.. 2024-01-05. MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography. https://doi.org/10.1101/2024.01.05.574336

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