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Active Learning to Classify Macromolecular Structures in situ for Less Supervision in Cryo-Electron Tomography

Xuefeng Du, Haohan Wang, Zhenxi Zhu, Xiangrui Zeng, Yi-Wei Chang, Jing Zhang, Eric Xing, Min Xu
2021 Bioinformatics  
Cryo-Electron Tomography (cryo-ET) is a 3D bioimaging tool that visualizes the structural and spatial organization of macromolecules at a near-native state in single cells, which has broad applications  ...  To alleviate this major labeling burden, we proposed a Hybrid Active Learning (HAL) framework for querying subtomograms for labelling from a large unlabeled subtomogram pool.  ...  Xing is removed from the author list according to his request. Mr. Zhenxi Zhu participated in this work in early 2019 as a small part of his undergraduate research training.  ... 
doi:10.1093/bioinformatics/btab123 pmid:33620460 fatcat:d4rhzxvg4bfhpfxy7ur4lucbeq

Automatic analysis of cryo-electron tomography using computer vision and machine learning

Min Xu
2021 Microscopy and Microanalysis  
Cryo-electron tomography (cryo-ET) is an emerging technology for the 3D visualization of structural organizations and interactions of subcellular components at near-native state and sub-molecular resolution  ...  In particular, we have developed a set of methods for the de novo structural pattern mining among cryo-ET data for the discovery of macromolecular structures without using any external structural template  ...  Active learning to classify macromolecular structures in situ for less supervision in cryo-electron tomography. Bioinformatics. doi:10.1093/bioinformatics/btab123 2.  ... 
doi:10.1017/s1431927621000908 fatcat:pz2gr2rw6ndo7bnxdchua775cy

Improved deep learning-based macromolecules structure classification from electron cryo-tomograms

Chengqian Che, Ruogu Lin, Xiangrui Zeng, Karim Elmaaroufi, John Galeotti, Min Xu
2018 Machine Vision and Applications  
With recent breakthroughs in Cellular Electron Cryo-Tomography (CECT) 3D imaging technology, it is now possible for researchers to gain accesses to fully study and understand the macro-molecular structures  ...  Specifically, we proposed a deep learning-based image classification approach for large-scale systematic macromolecular structure separation from CECT data.  ...  Recent breakthroughs in Cellular Electron Cryo Tomography (CECT) imaging technique enables the 3D visualization of macromolecular complex structures and their spatial organizations inside single cells  ... 
doi:10.1007/s00138-018-0949-4 pmid:31511756 pmcid:PMC6738941 fatcat:qh5kxzmyerhwnp3fj63lttbdki

Few Shot Domain Adaptation for in situ Macromolecule Structural Classification in Cryo-electron Tomograms

Liangyong Yu, Ran Li, Xiangrui Zeng, Hongyi Wang, Jie Jin, Ge Yang, Rui Jiang, Min Xu, Arne Elofsson
2020 Bioinformatics  
Motivation Cryo-Electron Tomography (cryo-ET) visualizes structure and spatial organization of macromolecules and their interactions with other subcellular components inside single cells in the close-to-native  ...  However often it is difficult to get enough high-quality annotated subtomogram data for supervised training due to the enormous expense of labeling.  ...  Cryo-electron Tomography (cryo-ET), as a revolutionary imaging technique for structural biology, enables the in situ 3D visualization of structural organization information of all subcellular components  ... 
doi:10.1093/bioinformatics/btaa671 pmid:32722755 pmcid:PMC8237843 fatcat:32omtn7yynfx7hka4zzv7sc3ry

Few-shot learning for classification of novel macromolecular structures in cryo-electron tomograms

Ran Li, Liangyong Yu, Bo Zhou, Xiangrui Zeng, Zhenyu Wang, Xiaoyan Yang, Jing Zhang, Xin Gao, Rui Jiang, Min Xu, Turkan Haliloglu
2020 PLoS Computational Biology  
role in structural biology in situ.  ...  Cryo-electron tomography (cryo-ET) provides 3D visualization of subcellular components in the near-native state and at sub-molecular resolutions in single cells, demonstrating an increasingly important  ...  part in structural biology in situ, and successful applications of cryo-ET to the study of considerable important macromolecular structures has been proposed [1] .  ... 
doi:10.1371/journal.pcbi.1008227 pmid:33175839 fatcat:4zwm6iz7ijhr5ajtmj3bhf42zu

Deep Learning Improves Macromolecules Localization and Identification in 3D Cellular Cryo-Electron Tomograms [article]

Emmanuel Moebel, Antonio Martinez-Sanchez, Damien Larivière, Eric Fourmentin, Julio Ortiz, Wolfgang Baumeister, Charles Kervrann
2020 bioRxiv   pre-print
abstractCryo-electron tomography (cryo-ET) allows one to visualize and study the 3D spatial distribution of macromolecules, in their native states and at nanometer resolution in single cells.  ...  Hence, we present a computational procedure that uses artificial neural networks to accurately localize several macromolecular species in cellular cryo-electron tomograms.  ...  Killinger for fruitful discussions about cryo-ET data analysis, and deep learning applied to large 3D volumes analysis, respectively.  ... 
doi:10.1101/2020.04.15.042747 fatcat:rgtheocj3racfcz5mi2aru57jm

DISCA: high-throughput cryo-ET structural pattern mining by deep unsupervised clustering [article]

Xiangrui Zeng, Anson Kahng, Liang Xue, Julia Mahamid, Yi-Wei Chang, Min Xu
2021 bioRxiv   pre-print
Cryo-electron tomography directly visualizes heterogeneous macromolecular structures in complex cellular environments, but existing computer-assisted sorting approaches are low-throughput or inherently  ...  Diverse structures emerging from sorted subsets enable systematic unbiased recognition of macromolecular complexes in situ.  ...  Acknowledgements This work was supported in part by U.S. NIH grants R01GM134020 and P41GM103712, NSF  ... 
doi:10.1101/2021.05.16.444381 fatcat:qul2vproqreexka46mttrri4tu

A convolutional autoencoder approach for mining features in cellular electron cryo-tomograms and weakly supervised coarse segmentation

Xiangrui Zeng, Miguel Ricardo Leung, Tzviya Zeev-Ben-Mordehai, Min Xu
2018 Journal of Structural Biology  
Cellular electron cryo-tomography enables the 3D visualization of cellular organization in the near-native state and at submolecular resolution.  ...  However, the contents of cellular tomograms are often complex, making it difficult to automatically isolate different in situ cellular components.  ...  Robert Murphy for suggestions. We thank Dr. Zachary Freyberg and Kai Wen Wang for help with manuscript preparation. We thank Stephanie Siegmund for providing technical help.  ... 
doi:10.1016/j.jsb.2017.12.015 pmid:29289599 pmcid:PMC6661905 fatcat:ucp2xrymrvh2fbejctzzkry2z4

Advanced Electron Microscopy of Nanophased Synthetic Polymers and Soft Complexes for Energy and Medicine Applications

Jihua Chen
2021 Nanomaterials  
Machine learning is expected to automate and facilitate image processing and information extraction of polymer and soft hybrid nanostructures in aspects such as dose-controlled imaging and structure analysis  ...  The recent progress in electron microscopy of nanostructured polymers and soft assemblies is important for applications in many different fields, including, but not limited to, mesoporous and nanoporous  ...  Acknowledgments: J.C. wishes to thank each one of the facility users over the years for collaborating.  ... 
doi:10.3390/nano11092405 pmid:34578720 pmcid:PMC8470047 fatcat:resycz3warc4nkl5yvn272uzk4

Morphomics via Next-generation Electron Microscopy [article]

Raku Son, Kenji Yamazawa, Akiko Oguchi, Mitsuo Suga, Masaru Tamura, Yasuhiro Murakawa, Satoshi Kume
2021 arXiv   pre-print
When attempting to observe these ultra-structures, the use of electron microscopy (EM) has become indispensable.  ...  The living body is composed of innumerable fine and complex structures and although these structures have been studied in the past, a vast amount of information pertaining to them still remains unknown  ...  We thank a member of the SAPOIN project in RIKEN for the regular and helpful discussion as well as Ms.  ... 
arXiv:2111.14373v1 fatcat:tv7jlahbhfhj3ij4y2tqqxkzs4

Correlated Multimodal Imaging in Life Sciences: Expanding the Biomedical Horizon

Andreas Walter, Perrine Paul-Gilloteaux, Birgit Plochberger, Ludek Sefc, Paul Verkade, Julia G. Mannheim, Paul Slezak, Angelika Unterhuber, Martina Marchetti-Deschmann, Manfred Ogris, Katja Bühler, Dror Fixler (+5 others)
2020 Frontiers in Physics  
The review is in line with major European initiatives, such as COMULIS (CA17121), a COST Action to promote and foster Correlated Multimodal Imaging in Life Sciences.  ...  challenges for its routine use in biomedical research: (1) Sample handling and preparation procedures that are compatible across modalities without compromising data quality, (2) soft-and hardware solutions  ...  Anything more inside will be too thick to image directly. Cryo-FIB-milling is currently the only way to acquire thin slices of frozen material for cryo-electron tomography (ET) [150] .  ... 
doi:10.3389/fphy.2020.00047 fatcat:ncyaxrt6ijgubp6sdgujyoq6yi

Advances in Electron Microscopy with Deep Learning

Jeffrey Ede
2020 Zenodo  
Highlights include a comprehensive review of deep learning in electron microscopy; large new electron microscopy datasets for machine learning, dataset search engines based on variational autoencoders,  ...  This doctoral thesis covers some of my advances in electron microscopy with deep learning.  ...  Acknowledgements Thanks go to Jeremy Sloan and Martin Lotz for internally reviewing this article.  ... 
doi:10.5281/zenodo.4598227 fatcat:hm2ksetmsvf37adjjefmmbakvq

Advances in Electron Microscopy with Deep Learning

Jeffrey Ede
2020 Zenodo  
Highlights include a comprehensive review of deep learning in electron microscopy; large new electron microscopy datasets for machine learning, dataset search engines based on variational autoencoders,  ...  This doctoral thesis covers some of my advances in electron microscopy with deep learning.  ...  Acknowledgements Thanks go to Jeremy Sloan and Martin Lotz for internally reviewing this article.  ... 
doi:10.5281/zenodo.4591029 fatcat:zn2hvfyupvdwlnvsscdgswayci

Advances in Electron Microscopy with Deep Learning

Jeffrey Ede
2020 Zenodo  
Highlights include a comprehensive review of deep learning in electron microscopy; large new electron microscopy datasets for machine learning, dataset search engines based on variational autoencoders,  ...  This doctoral thesis covers some of my advances in electron microscopy with deep learning.  ...  Acknowledgements Thanks go to Jeremy Sloan and Martin Lotz for internally reviewing this article.  ... 
doi:10.5281/zenodo.4399748 fatcat:63ggmnviczg6vlnqugbnrexsgy

The Native 3D Organization of Bacterial Polysomes

Florian Brandt, Stephanie A. Etchells, Julio O. Ortiz, Adrian H. Elcock, F. Ulrich Hartl, Wolfgang Baumeister
2009 Cell  
We employed cryoelectron tomography and a template-matching approach to map 70S ribosomes in vitrified bacterial translation extracts and in lysates of active E. coli spheroplasts.  ...  Recent advances have led to insights into the structure of the bacterial ribosome, but little is known about the 3D organization of ribosomes in the context of translating polysomes.  ...  CET is a powerful method to reconstruct the 3D electron densities of individual macromolecular objects in a close-to-native environment without the need to stain or fix the specimen (Lucic et al., 2005  ... 
doi:10.1016/j.cell.2008.11.016 pmid:19167328 fatcat:5f73vo24u5esvhph7oofdljwte
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