Article
Biochemical Research Methods
Jie E. Yang, Matthew R. Larson, Bryan S. Sibert, Joseph Y. Kim, Daniel Parrell, Juan C. Sanchez, Victoria Pappas, Anil Kumar, Kai Cai, Keith Thompson, Elizabeth R. Wright
Summary: In this paper, robust tools for montage parallel array cryo-tomography (MPACT) tailored for vitrified specimens are presented, which can image large fields of view while preserving high-resolution structural information. The combination of multiple techniques in MPACT supports studies that contextually define the three-dimensional architecture of cells, and it provides flexibility and efficient data processing and analysis.
Article
Multidisciplinary Sciences
Chentao Wen, Mami Matsumoto, Masato Sawada, Kazunobu Sawamoto, Koutarou D. Kimura
Summary: Recent advances in microscopy techniques, particularly in electron microscopy, have allowed for the acquisition of large quantities of high-precision 3D cell image stacks. However, the indistinct images often encountered in biomedical research pose a challenge for cell segmentation. Existing automatic segmentation methods, even when utilizing advanced deep learning techniques, often contain numerous mistakes. To effectively analyze 3D cell images, a semi-automated software solution is required that combines powerful deep learning techniques with the ability to perform post-processing and incorporate manual corrections. Seg2Link addresses this need by using deep learning predictions and watershed 2D+cross-slice linking to generate more accurate automatic segmentations, while also providing manual correction tools for refining the results.
SCIENTIFIC REPORTS
(2023)
Article
Chemistry, Analytical
Junling Chen, Hongru Li, Qiang Wu, Qiuyan Yan, Jiayin Sun, Feng Liang, Yi Liu, Hongda Wang
Summary: The study revealed the unique distribution of Protein tyrosine kinase-7 (PTK7) on the cell membrane, which is possibly related to the assembly relationship with lipid rafts, actin cytoskeleton, and membrane carbohydrate chains.
ANALYTICAL CHEMISTRY
(2021)
Article
Computer Science, Interdisciplinary Applications
Kisuk Lee, Ran Lu, Kyle Luther, H. Sebastian Seung
Summary: This study demonstrates that dense voxel embeddings learned through deep metric learning can accurately segment neurons from 3D electron microscopy images. A metric graph is constructed from the dense voxel embeddings generated by a convolutional network, and partitioning the graph with long-range edges as repulsive constraints results in precise initial segmentation, particularly useful for very thin objects. The convolutional embedding network is reused without modification to aggregate systematic splits caused by complex self-contact motifs, achieving state-of-the-art accuracy in reconstructing 3D neurons from brain images acquired through serial section electron microscopy. The proposed object-centered representation may have broader applications in automated neural circuit reconstruction.
IEEE TRANSACTIONS ON MEDICAL IMAGING
(2021)
Article
Multidisciplinary Sciences
Semih Barutcu, Selin Aslan, Aggelos K. Katsaggelos, Doga Gursoy
Summary: Computed tomography is widely used for reconstructing the three-dimensional structure of objects, but faces challenges in limited angle reconstruction. To address this, researchers have utilized generative models and deep networks to effectively constrain the solution space.
SCIENTIFIC REPORTS
(2021)
Article
Engineering, Chemical
Alexander T. Bridge, Matthew S. Santoso, Jessica A. Maisano, Alexander V. Hillsley, Joan F. Brennecke, Benny D. Freeman
Summary: This study proposes a rapid and accurate technique for quantifying the macroporosity in asymmetric membranes. The technique is validated by comparing results from X-ray computed tomography (XCT) and scanning electron microscopy (SEM). The study also demonstrates that the macroporosity can be approximated from limited 2D sampling, and using complementary descriptors can improve sensitivity.
JOURNAL OF MEMBRANE SCIENCE
(2022)
Article
Biochemical Research Methods
Romain F. Laine, Hannah S. Heil, Simao Coelho, Jonathon Nixon-Abell, Angelique Jimenez, Theresa Wiesner, Damian Martinez, Tommaso Galgani, Louise Regnier, Aki Stubb, Gautier Follain, Samantha Webster, Jesse Goyette, Aurelien Dauphin, Audrey Salles, Sian Culley, Guillaume Jacquemet, Bassam Hajj, Christophe Leterrier, Ricardo Henriques
Summary: This article presents an enhanced super-resolution radial fluctuations (eSRRF) method that improves image fidelity and resolution. The method incorporates automated parameter optimization and has been validated across various imaging modalities and biological systems. Additionally, eSRRF has been extended to three dimensions by combining it with multifocus microscopy, enabling live-cell volumetric super-resolution imaging.
Article
Biochemical Research Methods
Cong T. S. Van, Chrysanthe Preza
Summary: This study introduces a regularized three-dimensional model-based restoration method with positivity constraint for processing 3D data from structured illumination microscopy systems. The proposed method provides axial super resolution and improves 3D resolution compared to standard methods.
BIOMEDICAL OPTICS EXPRESS
(2021)
Article
Chemistry, Physical
Simon Collett, Joseph Torresi, Linda Earnest Silveira, Vi Khanh Truong, Dale Christiansen, Bang M. Tran, Elizabeth Vincan, Paul A. Ramsland, Aaron Elbourne
Summary: Cell cultures have been successfully used to study hepatitis C virus (HCV) for many years, with recent research suggesting that polarized cell systems are more suitable for studying HCV infection and dynamics.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2021)
Article
Computer Science, Interdisciplinary Applications
Anton Cid-Mejias, Raul Alonso-Calvo, Helena Gavilan, Jose Crespo, Victor Maojo
Summary: The study introduces a Deep Learning method based on Convolutional Neural Networks to detect, segment, infer orientations and reconstruct microscope images of nanoparticles using artificial datasets. The research successfully tested the method with various basic nanoparticle shapes, showing promising results in segmentation and reconstruction. The novelty of the study lies in the creation of artificial datasets resembling real nanoparticles photographs instead of using annotated images.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2021)
Article
Microbiology
Daria Tashyreva, Jiri Tyc, Ales Horak, Julius Lukes
Summary: This study provides a detailed three-dimensional model of a previously undescribed diplonemid species using serial block-face scanning and transmission electron microscopy. The study also describes the cell division process and identifies a novel, ultrastructurally complex organelle.
Article
Biochemistry & Molecular Biology
Ryan Lane, Anouk H. G. Wolters, Ben N. G. Giepmans, Jacob P. Hoogenboom
Summary: We developed a 3D image acquisition and reconstruction pipeline that integrates widefield fluorescence microscopy with scanning electron microscopy, overcoming the limitations of slow acquisition rates and difficulty in providing targeted biological information. By using cathodoluminescent markers, we achieved high precision EM-FM overlay. Our proof-of-concept on immunolabelled serial sections of tissues demonstrated expedited acquisition times and reduced data burden.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Medicine, General & Internal
Ai-bo Qin, Zi-shan Lin, Su-xia Wang, Hui Wang, Zhao Cui, Fu-de Zhou, Ming-hui Zhao
Summary: This study compared the clinicopathological and ultrastructural features of patients with mercury-associated membranous nephropathy (M-MN) and idiopathic membranous nephropathy (I-MN). The results showed that M-MN patients were younger, achieved complete remission more quickly, and had a lower relapse rate compared to I-MN patients. M-MN patients also exhibited less severe foot process effacement and a higher rate of mesangial electron-dense deposits.
AMERICAN JOURNAL OF THE MEDICAL SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Yi-Chi Wang, Thomas J. A. Slater, Gerard M. Leteba, Candace I. Lang, Zhong Lin Wang, Sarah J. Haigh
Summary: Tailoring the composition and morphology of nanoparticles is crucial for improving their catalytic performance. This study presents an in situ 3D imaging methodology using single particle reconstruction (SPR) that allows for the investigation of structural transformations and elemental redistribution in nanoparticles. The methodology is applied to study the restructuring of PtNi nanoparticles at elevated temperatures and reveals a transition from a disordered to an ordered phase. The changes in structure and elemental distribution are correlated with a decrease in catalytic activity. This in situ SPR methodology can be extended to study nanoparticle evolution in various environments.
Article
Cell Biology
Kiranjit K. Bains, Robert D. Young, Elena Koudouna, Philip N. Lewis, Andrew J. Quantock
Summary: Imaging techniques were used to study the three-dimensional microanatomy and spatiotemporal relationships of cells, extracellular matrix, and vasculature at the corneo-scleral limbus of developing and mature chicken eyes. Results showed the development of structures similar to Palisades of Vogt, associated with characteristics of stem cells, and direct cell-cell associations between corneal epithelial and stromal cells.
Article
Pathology
Pauline Ferraris, Partha K. Chandra, Rajesh Panigrahi, Fatma Aboulnasr, Srinivas Chava, Ramazan Kurt, Jean-Michel Pawlotsky, Ludwig Wilkens, Pamela Osterlund, Rune Hartmann, Luis A. Balart, Tong Wu, Srikanta Dash
AMERICAN JOURNAL OF PATHOLOGY
(2016)
Review
Virology
Srikanta Dash, Srinivas Chava, Yucel Aydin, Partha K. Chandra, Pauline Ferraris, Weina Chen, Luis A. Balart, Tong Wu, Robert F. Garry
Article
Virology
Sineewanlaya Wichit, Pauline Ferraris, Valerie Choumet, Dorothee Misse
CURRENT OPINION IN VIROLOGY
(2016)
Article
Infectious Diseases
Sineewanlaya Wichit, Fode Diop, Rodolphe Hamel, Loic Talignani, Pauline Ferraris, Sylvie Cornelie, Florian Liegeois, Frederic Thomas, Hans Yssel, Dorothe Misse
INFECTION GENETICS AND EVOLUTION
(2017)
Article
Infectious Diseases
Rodolphe Hamel, Pauline Ferraris, Sineewanlaya Wichit, Fode Diop, Loic Talignani, Julien Pompon, Deborah Garcia, Florian Liegeois, Amadou A. Sall, Hans Yssel, Dorothee Misse
INFECTION GENETICS AND EVOLUTION
(2017)
Article
Biochemistry & Molecular Biology
Benita Wolf, Fode Diop, Pauline Ferraris, Sineewanlaya Wichit, Coralie Busso, Dorothee Misse, Pierre Gonczy
Article
Virology
Rajesh Panigrahi, Partha K. Chandra, Pauline Ferraris, Ramazan Kurt, Kyoungsub Song, Robert F. Garry, Krzysztof Reiss, Imogen R. Coe, Tomomi Furihata, Luis A. Balart, Tong Wu, Srikanta Dash
JOURNAL OF VIROLOGY
(2015)
Article
Multidisciplinary Sciences
Fode Diop, Thomas Vial, Pauline Ferraris, Sineewanlaya Wichit, Michele Bengue, Rodolphe Hamel, Ldic Talignani, Florian Liegeois, Julien Pompon, Hans Yssel, Guillaume Marti, Dorothee Misse
Article
Multidisciplinary Sciences
Sineewanlaya Wichit, Rodolphe Hamel, Eric Bernard, Loic Talignani, Fode Diop, Pauline Ferraris, Florian Liegeois, Peeraya Ekchariyawat, Natthanej Luplertlop, Pornapat Surasombatpattana, Frederic Thomas, Andres Merits, Valerie Choumet, Pierre Roques, Hans Yssel, Laurence Briant, Dorothee Misse
SCIENTIFIC REPORTS
(2017)
Article
Biochemistry & Molecular Biology
Sineewanlaya Wichit, Rodolphe Hamel, Andreas Zanzoni, Fode Diop, Alexandra Cribier, Loic Talignani, Abibatou Diack, Pauline Ferraris, Florian Liegeois, Serge Urbach, Peeraya Ekchariyawat, Andres Merits, Hans Yssel, Monsef Benkirane, Dorothee Misse
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2019)
Review
Immunology
Pauline Ferraris, Hans Yssel, Dorothee Misse
MICROBES AND INFECTION
(2019)
Article
Virology
Michele Bengue, Pauline Ferraris, Cecile Baronti, Cheikh Tidiane Diagne, Loic Talignani, Sineewanlaya Wichit, Florian Liegeois, Catherine Bisbal, Antoine Nougairede, Dorothee Misse
Article
Virology
Michele Bengue, Pauline Ferraris, Jonathan Barthelemy, Cheikh Tidiane Diagne, Rodolphe Hamel, Florian Liegeois, Antoine Nougairede, Xavier de Lamballerie, Yannick Simonin, Julien Pompon, Sara Salinas, Dorothee Misse
Summary: The study indicates that MAYV and CHIKV induce different antiviral responses in astrocytes, with MAYV being more susceptible to the antiviral effects of interferons.
Review
Infectious Diseases
Pauline Ferraris, Sineewanlaya Wichit, Nadege Cordel, Dorothee Misse
Summary: Managing emerging infectious diseases is a current challenge in microbiology and epidemiology, with climate change and global warming favoring the emergence of new pathogens. The recent Zika virus epidemic has highlighted the importance of studying viruses responsible for sporadic infections. Understanding key factors involved in emerging infections is crucial for implementing specific monitoring.
INFECTION GENETICS AND EVOLUTION
(2021)
Article
Immunology
Pauline Ferraris, Marielle Cochet, Rodolphe Hamel, Ivan Gladwyn-Ng, Christian Alfan, Fode Diop, Deborah Garcia, Loic Talignani, Claudia N. Montero-Menei, Antoine Nougairede, Hans Yssel, Laurent Nguyen, Muriel Coulpier, Dorothee Misse
EMERGING MICROBES & INFECTIONS
(2019)
