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
Radiology, Nuclear Medicine & Medical Imaging
Mary E. Hall, Marianne S. Black, Garry E. Gold, Marc E. Levenston
Summary: The study demonstrated the utility of a 2D watershed algorithm for accurately identifying cartilage boundaries in CT arthrograms of the knee, even with increasing boundary blurring. The results indicated that the watershed lines were closer to the cartilage surface in areas where soft tissues were in direct contact with each other.
QUANTITATIVE IMAGING IN MEDICINE AND SURGERY
(2022)
Article
Biochemistry & Molecular Biology
Adham Aleid, Khalid Alhussaini, Mohammed Almijalli, Ali S. Saad
Summary: This study investigated the interaction and uptake of SPIO nanoparticles in M1 and M2 macrophages, and extracted the quantity of particles using image processing techniques. The results are important for targeted drug delivery and assessing the safety impact of SPIO nanoparticles in nanomedicine.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Computer Science, Information Systems
Ying Yu, Chunping Wang, Qiang Fu, Renke Kou, Fuyu Huang, Boxiong Yang, Tingting Yang, Mingliang Gao
Summary: Image segmentation, a research hotspot in the fields of image processing and computer vision, aims to divide an image into meaningful and non-overlapping regions, playing a vital role in natural scene understanding. This paper systematically reviews the advancements in image segmentation methods, focusing on classic segmentation, collaborative segmentation, and deep learning-based semantic segmentation. The main algorithms, key techniques, advantages, and limitations of different segmentation models are discussed, and the challenges and development trends in image segmentation techniques are analyzed.
Article
Biochemistry & Molecular Biology
Maria Narciso, Jorge Otero, Daniel Navajas, Ramon Farre, Isaac Almendros, Nuria Gavara
Summary: A new image processing algorithm has been developed for quantitative analysis of DNA content in (de)cellularized tissues, offering a faster, simpler, and more comprehensive alternative to traditional methods. This method can be applied to both native and decellularized tissues, providing a means to quantify DNA content and assess decellularization procedures.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Computer Science, Artificial Intelligence
Fengnan Quan, Bo Lang
Summary: In this paper, the authors propose a self-supervised generative adversarial network (GAN) called GIGAN, which can generate the complete appearance of objects without labeled invisible part information. They introduce two cycle transformation networks, CycleIncomplete (CycleI) and CycleComplete (CycleC), that share parameters to improve mask completion accuracy. The authors also propose a conditional normalization module to enhance content recovery ability and combine it with the inferred complete mask output. Experimental results show that their method achieves improvements in l(1) error, mean intersection-over-union (mIOU), and Frechet inception distance (FID) on the COCOA and KINS datasets compared to existing self-supervised learning models.
IET IMAGE PROCESSING
(2023)
Article
Neurosciences
Vladan Lucic
Summary: This article reviews the importance of electron microscopy in the study of neuronal synapse structures and discusses the use of image processing software methods. Special attention is given to the application of recent cryo-electron microscopy and tomography methods in molecular level analysis.
CURRENT OPINION IN NEUROBIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Zhixun Li, Wenjing Du, Jiong Yang, De-Hua Lai, Zhao-Rong Lun, Qiang Guo
Summary: The fine structure of Toxoplasma gondii in its native state is visualized using cryo-electron tomography. The cytoskeleton is found to originate from microtubules, which provides a reference for further studies.
Article
Chemistry, Analytical
Mengfan Xue, Lu Han, Yiran Song, Fan Rao, Dongliang Peng
Summary: The study introduces a learning-based method for lung lobe segmentation, which combines local fissures, the whole lung, and prior pulmonary anatomy knowledge for robust and accurate segmentation in COPD patients. The method performs comparably to a former approach but demonstrates greater robustness in cases with morphological specificity.
Article
Computer Science, Artificial Intelligence
Lukasz Karbowiak, Janusz Bobulski
Summary: This article introduces the importance of background segmentation and proposes a method to compare algorithms under severe weather conditions. Through testing in different weather conditions, interesting differences in detail detection and detection noise were observed.
PEERJ COMPUTER SCIENCE
(2022)
Article
Computer Science, Artificial Intelligence
Pengshuai Yin, Yanwu Xu, Jinhui Zhu, Jiang Liu, Chang'an Yi, Huichou Huang, Qingyao Wu
Summary: The study introduces a level set based deep learning method for optic disc and cup segmentation, addressing the challenge of injecting domain-specific knowledge into existing segmentation networks. By adding constraints and considering pixel relationships, the proposed method effectively solves the problem. Experimental results confirm the effectiveness of the approach.
Review
Biochemistry & Molecular Biology
Paula P. Navarro
Summary: This article reviews the hardware and software developments in quantitative cryo-electron tomography, discusses its importance and limitations in biological research. Quantitative cryo-electron tomography can be used to visualize the three-dimensional structure of biological systems, helping us understand changes in cellular structure and function.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Computer Science, Artificial Intelligence
Pengyi Hao, Kangjian Shi, Shuyuan Tian, Fuli Wu
Summary: Medical image segmentation from noisy labels is a challenging task. In this study, a novel uncertainty-aware iterative learning (UaIL) approach is proposed to address issues related to noisy annotations. UaIL trains two deep networks iteratively using original and augmented images, with a joint loss function that includes softened label loss, hard label loss, and consistency loss. Experimental results on two public datasets show that UaIL outperforms competing approaches, especially when dealing with serious label noises. UaIL is also validated on a private dataset, demonstrating its applicability in real-world scenarios with noisy labels.
IET IMAGE PROCESSING
(2023)
Article
Computer Science, Artificial Intelligence
Marjan Vatanpour, Javad Haddadnia
Summary: The proposed method for automatic segmentation of brain tumours achieves better performance on tumour core and whole tumour compared to other segmentation approaches, leveraging deep learning methods and attention mechanism.
IET IMAGE PROCESSING
(2023)
Article
Chemistry, Multidisciplinary
Maria Moncho-Santonja, Silvia Aparisi-Navarro, Beatriz Defez, Guillermo Peris-Fajarnes
Summary: This study aims to analyze the segmentation methods developed for acne vulgaris images so far, including the processing techniques, image modalities, and results. The results show that there are two types of methods: those based on classical image processing techniques and those based on machine learning algorithms. Currently, there is no preference for one group of methods over the other, and the lack of uniformity in result evaluation makes method comparison difficult. The preferred image modality is conventional photography, and there is a research gap in the application of segmentation algorithms to other useful acne vulgaris image modalities such as fluorescence imaging.
APPLIED SCIENCES-BASEL
(2023)
Article
Multidisciplinary Sciences
Ralf F. Ziesche, Tobias Arlt, Donal P. Finegan, Thomas M. M. Heenan, Alessandro Tengattini, Daniel Baum, Nikolay Kardjilov, Henning Markoetter, Ingo Manke, Winfried Kockelmann, Dan J. L. Brett, Paul R. Shearing
NATURE COMMUNICATIONS
(2020)
Article
Biology
Sider Penkov, Bharath Kumar Raghuraman, Cihan Erkut, Jana Oertel, Roberta Galli, Eduardo Jacobo Miranda Ackerman, Daniela Vorkel, Jean-Marc Verbavatz, Edmund Koch, Karim Fahmy, Andrej Shevchenko, Teymuras V. Kurzchalia
Article
Biology
Griselda Velez-Aguilera, Sylvia Nkombo Nkoula, Batool Ossareh-Nazari, Jana Link, Dimitra Paouneskou, Lucie Van Hove, Nicolas Joly, Nicolas Tavernier, Jean-Marc Verbavatz, Verena Jantsch, Lionel Pintard
Article
Dentistry, Oral Surgery & Medicine
Ana Prates Soares, Daniel Baum, Bernhard Hesse, Andreas Kupsch, Bernd R. Mueller, Paul Zaslansky
Summary: This study aimed to identify and characterize damage to fiberglass posts using PCE-CT and SXRR imaging methods. The findings revealed significant differences in morphological characteristics of damage-affected areas caused by trimming, highlighting the critical importance of the integrity of glass fibers in the posts for their functionality.
Article
Computer Science, Software Engineering
Felix Herter, Hans-Christian Hege, Markus Hadwiger, Verena Lepper, Daniel Baum
Summary: This study addresses the challenge of analyzing thin, curved structures in volumetric data by rendering spatially transformed views, allowing for unobstructed visualization of the entire structure and enabling simple and intuitive navigation. The approach is based on ray-casting and uses guiding surface meshes to define transformed views, supplemented by interactive local modifications for visual inspection of structures.
COMPUTER GRAPHICS FORUM
(2021)
Article
Microscopy
Norbert Lindow, Florian N. Bruenig, Vincent J. Dercksen, Gunar Fabig, Robert Kiewisz, Stefanie Redemann, Thomas Mueller-Reichert, Steffen Prohaska, Daniel Baum
Summary: A software-assisted workflow for aligning and matching filamentous structures across a 3D stack of serial images has been developed, combining automatic methods, visual validation, and interactive correction. User interaction is key to continuously improving results by correcting landmarks or matches of filaments, with a visual quality assessment allowing a balance between quality and manual labor. This interdisciplinary collaboration between computer scientists and cell biologists aims to investigate cell division by quantitatively analyzing microtubules in mitotic and meiotic spindles.
JOURNAL OF MICROSCOPY
(2021)
Article
Multidisciplinary Sciences
Jing Xie, Javad Najafi, Remi Le Borgne, Jean-Marc Verbavatz, Catherine Durieu, Jeremy Salle, Nicolas Minc
Summary: Cells are filled with macromolecules and polymer networks that provide viscous and elastic properties to the cytoplasm. Using magnetic tweezers, researchers found that the cytoplasm can exert reactive forces to move organelles back to their original positions. These findings have important implications for cell division positioning and cellular organization.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Physiology
Alice Dussouchaud, Julieta Jacob, Charles Secq, Jean-Marc Verbavatz, Martina Moras, Jerome Larghero, Claudio M. Fader, Mariano A. Ostuni, Sophie D. Lefevre
Summary: During human erythroblast differentiation, mitochondria are progressively cleared and lose contact with the endoplasmic reticulum (ER) and nucleus (NAM). The number of endosomes and multivesicular bodies (MVBs) involved in iron traffic and heme synthesis increases during differentiation, as well as autophagosomes. Glycogen accumulation is observed in the OrthoE stage.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Anatomy & Morphology
Lennart Eigen, Daniel Baum, Mason N. Dean, Daniel Werner, Jan Woelfer, John A. Nyakatura
Summary: Biological armors, such as the carapace of boxfish, derive their mechanical integrity from geometric architectures involving tessellations. The carapace of boxfish grows with the fish, with the number of scutes remaining constant but increasing in volume, thickness, and width with age. The carapace is predominantly flat, with thicker scutes at the edges, and the overall morphology allows for a relatively straightforward growth system of this tessellated architecture.
JOURNAL OF ANATOMY
(2022)
Article
Computer Science, Software Engineering
Natalia Mikula, Tom Doerffel, Daniel Baum, Hans-Christian Hege
Summary: Our ability to understand complex phenomena relies on recognizing and relating structures. A systematic approach and interactive tool can be used to obtain precise definitions of spatiotemporal structures, facilitating automated data analysis and the development of phenomenological models.
COMPUTER GRAPHICS FORUM
(2022)
Article
Multidisciplinary Sciences
Joy Lachat, Alice Pascault, Delphine Thibaut, Remi Le Borgne, Jean-Marc Verbavatz, Allon Weiner
Summary: The opportunistic fungal pathogen Candida albicans can invade host cells and cause infection. This study investigates the invasion process of Candida albicans using live-cell imaging and a damage-sensitive reporter gene. The results show that invasion can result in host cell membrane breaching or cell death, or traversal of host cells without membrane breaching.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Priyanka Fernandes, Manon Loubens, Remi Le Borgne, Carine Marinach, Beatrice Ardin, Sylvie Briquet, Laetitia W. Vincensini, Soumia Hamada, Benedicte W. Hoareau-Coudert, Jean-Marc Verbavatz, Allon W. Weiner, Olivier Silvie
Summary: AMA1 and RONs facilitate host cell invasion across Plasmodium invasive stages and may represent potential targets for blocking malaria transmission.
Article
Multidisciplinary Sciences
Kaitlyn Becker, Clark Teeple, Nicholas Charles, Yeonsu Jung, Daniel Baum, James C. Weaver, L. Mahadevan, Robert Wood
Summary: Grasping is sensitive to variations in size, weight, and shape in both biological and engineered mechanisms. Through experimental evaluation and computational modeling, this study explains the grasping performance of a strategy involving flexible filaments in contact with complex objects. The findings highlight the potential of active collective entanglement of filament arrays in enabling soft and adaptable grasping.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Soledad Ferreras, Neha Pratap Singh, Remi Le Borgne, Philippe Bun, Thomas Binz, Robert G. Parton, Jean-Marc Verbavatz, Christian Vannier, Thierry Galli
Summary: A synthetic biological approach using Caveolin protein in Escherichia coli has been developed to study membrane fusion. The coexpression of SNAREs led to the formation of protein complexes and elongation of cells. This assay provides a simple organism model for studying the structure and function of SNAREs.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Proceedings Paper
Computer Science, Artificial Intelligence
Martha Paskin, Daniel Baum, Mason N. Dean, Christoph Von Tycowicz
Summary: 3D shapes provide more information than 2D images, but it is often difficult to acquire 3D shapes compared to 2D images. This paper presents a new approach based on Kendall shape space to reconstruct 3D shapes from single monocular 2D images. The method is applied to study the feeding behavior of the basking shark, demonstrating its robustness compared to previous methods.
COMPUTER VISION - ECCV 2022, PT II
(2022)
