Article
Robotics
Zhongliang Jiang, Yuan Gao, Le Xie, Nassir Navab
Summary: This paper proposes a vision-based approach for autonomous robotic ultrasound limb scanning. By utilizing an MRI template and incorporating channel attention modules into a neural network, it effectively segments and reconstructs the targeted 3D vessels for robotic ultrasound acquisition.
IEEE ROBOTICS AND AUTOMATION LETTERS
(2022)
Article
Gastroenterology & Hepatology
Nazli Khodayari, Regina Oshins, Alek M. Aranyos, Sergio Duarte, Sayedamin Mostofizadeh, Yuanqing Lu, Mark Brantly
Summary: We characterized a mouse model of human alpha-1 antitrypsin deficiency with a strong manifestation of liver disease, which can be used as an in vivo tool for testing preventive and therapeutic reagents. Our data explored the altered immunophenotype of alpha-1 antitrypsin-deficient liver macrophages and suggested a relationship between acute inflammation, immune response, and fibrosis.
AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY
(2022)
Article
Computer Science, Interdisciplinary Applications
Maryam Sadeghi, Arnau Ramos-Prats, Pedro Neto, Federico Castaldi, Devin Crowley, Pawel Matulewicz, Enrica Paradiso, Wolfgang Freysinger, Francesco Ferraguti, Georg Goebel
Summary: To accurately investigate the anatomical organization of neural circuits in the brain, it is crucial to map experimental brain data onto a standardized coordinate system. We propose a computational tool called AMBIA that can accurately map 2D mouse brain slices onto a 3D brain model with minimal human intervention. The tool performs at a human expert level in terms of localization and registration.
Article
Veterinary Sciences
Perumalraja Kirthika, Sungwoo Park, Vijayakumar Jawalagatti, John Hwa Lee
Summary: This study established a C57BL/6 mouse model to evaluate the progression and lesions of proliferative enteropathy (PE) caused by L. intracellularis, and found that the infection could modulate the immune responses of mice. This model contributes to the study of L. intracellularis infection and the development of potential vaccination and therapeutic strategies.
JOURNAL OF VETERINARY SCIENCE
(2022)
Article
Toxicology
Kristal A. Rychlik, Emily J. Illingworth, Ian F. Sanchez, Sarah E. Attreed, Prithvi Sinha, Kevin M. Casin, Nicole Taube, Jeff Loube, Rokeya Tasneen, Raihan Kabir, Eric Nuermberger, Wayne Mitzner, Mark J. Kohr, Fenna C. M. Sille
Summary: This study aimed to characterize the long-term impact of mid-pregnancy arsenic exposure on the lung, heart, and immune system. The results suggest that prenatal arsenic exposure can affect lung and immune cell function, potentially increasing the risk of respiratory diseases.
TOXICOLOGY LETTERS
(2023)
Article
Computer Science, Interdisciplinary Applications
Johanna Perens, Casper Gravesen Salinas, Urmas Roostalu, Jacob Lercke Skytte, Carsten Gundlach, Jacob Hecksher-Sorensen, Anders Bjorholm Dahl, Tim B. Dyrby
Summary: Magnetic resonance imaging (MRI) and light-sheet fluorescence microscopy (LSFM) are technologies that allow non-invasive imaging of whole mouse brains in three dimensions. This study developed a bidirectional multimodal atlas framework to facilitate the translation of LSFM recorded brains to non-distorted templates, improving research on neuroscience, disease progression, and drug efficacy.
Article
Mathematical & Computational Biology
Jan Krepl, Francesco Casalegno, Emilie Delattre, Csaba Ero, Huanxiang Lu, Daniel Keller, Dimitri Rodarie, Henry Markram, Felix Schurmann
Summary: This study introduces a supervised learning model for gene expression image registration using deep learning, which produces accurate and smooth predictions, outperforming traditional approaches in aligning complex brain structures.
FRONTIERS IN NEUROINFORMATICS
(2021)
Article
Veterinary Sciences
Seoung-Woo Lee, Su-Min Baek, Young-Jin Lee, Jin-Kyu Park
Summary: A 70-week-old female mouse with mesenteric lymph node metastatic lymphoma showed signs of anorexia, lethargy, and enlarged abdomen. The tumor had spread to various organs, and microscopic examination revealed neoplastic cells with characteristic features. This case highlights the potential risk of lymphoma development associated with SMP30 depletion.
ACTA VETERINARIA-BEOGRAD
(2022)
Proceedings Paper
Engineering, Biomedical
Sehastien Piluso, Nicolas Souedet, Caroline Jan, Cedric Clouchoux, Thierry Delzescaux
Summary: In this paper, a new method is proposed to automatically segment single 2D coronal slices within a 3D volume of atlas using linear registration, with high accuracy and robustness. This method addresses a significant challenge in current brain histological data analysis.
2021 43RD ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE & BIOLOGY SOCIETY (EMBC)
(2021)
Proceedings Paper
Computer Science, Interdisciplinary Applications
Justinas Antanavicius, Roberto Leiras, Raghavendra Selvan
Summary: Registering mouse brain microscopy images to a reference atlas is crucial for understanding brain circuits. However, existing registration methods face challenges such as missing data, different cutting angles, and high-resolution image identification. This study proposes using convolutional neural networks to learn a low-dimensional embedding space for image identification. The experimental results demonstrate that our method outperforms existing methods in terms of accuracy.
BIOMEDICAL IMAGE REGISTRATION (WBIR 2022)
(2022)
Proceedings Paper
Computer Science, Interdisciplinary Applications
Maryam Sadeghi, Pedro Neto, Arnau Ramos-Prats, Federico Castaldi, Enrica Paradiso, Naghmeh Mahmoodian, Francesco Ferraguti, Georg Goebel
Summary: This study introduces a deep learning-based approach to automatically detect the position and angle of mouse brain sections in a 3D reference atlas. The proposed method outperforms traditional 2D or 3D registration methods in terms of accuracy, efficiency, and robustness to histological artifacts.
MEDICAL IMAGING 2022: IMAGE PROCESSING
(2022)
Article
Biochemical Research Methods
Tamim Abdelaal, Paul de Raadt, Boudewijn P. F. Lelieveldt, Marcel J. T. Reinders, Ahmed Mahfouz
Article
Computer Science, Software Engineering
Antonios Somarakis, Vincent Van Unen, Frits Koning, Boudewijn Lelieveldt, Thomas Hollt
Summary: Imaging Mass Cytometry allows for precise characterization and spatial mapping of cell types in tissues, but the resulting data poses challenges for analysis. An interactive visual analysis tool, ImaCytE, was developed in collaboration with domain experts to help users analyze cell types and microenvironments, aiding in the understanding of tissue architecture and function. The effectiveness of this workflow and tool was demonstrated through a case study conducted by a collaborating specialist.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2021)
Article
Computer Science, Software Engineering
Antonios Somarakis, Marieke E. Ijsselsteijn, Sietse J. Luk, Boyd Kenkhuis, Noel F. C. C. de Miranda, Boudewijn P. F. Lelieveldt, Thomas Hollt
Summary: Spatially-resolved omics-data can help researchers distinguish cell types in tissues and explore their interactions. Clinical researchers perform large-scale cohort studies to understand diseases, requiring explorative data analysis. The interactive visual analysis workflow enables the comparison of spatially-resolved omics-data cohorts.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2021)
Article
Immunology
Sanne E. de Jong, Vincent van Unen, Mikhael D. Manurung, Koen A. Stam, Jelle J. Goeman, Simon P. Jochems, Thomas Hollt, Nicola Pezzotti, Yoanne D. Mouwenda, Madeleine Eunice Betouke Ongwe, Freia-Raphaella Lorenz, Yvonne C. M. Kruize, Shohreh Azimi, Marion H. Konig, Anna Vilanova, Elmar Eisemann, Boudewijn P. F. Lelieveldt, Meta Roestenberg, B. Kim Lee Sim, Marcel J. T. Reinders, Rolf Fendel, Stephen L. Hoffman, Peter G. Kremsner, Frits Koning, Benjamin Mordmuller, Bertrand Lell, Maria Yazdanbakhsh
Summary: Controlled human infections were used to compare immune responses of Europeans and Africans to Plasmodium falciparum, revealing differences in immune cell populations and gene expression profiles. Africans capable of controlling parasitemia were characterized by specific immune cell clusters and transcriptional responses after inoculation. These findings provide insights for developing effective malaria vaccines in endemic regions.
Article
Biochemical Research Methods
Marieke E. Ijsselsteijn, Antonios Somarakis, Boudewijn P. F. Lelieveldt, Thomas Hollt, Noel F. C. C. Miranda
Summary: This study examines the impact of immunodetection-related signal intensity fluctuations on IMC analysis and phenotype identification in 12 colorectal cancer tissues and proposes a workflow for normalizing IMC data through semi-automated background removal.
Article
Computer Science, Software Engineering
Zixia Zhou, Xinrui Zu, Yuanyuan Wang, Boudewijn P. F. Lelieveldt, Qian Tao
Summary: In this article, we propose a method to embed high-dimensional data onto a low-dimensional manifold using deep embedding networks and mathematics-guided rules, combined with a recursive strategy to boost embedding performance. Our proposed method outperforms traditional embedding methods in terms of preserving local and global structures, showing improved embedding performance on a range of public datasets.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2022)
Article
Medicine, Legal
Martin Baiker-Sorensen, Koen Herlaar
Summary: This article examines the properties of knife blades and cutting marks, finding that the relationship between corresponding properties of blades and marks depends on the knife type. Mark properties are only specific for a particular knife brand and model assuming a specific knife type.
INTERNATIONAL JOURNAL OF LEGAL MEDICINE
(2022)
Article
Radiology, Nuclear Medicine & Medical Imaging
Kirsten Koolstra, Peter Bornert, Boudewijn P. F. Lelieveldt, Andrew Webb, Oleh Dzyubachyk
Summary: The study visualized the encoding capability of MRF dictionaries using t-SNE, showing clear differences between different MRF sequences in a color-coded map. The technique was validated using quantitative measures and could be used as a confirmation tool in MRF sequence optimization.
MAGNETIC RESONANCE MATERIALS IN PHYSICS BIOLOGY AND MEDICINE
(2022)
Article
Multidisciplinary Sciences
Trygve E. Bakken, Nikolas L. Jorstad, Qiwen Hu, Blue B. Lake, Wei Tian, Brian E. Kalmbach, Megan Crow, Rebecca D. Hodge, Fenna M. Krienen, Staci A. Sorensen, Jeroen Eggermont, Zizhen Yao, Brian D. Aevermann, Andrew I. Aldridge, Anna Bartlett, Darren Bertagnolli, Tamara Casper, Rosa G. Castanon, Kirsten Crichton, Tanya L. Daigle, Rachel Dalley, Nick Dee, Nikolai Dembrow, Dinh Diep, Song-Lin Ding, Weixiu Dong, Rongxin Fang, Stephan Fischer, Melissa Goldman, Jeff Goldy, Lucas T. Graybuck, Brian R. Herb, Xiaomeng Hou, Jayaram Kancherla, Matthew Kroll, Kanan Lathia, Baldur van Lew, Yang Eric Li, Christine S. Liu, Hanqing Liu, Jacinta D. Lucero, Anup Mahurkar, Delissa McMillen, Jeremy A. Miller, Marmar Moussa, Joseph R. Nery, Philip R. Nicovich, Sheng-Yong Niu, Joshua Orvis, Julia K. Osteen, Scott Owen, Carter R. Palmer, Thanh Pham, Nongluk Plongthongkum, Olivier Poirion, Nora M. Reed, Christine Rimorin, Angeline Rivkin, William J. Romanow, Adriana E. Sedeno-Cortes, Kimberly Siletti, Saroja Somasundaram, Josef Sulc, Michael Tieu, Amy Torkelson, Herman Tung, Xinxin Wang, Fangming Xie, Anna Marie Yanny, Renee Zhang, Seth A. Ament, M. Margarit Behrens, Hector Corrada Bravo, Jerold Chun, Alexander Dobin, Jesse Gillis, Ronna Hertzano, Patrick R. Hof, Thomas Hollt, Gregory D. Horwitz, C. Dirk Keene, Peter Kharchenko, Andrew L. Ko, Boudewijn P. Lelieveldt, Chongyuan Luo, Eran A. Mukamel, Antonio Pinto-Duarte, Sebastian Preissl, Aviv Regev, Bing Ren, Richard H. Scheuermann, Kimberly Smith, William J. Spain, Owen R. White, Christof Koch, Michael Hawrylycz, Bosiljka Tasic, Evan Z. Macosko, Steven A. McCarroll, Jonathan T. Ting, Hongku Zeng, Kun Zhang, Guoping Feng, Joseph R. Ecker, Sten Linnarsson, Ed S. Lein
Summary: The research reveals a broadly conserved cellular makeup of the primary motor cortex in humans, marmoset monkeys, and mice, with species-specific specializations. Few cell-type marker genes are conserved across species, indicating some candidate genes and regulatory mechanisms responsible for functional identity of cell types and their species-specific adaptations.
Article
Biochemistry & Molecular Biology
Olena Vepris, Christina Eich, Yansong Feng, Gaston Fuentes, Hong Zhang, Eric L. Kaijzel, Luis J. Cruz
Summary: This study successfully used PLGA-NPs as a delivery vehicle for TTA-UC and demonstrated its integrity and suitability in vivo, providing a proof-of-concept for the development of advanced nanocarriers for simultaneous in vivo molecular imaging and drug delivery.
Article
Immunology
Vincent Van Unen, Laura F. Ouboter, Na Li, Mette Schreurs, Tamim Abdelaal, Yvonne Kooy-Winkelaar, Guillaume Beyrend, Thomas Hoellt, P. W. Jeroen Maljaars, M. Luisa Mearin, Ahmed Mahfouz, Anne M. C. Witte, Cornelis H. M. Clemens, Sunje Abraham, Johanna C. Escher, Boudewijn P. F. Lelieveldt, M. Fernanda Pascutti, Andrea E. van der Meulen E. De Jong, Frits Koning
Summary: This study identifies immune cell types associated with inflammatory bowel disease (IBD) and reveals their spatial distribution in inflamed biopsies from a subset of patients. These findings contribute to understanding disease heterogeneity and may guide the development of targeted therapeutics in IBD.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Oncology
Thomas P. Brouwer, Natasja L. de Vries, Tamim Abdelaal, Ricki T. Krog, Zheng Li, Dina Ruano, Arantza Farina, Boudewijn P. F. Lelieveldt, Hans Morreau, Bert A. Bonsing, Alexander L. Vahrmeijer, Frits Koning, Noel F. C. C. de Miranda
Summary: This study reveals an immunosuppressive landscape in PDAC tissues, with a depletion of cytotoxic T cells and an enrichment of regulatory T cells and B cells. The potential of ILC1-like cells in PDAC to act against tumors may be explored in therapeutic settings. Moreover, the immune cell composition of the PDAC microenvironment can be reflected in blood samples isolated from the portal vein.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2022)
Article
Computer Science, Artificial Intelligence
Olaf M. Neve, Yunjie Chen, Qian Tao, Stephan R. Romeijn, Nick P. de Boer, Willem Grootjans, Mark C. Kruit, Boudewijn P. F. Lelieveldt, Jeroen C. Jansen, Erik F. Hensen, Berit M. Verbist, Marius Staring
Summary: This study developed an automated method for measuring vestibular schwannoma on contrast-enhanced T1- and T2-weighted MRI scans. The convolutional neural network model achieved accurate delineation of the tumor and differentiation between intrameatal and extrameatal tumor parts.
RADIOLOGY-ARTIFICIAL INTELLIGENCE
(2022)
Proceedings Paper
Computer Science, Artificial Intelligence
Patricia M. Johnson, Geunu Jeong, Kerstin Hammernik, Jo Schlemper, Chen Qin, Jinming Duan, Daniel Rueckert, Jingu Lee, Nicola Pezzotti, Elwin De Weerdt, Sahar Yousefi, Mohamed S. Elmahdy, Jeroen Hendrikus Franciscus Van Gemert, Christophe Schuelke, Mariya Doneva, Tim Nielsen, Sergey Kastryulin, Boudewijn P. F. Lelieveldt, Matthias J. P. Van Osch, Marius Staring, Eric Z. Chen, Puyang Wang, Xiao Chen, Terrence Chen, Vishal M. Patel, Shanhui Sun, Hyungseob Shin, Yohan Jun, Taejoon Eo, Sewon Kim, Taeseong Kim, Dosik Hwang, Patrick Putzky, Dimitrios Karkalousos, Jonas Teuwen, Nikita Miriakov, Bart Bakker, Matthan Caan, Max Welling, Matthew J. Muckley, Florian Knoll
Summary: The 2019 fastMRI challenge aimed to advance research in the field of machine learning for MR image reconstruction. Despite differences in model architecture and training, the study found that all methods performed very similarly in terms of generalization performance under various perturbations.
MACHINE LEARNING FOR MEDICAL IMAGE RECONSTRUCTION (MLMIR 2021)
(2021)
Article
Computer Science, Information Systems
Hessam Sokooti, Sahar Yousefi, Mohamed S. Elmahdy, Boudewijn P. F. Lelieveldt, Marius Staring
Summary: In this paper, a supervised method using CNNs to predict registration misalignment is proposed. By leveraging hierarchical predictions and multi-resolution information through LSTM, the system achieves better registration results and higher accuracy in chest CT scans.