@article{WengHeidenreichMetzetal.2021, author = {Weng, Andreas M. and Heidenreich, Julius F. and Metz, Corona and Veldhoen, Simon and Bley, Thorsten A. and Wech, Tobias}, title = {Deep learning-based segmentation of the lung in MR-images acquired by a stack-of-spirals trajectory at ultra-short echo-times}, series = {BMC Medical Imaging}, volume = {21}, journal = {BMC Medical Imaging}, doi = {10.1186/s12880-021-00608-1}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-260520}, year = {2021}, abstract = {Background Functional lung MRI techniques are usually associated with time-consuming post-processing, where manual lung segmentation represents the most cumbersome part. The aim of this study was to investigate whether deep learning-based segmentation of lung images which were scanned by a fast UTE sequence exploiting the stack-of-spirals trajectory can provide sufficiently good accuracy for the calculation of functional parameters. Methods In this study, lung images were acquired in 20 patients suffering from cystic fibrosis (CF) and 33 healthy volunteers, by a fast UTE sequence with a stack-of-spirals trajectory and a minimum echo-time of 0.05 ms. A convolutional neural network was then trained for semantic lung segmentation using 17,713 2D coronal slices, each paired with a label obtained from manual segmentation. Subsequently, the network was applied to 4920 independent 2D test images and results were compared to a manual segmentation using the S{\o}rensen-Dice similarity coefficient (DSC) and the Hausdorff distance (HD). Obtained lung volumes and fractional ventilation values calculated from both segmentations were compared using Pearson's correlation coefficient and Bland Altman analysis. To investigate generalizability to patients outside the CF collective, in particular to those exhibiting larger consolidations inside the lung, the network was additionally applied to UTE images from four patients with pneumonia and one with lung cancer. Results The overall DSC for lung tissue was 0.967 ± 0.076 (mean ± standard deviation) and HD was 4.1 ± 4.4 mm. Lung volumes derived from manual and deep learning based segmentations as well as values for fractional ventilation exhibited a high overall correlation (Pearson's correlation coefficent = 0.99 and 1.00). For the additional cohort with unseen pathologies / consolidations, mean DSC was 0.930 ± 0.083, HD = 12.9 ± 16.2 mm and the mean difference in lung volume was 0.032 ± 0.048 L. Conclusions Deep learning-based image segmentation in stack-of-spirals based lung MRI allows for accurate estimation of lung volumes and fractional ventilation values and promises to replace the time-consuming step of manual image segmentation in the future.}, language = {en} } @article{RichterWechWengetal.2020, author = {Richter, Julian A. J. and Wech, Tobias and Weng, Andreas M. and Stich, Manuel and Weick, Stefan and Breuer, Kathrin and Bley, Thorsten A. and K{\"o}stler, Herbert}, title = {Free-breathing self-gated 4D lung MRI using wave-CAIPI}, series = {Magnetic Resonance in Medicine}, volume = {84}, journal = {Magnetic Resonance in Medicine}, number = {6}, doi = {10.1002/mrm.28383}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-218075}, pages = {3223 -- 3233}, year = {2020}, abstract = {Purpose The aim of this study was to compare the wave-CAIPI (controlled aliasing in parallel imaging) trajectory to the Cartesian sampling for accelerated free-breathing 4D lung MRI. Methods The wave-CAIPI k-space trajectory was implemented in a respiratory self-gated 3D spoiled gradient echo pulse sequence. Trajectory correction applying the gradient system transfer function was used, and images were reconstructed using an iterative conjugate gradient SENSE (CG SENSE) algorithm. Five healthy volunteers and one patient with squamous cell carcinoma in the lung were examined on a clinical 3T scanner, using both sampling schemes. For quantitative comparison of wave-CAIPI and standard Cartesian imaging, the normalized mutual information and the RMS error between retrospectively accelerated acquisitions and their respective references were calculated. The SNR ratios were investigated in a phantom study. Results The obtained normalized mutual information values indicate a lower information loss due to acceleration for the wave-CAIPI approach. Average normalized mutual information values of the wave-CAIPI acquisitions were 10\% higher, compared with Cartesian sampling. Furthermore, the RMS error of the wave-CAIPI technique was lower by 19\% and the SNR was higher by 14\%. Especially for short acquisition times (down to 1 minute), the undersampled Cartesian images showed an increased artifact level, compared with wave-CAIPI. Conclusion The application of the wave-CAIPI technique to 4D lung MRI reduces undersampling artifacts, in comparison to a Cartesian acquisition of the same scan time. The benefit of wave-CAIPI sampling can therefore be traded for shorter examinations, or enhancing image quality of undersampled 4D lung acquisitions, keeping the scan time constant.}, language = {en} } @article{SagivMichaeliAssietal.2015, author = {Sagiv, Jitka Y. and Michaeli, Janna and Assi, Simaan and Mishalian, Inbal and Kisos, Hen and Levy, Liran and Damti, Pazzit and Lumbroso, Delphine and Polyansky, Lola and Sionov, Ronit V. and Ariel, Amiram and Hovav, Avi-Hai and Henke, Erik and Fridlender, Zvi G. and Granot, Zvi}, title = {Phenotypic diversity and plasticity in circulating neutrophil subpopulations in cancer}, series = {Cell Reports}, volume = {10}, journal = {Cell Reports}, number = {4}, doi = {10.1016/j.celrep.2014.12.039}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-144102}, pages = {562-573}, year = {2015}, abstract = {Controversy surrounds neutrophil function in cancer because neutrophils were shown to provide both pro-and antitumor functions. We identified a heterogeneous subset of low-density neutrophils (LDNs) that appear transiently in self-resolving inflammation but accumulate continuously with cancer progression. LDNs display impaired neutrophil function and immunosuppressive properties, characteristics that are in stark contrast to those of mature, high-density neutrophils (HDNs). LDNs consist of both immature myeloid-derived suppressor cells (MDSCs) and mature cells that are derived from HDNs in a TGF-beta-dependent mechanism. Our findings identify three distinct populations of circulating neutrophils and challenge the concept that mature neutrophils have limited plasticity. Furthermore, our findings provide a mechanistic explanation to mitigate the controversy surrounding neutrophil function in cancer.}, language = {en} } @article{WillemsUrlichsSeidenspinneretal.2012, author = {Willems, Coen H. M. P. and Urlichs, Florian and Seidenspinner, Silvia and Kunzmann, Steffen and Speer, Christian P. and Kramer, Boris W.}, title = {Poractant alfa (Curosurf (R)) increases phagocytosis of apoptotic neutrophils by alveolar macrophages in vivo}, series = {Respiratory Research}, volume = {13}, journal = {Respiratory Research}, number = {17}, doi = {10.1186/1465-9921-13-17}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-130721}, year = {2012}, abstract = {Background: Clearance of apoptotic neutrophils in the lung is an essential process to limit inflammation, since they could become a pro-inflammatory stimulus themselves. The clearance is partially mediated by alveolar macrophages, which phagocytose these apoptotic cells. The phagocytosis of apoptotic immune cells by monocytes in vitro has been shown to be augmented by several constituents of pulmonary surfactant, e. g. phospholipids and hydrophobic surfactant proteins. In this study, we assessed the influence of exogenous poractant alfa (Curosurf (R)) instillation on the in vivo phagocytosis of apoptotic neutrophils by alveolar macrophages. Methods: Poractant alfa (200 mg/kg) was instilled intratracheally in the lungs of three months old adult male C57/Black 6 mice, followed by apoptotic neutrophil instillation. Bronchoalveloar lavage was performed and alveolar macrophages and neutrophils were counted. Phagocytosis of apoptotic neutrophils was quantified by determining the number of apoptotic neutrophils per alveolar macrophages. Results: Exogenous surfactant increased the number of alveolar macrophages engulfing apoptotic neutrophils 2.6 fold. The phagocytosis of apoptotic neutrophils was increased in the presence of exogenous surfactant by a 4.7 fold increase in phagocytosed apoptotic neutrophils per alveolar macrophage. Conclusions: We conclude that the anti-inflammatory properties of surfactant therapy may be mediated in part by increased numbers of alveolar macrophages and increased phagocytosis of apoptotic neutrophils by alveolar macrophages.}, language = {en} } @article{BiedererBeerHirschetal.2012, author = {Biederer, J. and Beer, M. and Hirsch, W. and Wild, J. and Fabel, M. and Puderbach, M. and Van Beek, E. J. R.}, title = {MRI of the lung (2/3). Why … when … how?}, series = {Insights into Imaging}, volume = {3}, journal = {Insights into Imaging}, number = {4}, doi = {10.1007/s13244-011-0146-8}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-124268}, pages = {355-371}, year = {2012}, abstract = {Background Among the modalities for lung imaging, proton magnetic resonance imaging (MRI) has been the latest to be introduced into clinical practice. Its value to replace X-ray and computed tomography (CT) when radiation exposure or iodinated contrast material is contra-indicated is well acknowledged: i.e. for paediatric patients and pregnant women or for scientific use. One of the reasons why MRI of the lung is still rarely used, except in a few centres, is the lack of consistent protocols customised to clinical needs. Methods This article makes non-vendor-specific protocol suggestions for general use with state-of-the-art MRI scanners, based on the available literature and a consensus discussion within a panel of experts experienced in lung MRI. Results Various sequences have been successfully tested within scientific or clinical environments. MRI of the lung with appropriate combinations of these sequences comprises morphological and functional imaging aspects in a single examination. It serves in difficult clinical problems encountered in daily routine, such as assessment of the mediastinum and chest wall, and even might challenge molecular imaging techniques in the near future. Conclusion This article helps new users to implement appropriate protocols on their own MRI platforms. Main Messages • MRI of the lung can be readily performed on state-of-the-art 1.5-T MRI scanners. • Protocol suggestions based on the available literature facilitate its use for routine • MRI offers solutions for complicated thoracic masses with atelectasis and chest wall invasion. • MRI is an option for paediatrics and science when CT is contra-indicated}, language = {en} } @article{WildMarshallBocketal.2012, author = {Wild, J. M. and Marshall, H. and Bock, M. and Schad, L. R. and Jakob, P. M. and Puderbach, M. and Molinari, F. and Van Beek, E. J. R. and Biederer, J.}, title = {MRI of the lung (1/3): methods}, series = {Insights into Imaging}, volume = {3}, journal = {Insights into Imaging}, number = {4}, doi = {10.1007/s13244-012-0176-x}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-124238}, pages = {345-353}, year = {2012}, abstract = {Proton magnetic resonance imaging (MRI) has recently emerged as a clinical tool to image the lungs. This paper outlines the current technical aspects of MRI pulse sequences, radiofrequency (RF) coils and MRI system requirements needed for imaging the pulmonary parenchyma and vasculature. Lung MRI techniques are presented as a "technical toolkit", from which MR protocols will be composed in the subsequent papers for comprehensive imaging of lung disease and function (parts 2 and 3). This paper is pitched at MR scientists, technicians and radiologists who are interested in understanding and establishing lung MRI methods. Images from a 1.5 T scanner are used for illustration of the sequences and methods that are highlighted. Main Messages • Outline of the hardware and pulse sequence requirements for proton lung MRI • Overview of pulse sequences for lung parenchyma, vascular and functional imaging with protons • Demonstration of the pulse-sequence building blocks for clinical lung MRI protocols}, language = {en} }