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ORCIDChristian F. Baumgartner
Person information
- affiliation: University of Tübingen, Germany
- affiliation (former): ETH Zurich, Switzerland
- affiliation (former): Imperial College London
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Journal Articles
- 2024
[j11]Shadi Albarqouni, Christian F. Baumgartner, Qi Dou, Ender Konukoglu, Bjoern H. Menze, Archana Venkataraman:
Editorial for the Special Issue on the 2022 Medical Imaging with Deep Learning Conference. Medical Image Anal. 98: 103308 (2024)- [j10]Lisa M. Koch
, Christian F. Baumgartner, Philipp Berens:
Distribution shift detection for the postmarket surveillance of medical AI algorithms: a retrospective simulation study. npj Digit. Medicine 7(1) (2024) - 2022
- [j9]Kerem Can Tezcan, Neerav Karani, Christian F. Baumgartner, Ender Konukoglu:
Sampling Possible Reconstructions of Undersampled Acquisitions in MR Imaging With a Deep Learned Prior. IEEE Trans. Medical Imaging 41(7): 1885-1896 (2022) - 2021
- [j8]Krishna Chaitanya, Neerav Karani, Christian F. Baumgartner, Ertunc Erdil, Anton S. Becker, Olivio Donati, Ender Konukoglu:
Semi-supervised task-driven data augmentation for medical image segmentation. Medical Image Anal. 68: 101934 (2021) - 2019
- [j7]Kerem Can Tezcan, Christian F. Baumgartner, Roger Luechinger, Klaas P. Pruessmann, Ender Konukoglu:
MR Image Reconstruction Using Deep Density Priors. IEEE Trans. Medical Imaging 38(7): 1633-1642 (2019) - 2018
- [j6]Lisa M. Koch, Martin Rajchl, Wenjia Bai, Christian F. Baumgartner, Tong Tong, Jonathan Passerat-Palmbach, Paul Aljabar, Daniel Rueckert:
Multi-Atlas Segmentation Using Partially Annotated Data: Methods and Annotation Strategies. IEEE Trans. Pattern Anal. Mach. Intell. 40(7): 1683-1696 (2018) - [j5]Olivier Bernard, Alain Lalande, Clément Zotti, Frederic Cervenansky, Xin Yang, Pheng-Ann Heng, Irem Cetin, Karim Lekadir, Oscar Camara, Miguel Ángel González Ballester, Gerard Sanroma, Sandy Napel, Steffen E. Petersen, Georgios Tziritas, Elias Grinias, Mahendra Khened, Alex Varghese, Ganapathy Krishnamurthi, Marc-Michel Rohé, Xavier Pennec, Maxime Sermesant, Fabian Isensee, Paul Jäger, Klaus H. Maier-Hein, Peter M. Full, Ivo Wolf, Sandy Engelhardt, Christian F. Baumgartner, Lisa M. Koch, Jelmer M. Wolterink, Ivana Isgum, Yeonggul Jang, Yoonmi Hong, Jay Patravali, Shubham Jain, Olivier Humbert, Pierre-Marc Jodoin:
Deep Learning Techniques for Automatic MRI Cardiac Multi-Structures Segmentation and Diagnosis: Is the Problem Solved? IEEE Trans. Medical Imaging 37(11): 2514-2525 (2018) - 2017
- [j4]Christian F. Baumgartner, Christoph Kolbitsch, Jamie R. McClelland, Daniel Rueckert, Andrew P. King:
Autoadaptive motion modelling for MR-based respiratory motion estimation. Medical Image Anal. 35: 83-100 (2017) - [j3]Xin Chen, Muhammad Usman, Christian F. Baumgartner, Daniel R. Balfour, Paul K. Marsden, Andrew J. Reader, Claudia Prieto, Andrew P. King:
High-Resolution Self-Gated Dynamic Abdominal MRI Using Manifold Alignment. IEEE Trans. Medical Imaging 36(4): 960-971 (2017) - [j2]Christian F. Baumgartner, Konstantinos Kamnitsas, Jacqueline Matthew, Tara P. Fletcher, Sandra Smith, Lisa M. Koch, Bernhard Kainz, Daniel Rueckert:
SonoNet: Real-Time Detection and Localisation of Fetal Standard Scan Planes in Freehand Ultrasound. IEEE Trans. Medical Imaging 36(11): 2204-2215 (2017) - 2014
- [j1]Christian F. Baumgartner, Christoph Kolbitsch, Daniel R. Balfour, Paul K. Marsden, Jamie R. McClelland, Daniel Rueckert, Andrew P. King:
High-resolution dynamic MR imaging of the thorax for respiratory motion correction of PET using groupwise manifold alignment. Medical Image Anal. 18(7): 939-952 (2014)
Conference and Workshop Papers
- 2023
- [c21]Paul Fischer, Thomas Küstner, Christian F. Baumgartner:
Uncertainty Estimation and Propagation in Accelerated MRI Reconstruction. UNSURE@MICCAI 2023: 84-94 - [c20]Susu Sun, Lisa M. Koch, Christian F. Baumgartner:
Right for the Wrong Reason: Can Interpretable ML Techniques Detect Spurious Correlations? MICCAI (2) 2023: 425-434 - [c19]Kerol R. Djoumessi Donteu, Indu Ilanchezian, Laura Kühlewein, Hanna Faber, Christian F. Baumgartner, Bubacarr Bah, Philipp Berens, Lisa M. Koch:
Sparse Activations for Interpretable Disease Grading. MIDL 2023: 1-17 - [c18]Susu Sun, Stefano Woerner, Andreas K. Maier, Lisa M. Koch, Christian F. Baumgartner:
Inherently Interpretable Multi-Label Classification Using Class-Specific Counterfactuals. MIDL 2023: 937-956 - 2022
- [c17]Jan Nikolas Morshuis, Sergios Gatidis, Matthias Hein, Christian F. Baumgartner:
Adversarial Robustness of MR Image Reconstruction Under Realistic Perturbations. MLMIR@MICCAI 2022: 24-33 - 2019
- [c16]Krishna Chaitanya, Neerav Karani, Christian F. Baumgartner, Anton S. Becker, Olivio Donati, Ender Konukoglu:
Semi-supervised and Task-Driven Data Augmentation. IPMI 2019: 29-41 - [c15]Christian F. Baumgartner, Kerem Can Tezcan, Krishna Chaitanya, Andreas M. Hötker, Urs J. Muehlematter, Khoschy Schawkat, Anton S. Becker, Olivio Donati, Ender Konukoglu:
PHiSeg: Capturing Uncertainty in Medical Image Segmentation. MICCAI (2) 2019: 119-127 - [c14]Robin Brügger, Christian F. Baumgartner, Ender Konukoglu:
A Partially Reversible U-Net for Memory-Efficient Volumetric Image Segmentation. MICCAI (3) 2019: 429-437 - 2018
- [c13]Christian F. Baumgartner, Lisa M. Koch, Kerem Can Tezcan, Jia Xi Ang, Ender Konukoglu:
Visual Feature Attribution Using Wasserstein GANs. CVPR 2018: 8309-8319 - [c12]Matthew Sinclair, Christian F. Baumgartner, Jacqueline Matthew, Wenjia Bai, Juan Cerrolaza Martinez, Yuanwei Li, Sandra Smith, Caroline L. Knight, Bernhard Kainz, Joseph V. Hajnal, Andrew P. King, Daniel Rueckert:
Human-level Performance On Automatic Head Biometrics In Fetal Ultrasound Using Fully Convolutional Neural Networks. EMBC 2018: 714-717 - [c11]Qingjie Meng, Christian F. Baumgartner, Matthew Sinclair, James Housden, Martin Rajchl, Alberto Gómez, Benjamin Hou, Nicolas Toussaint, Veronika A. M. Zimmer, Jeremy Tan, Jacqueline Matthew, Daniel Rueckert, Julia A. Schnabel, Bernhard Kainz:
Automatic Shadow Detection in 2D Ultrasound Images. DATRA/PIPPI@MICCAI 2018: 66-75 - [c10]Yigit Baran Can, Krishna Chaitanya, Basil Mustafa, Lisa M. Koch, Ender Konukoglu, Christian F. Baumgartner:
Learning to Segment Medical Images with Scribble-Supervision Alone. DLMIA/ML-CDS@MICCAI 2018: 236-244 - [c9]Jana Kemnitz, Christian F. Baumgartner, Wolfgang Wirth, Felix Eckstein, Sebastian K. Eder, Ender Konukoglu:
Combining Heterogeneously Labeled Datasets For Training Segmentation Networks. MLMI@MICCAI 2018: 276-284 - [c8]Neerav Karani, Krishna Chaitanya, Christian F. Baumgartner, Ender Konukoglu:
A Lifelong Learning Approach to Brain MR Segmentation Across Scanners and Protocols. MICCAI (1) 2018: 476-484 - 2017
- [c7]Ramin M. Hasani, Dieter Haerle, Christian F. Baumgartner, Alessio R. Lomuscio, Radu Grosu:
Compositional neural-network modeling of complex analog circuits. IJCNN 2017: 2235-2242 - [c6]Konstantinos Kamnitsas, Christian F. Baumgartner, Christian Ledig, Virginia F. J. Newcombe, Joanna P. Simpson, Andrew D. Kane, David K. Menon, Aditya V. Nori, Antonio Criminisi, Daniel Rueckert, Ben Glocker:
Unsupervised Domain Adaptation in Brain Lesion Segmentation with Adversarial Networks. IPMI 2017: 597-609 - [c5]Christian F. Baumgartner, Lisa M. Koch, Marc Pollefeys, Ender Konukoglu:
An Exploration of 2D and 3D Deep Learning Techniques for Cardiac MR Image Segmentation. STACOM@MICCAI 2017: 111-119 - 2016
- [c4]Christian F. Baumgartner, Konstantinos Kamnitsas, Jacqueline Matthew, Sandra Smith, Bernhard Kainz, Daniel Rueckert:
Real-Time Standard Scan Plane Detection and Localisation in Fetal Ultrasound Using Fully Convolutional Neural Networks. MICCAI (2) 2016: 203-211 - 2015
- [c3]Christian F. Baumgartner, Alberto Gómez, Lisa M. Koch, Richard James Housden, Christoph Kolbitsch, Jamie R. McClelland, Daniel Rueckert, Andy P. King:
Self-Aligning Manifolds for Matching Disparate Medical Image Datasets. IPMI 2015: 363-374 - 2014
- [c2]Christian F. Baumgartner, Christoph Kolbitsch, Jamie R. McClelland, Daniel Rueckert, Andy P. King:
Autoadaptive motion modelling. ISBI 2014: 457-460 - 2013
- [c1]Christian F. Baumgartner, Christoph Kolbitsch, Jamie McClelland, Daniel Rueckert, Andrew P. King:
Groupwise Simultaneous Manifold Alignment for High-Resolution Dynamic MR Imaging of Respiratory Motion. IPMI 2013: 232-243
Parts in Books or Collections
- 2017
- [p2]Christian F. Baumgartner, Ozan Oktay, Daniel Rueckert:
Fully Convolutional Networks in Medical Imaging: Applications to Image Enhancement and Recognition. Deep Learning and Convolutional Neural Networks for Medical Image Computing 2017: 159-179 - 2014
- [p1]Ofer Pasternak, Klaus H. Maier-Hein, Christian F. Baumgartner, Martha Elizabeth Shenton, Yogesh Rathi, Carl-Fredrik Westin:
The Estimation of Free-Water Corrected Diffusion Tensors. Visualization and Processing of Tensors and Higher Order Descriptors for Multi-Valued Data 2014: 249-270
Editorship
- 2023
- [e7]Carole H. Sudre, Christian F. Baumgartner, Adrian V. Dalca, Raghav Mehta, Chen Qin, William M. Wells:
Uncertainty for Safe Utilization of Machine Learning in Medical Imaging - 5th International Workshop, UNSURE 2023, Held in Conjunction with MICCAI 2023, Vancouver, BC, Canada, October 12, 2023, Proceedings. Lecture Notes in Computer Science 14291, Springer 2023, ISBN 978-3-031-44335-0 [contents] - [e6]Jonghye Woo, Alessa Hering, Wilson Silva, Xiang Li, Huazhu Fu, Xiaofeng Liu, Fangxu Xing, Sanjay Purushotham, Tejas Sudharshan Mathai, Pritam Mukherjee, Max De Grauw, Regina Beets-Tan, Valentina Corbetta, Elmar Kotter, Mauricio Reyes, Christian F. Baumgartner, Quanzheng Li, Richard M. Leahy, Bin Dong, Hao Chen, Yuankai Huo, Jinglei Lv, Xinxing Xu, Xiaomeng Li, Dwarikanath Mahapatra, Li Cheng, Caroline Petitjean, Benoît Presles:
Medical Image Computing and Computer Assisted Intervention - MICCAI 2023 Workshops - MTSAIL 2023, LEAF 2023, AI4Treat 2023, MMMI 2023, REMIA 2023, Held in Conjunction with MICCAI 2023, Vancouver, BC, Canada, October 8-12, 2023, Proceedings. Lecture Notes in Computer Science 14394, Springer 2023, ISBN 978-3-031-47424-8 [contents] - 2022
- [e5]Carole H. Sudre, Christian F. Baumgartner, Adrian V. Dalca, Chen Qin, Ryutaro Tanno, Koen Van Leemput, William M. Wells III:
Uncertainty for Safe Utilization of Machine Learning in Medical Imaging - 4th International Workshop, UNSURE 2022, Held in Conjunction with MICCAI 2022, Singapore, September 18, 2022, Proceedings. Lecture Notes in Computer Science 13563, Springer 2022, ISBN 978-3-031-16748-5 [contents] - [e4]Ender Konukoglu, Bjoern H. Menze, Archana Venkataraman, Christian F. Baumgartner, Qi Dou, Shadi Albarqouni:
International Conference on Medical Imaging with Deep Learning, MIDL 2022, 6-8 July 2022, Zurich, Switzerland. Proceedings of Machine Learning Research 172, PMLR 2022 [contents] - 2021
- [e3]Carole H. Sudre, Roxane Licandro, Christian F. Baumgartner, Andrew Melbourne, Adrian V. Dalca, Jana Hutter, Ryutaro Tanno, Esra Abaci Turk, Koen Van Leemput, Jordina Torrents-Barrena, William M. Wells III, Christopher K. Macgowan:
Uncertainty for Safe Utilization of Machine Learning in Medical Imaging, and Perinatal Imaging, Placental and Preterm Image Analysis - 3rd International Workshop, UNSURE 2021, and 6th International Workshop, PIPPI 2021 Held in Conjunction with MICCAI 2021, Strasbourg, France, October 1, 2021, Proceedings. Lecture Notes in Computer Science 12959, Springer 2021, ISBN 978-3-030-87734-7 [contents] - 2020
- [e2]Carole H. Sudre, Hamid Fehri, Tal Arbel, Christian F. Baumgartner, Adrian V. Dalca, Ryutaro Tanno, Koen Van Leemput, William M. Wells III, Aristeidis Sotiras, Bartlomiej W. Papiez, Enzo Ferrante, Sarah Parisot:
Uncertainty for Safe Utilization of Machine Learning in Medical Imaging, and Graphs in Biomedical Image Analysis - Second International Workshop, UNSURE 2020, and Third International Workshop, GRAIL 2020, Held in Conjunction with MICCAI 2020, Lima, Peru, October 8, 2020, Proceedings. Lecture Notes in Computer Science 12443, Springer 2020, ISBN 978-3-030-60364-9 [contents] - 2019
- [e1]Hayit Greenspan, Ryutaro Tanno, Marius Erdt, Tal Arbel, Christian F. Baumgartner, Adrian V. Dalca, Carole H. Sudre, William M. Wells III, Klaus Drechsler, Marius George Linguraru, Cristina Oyarzun Laura, Raj Shekhar, Stefan Wesarg, Miguel Ángel González Ballester:
Uncertainty for Safe Utilization of Machine Learning in Medical Imaging and Clinical Image-Based Procedures - First International Workshop, UNSURE 2019, and 8th International Workshop, CLIP 2019, Held in Conjunction with MICCAI 2019, Shenzhen, China, October 17, 2019, Proceedings. Lecture Notes in Computer Science 11840, Springer 2019, ISBN 978-3-030-32688-3 [contents]
Informal and Other Publications
- 2024
- [i31]Stefano Woerner, Arthur Jaques, Christian F. Baumgartner:
A comprehensive and easy-to-use multi-domain multi-task medical imaging meta-dataset (MedIMeta). CoRR abs/2404.16000 (2024) - [i30]Susu Sun, Stefano Woerner, Andreas K. Maier, Lisa M. Koch, Christian F. Baumgartner:
Attri-Net: A Globally and Locally Inherently Interpretable Model for Multi-Label Classification Using Class-Specific Counterfactuals. CoRR abs/2406.05477 (2024) - [i29]Paul Fischer, Hannah Willms, Moritz Schneider, Daniela Thorwarth, Michael Muehlebach, Christian F. Baumgartner:
Subgroup-Specific Risk-Controlled Dose Estimation in Radiotherapy. CoRR abs/2407.08432 (2024) - [i28]Leonard Siegert, Paul Fischer, Mattias P. Heinrich, Christian F. Baumgartner:
PULPo: Probabilistic Unsupervised Laplacian Pyramid Registration. CoRR abs/2407.10567 (2024) - [i27]Anna M. Wundram, Paul Fischer, Michael Muehlebach, Lisa M. Koch, Christian F. Baumgartner:
Conformal Performance Range Prediction for Segmentation Output Quality Control. CoRR abs/2407.13307 (2024) - [i26]Jan Nikolas Morshuis, Matthias Hein, Christian F. Baumgartner:
Segmentation-guided MRI reconstruction for meaningfully diverse reconstructions. CoRR abs/2407.18026 (2024) - [i25]Stefano Woerner, Christian F. Baumgartner:
Navigating Data Scarcity using Foundation Models: A Benchmark of Few-Shot and Zero-Shot Learning Approaches in Medical Imaging. CoRR abs/2408.08058 (2024) - 2023
- [i24]Jaivardhan Kapoor, Jakob H. Macke, Christian F. Baumgartner:
Multiscale Metamorphic VAE for 3D Brain MRI Synthesis. CoRR abs/2301.03588 (2023) - [i23]Martin Paulikat, Christian M. Schürch, Christian F. Baumgartner:
Studying Therapy Effects and Disease Outcomes in Silico using Artificial Counterfactual Tissue Samples. CoRR abs/2302.03120 (2023) - [i22]Susu Sun, Stefano Woerner, Andreas Maier, Lisa M. Koch, Christian F. Baumgartner:
Inherently Interpretable Multi-Label Classification Using Class-Specific Counterfactuals. CoRR abs/2303.00500 (2023) - [i21]Lisa M. Koch, Christian M. Schürch, Christian F. Baumgartner, Arthur Gretton, Philipp Berens:
Deep Hypothesis Tests Detect Clinically Relevant Subgroup Shifts in Medical Images. CoRR abs/2303.04862 (2023) - [i20]Susu Sun, Lisa M. Koch, Christian F. Baumgartner:
Right for the Wrong Reason: Can Interpretable ML Techniques Detect Spurious Correlations? CoRR abs/2307.12344 (2023) - [i19]Paul Fischer, Thomas Küstner, Christian F. Baumgartner:
Uncertainty Estimation and Propagation in Accelerated MRI Reconstruction. CoRR abs/2308.02631 (2023) - [i18]Alexander Frötscher, Jaivardhan Kapoor, Thomas Wolfers, Christian F. Baumgartner:
Unsupervised Anomaly Detection using Aggregated Normative Diffusion. CoRR abs/2312.01904 (2023) - 2022
- [i17]Jan Nikolas Morshuis, Sergios Gatidis, Matthias Hein, Christian F. Baumgartner:
Adversarial Robustness of MR Image Reconstruction under Realistic Perturbations. CoRR abs/2208.03161 (2022) - 2020
- [i16]Esther Puyol-Antón, Bram Ruijsink, Christian F. Baumgartner, Matthew Sinclair, Ender Konukoglu, Reza Razavi, Andrew P. King:
Automated quantification of myocardial tissue characteristics from native T1 mapping using neural networks with Bayesian inference for uncertainty-based quality-control. CoRR abs/2001.11711 (2020) - [i15]Krishna Chaitanya, Neerav Karani, Christian F. Baumgartner, Anton S. Becker, Olivio Donati, Ender Konukoglu:
Semi-supervised Task-driven Data Augmentation for Medical Image Segmentation. CoRR abs/2007.05363 (2020) - [i14]Kerem Can Tezcan, Christian F. Baumgartner, Ender Konukoglu:
Sampling possible reconstructions of undersampled acquisitions in MR imaging. CoRR abs/2010.00042 (2020) - 2019
- [i13]Krishna Chaitanya, Neerav Karani, Christian F. Baumgartner, Olivio Donati, Anton S. Becker, Ender Konukoglu:
Semi-Supervised and Task-Driven Data Augmentation. CoRR abs/1902.05396 (2019) - [i12]Christian F. Baumgartner, Kerem Can Tezcan, Krishna Chaitanya, Andreas M. Hötker, Urs J. Muehlematter, Khoschy Schawkat, Anton S. Becker, Olivio Donati, Ender Konukoglu:
PHiSeg: Capturing Uncertainty in Medical Image Segmentation. CoRR abs/1906.04045 (2019) - [i11]Robin Brügger, Christian F. Baumgartner, Ender Konukoglu:
A Partially Reversible U-Net for Memory-Efficient Volumetric Image Segmentation. CoRR abs/1906.06148 (2019) - 2018
- [i10]Matthew Sinclair, Christian F. Baumgartner, Jacqueline Matthew, Wenjia Bai, Juan Cerrolaza Martinez, Yuanwei Li, Sandra Smith, Caroline L. Knight, Bernhard Kainz, Joseph V. Hajnal, Andrew P. King, Daniel Rueckert:
Human-level Performance On Automatic Head Biometrics In Fetal Ultrasound Using Fully Convolutional Neural Networks. CoRR abs/1804.09102 (2018) - [i9]Neerav Karani, Krishna Chaitanya, Christian F. Baumgartner, Ender Konukoglu:
A Lifelong Learning Approach to Brain MR Segmentation Across Scanners and Protocols. CoRR abs/1805.10170 (2018) - [i8]Yigit Baran Can, Krishna Chaitanya, Basil Mustafa, Lisa M. Koch, Ender Konukoglu, Christian F. Baumgartner:
Learning to Segment Medical Images with Scribble-Supervision Alone. CoRR abs/1807.04668 (2018) - [i7]Jana Kemnitz, Christian F. Baumgartner, Wolfgang Wirth, Felix Eckstein, Sebastian K. Eder, Ender Konukoglu:
Combining Heterogeneously Labeled Datasets For Training Segmentation Networks. CoRR abs/1807.08935 (2018) - 2017
- [i6]Christian F. Baumgartner, Lisa M. Koch, Marc Pollefeys, Ender Konukoglu:
An Exploration of 2D and 3D Deep Learning Techniques for Cardiac MR Image Segmentation. CoRR abs/1709.04496 (2017) - [i5]Christian F. Baumgartner, Lisa M. Koch, Kerem Can Tezcan, Jia Xi Ang, Ender Konukoglu:
Visual Feature Attribution using Wasserstein GANs. CoRR abs/1711.08998 (2017) - [i4]Kerem Can Tezcan, Christian F. Baumgartner, Ender Konukoglu:
MR image reconstruction using the learned data distribution as prior. CoRR abs/1711.11386 (2017) - 2016
- [i3]Lisa M. Koch, Martin Rajchl, Wenjia Bai, Christian F. Baumgartner, Tong Tong, Jonathan Passerat-Palmbach, Paul Aljabar, Daniel Rueckert:
Multi-Atlas Segmentation using Partially Annotated Data: Methods and Annotation Strategies. CoRR abs/1605.00029 (2016) - [i2]Christian F. Baumgartner, Konstantinos Kamnitsas, Jacqueline Matthew, Tara P. Fletcher, Sandra Smith, Lisa M. Koch, Bernhard Kainz, Daniel Rueckert:
Real-Time Detection and Localisation of Fetal Standard Scan Planes in 2D Freehand Ultrasound. CoRR abs/1612.05601 (2016) - [i1]Konstantinos Kamnitsas, Christian F. Baumgartner, Christian Ledig, Virginia F. J. Newcombe, Joanna P. Simpson, Andrew D. Kane, David K. Menon, Aditya V. Nori, Antonio Criminisi, Daniel Rueckert, Ben Glocker:
Unsupervised domain adaptation in brain lesion segmentation with adversarial networks. CoRR abs/1612.08894 (2016)
Coauthor Index
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