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Toader B, Boulanger J, Korolev Y, Lenz MO, Manton J, Schönlieb CB, Mureşan L. Image Reconstruction in Light-Sheet Microscopy: Spatially Varying Deconvolution and Mixed Noise. J Math Imaging Vis 2022; 64:968-992. [PMID: 36329880 PMCID: PMC7613773 DOI: 10.1007/s10851-022-01100-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 04/23/2022] [Indexed: 06/16/2023]
Abstract
We study the problem of deconvolution for light-sheet microscopy, where the data is corrupted by spatially varying blur and a combination of Poisson and Gaussian noise. The spatial variation of the point spread function of a light-sheet microscope is determined by the interaction between the excitation sheet and the detection objective PSF. We introduce a model of the image formation process that incorporates this interaction and we formulate a variational model that accounts for the combination of Poisson and Gaussian noise through a data fidelity term consisting of the infimal convolution of the single noise fidelities, first introduced in L. Calatroni et al. (SIAM J Imaging Sci 10(3):1196-1233, 2017). We establish convergence rates and a discrepancy principle for the infimal convolution fidelity and the inverse problem is solved by applying the primal-dual hybrid gradient (PDHG) algorithm in a novel way. Numerical experiments performed on simulated and real data show superior reconstruction results in comparison with other methods.
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Affiliation(s)
- Bogdan Toader
- Cambridge Advanced Imaging Centre, University of Cambridge, Anatomy School, Downing Street, Cambridge, CB2 3DY UK
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge, CB3 0WA UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY UK
| | - Jérôme Boulanger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH UK
| | - Yury Korolev
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge, CB3 0WA UK
| | - Martin O. Lenz
- Cambridge Advanced Imaging Centre, University of Cambridge, Anatomy School, Downing Street, Cambridge, CB2 3DY UK
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR UK
| | - James Manton
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH UK
| | - Carola-Bibiane Schönlieb
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge, CB3 0WA UK
| | - Leila Mureşan
- Cambridge Advanced Imaging Centre, University of Cambridge, Anatomy School, Downing Street, Cambridge, CB2 3DY UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY UK
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR UK
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Rossignoli G, Krämer K, Lugarà E, Alrashidi H, Pope S, De La Fuente Barrigon C, Barwick K, Bisello G, Ng J, Counsell J, Lignani G, Heales SJR, Bertoldi M, Barral S, Kurian MA. Aromatic l-amino acid decarboxylase deficiency: a patient-derived neuronal model for precision therapies. Brain 2021; 144:2443-2456. [PMID: 33734312 PMCID: PMC8418346 DOI: 10.1093/brain/awab123] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 01/25/2021] [Accepted: 02/08/2021] [Indexed: 11/13/2022] Open
Abstract
Aromatic l-amino acid decarboxylase (AADC) deficiency is a complex inherited neurological disorder of monoamine synthesis which results in dopamine and serotonin deficiency. The majority of affected individuals have variable, though often severe cognitive and motor delay, with a complex movement disorder and high risk of premature mortality. For most, standard pharmacological treatment provides only limited clinical benefit. Promising gene therapy approaches are emerging, though may not be either suitable or easily accessible for all patients. To characterize the underlying disease pathophysiology and guide precision therapies, we generated a patient-derived midbrain dopaminergic neuronal model of AADC deficiency from induced pluripotent stem cells. The neuronal model recapitulates key disease features, including absent AADC enzyme activity and dysregulated dopamine metabolism. We observed developmental defects affecting synaptic maturation and neuronal electrical properties, which were improved by lentiviral gene therapy. Bioinformatic and biochemical analyses on recombinant AADC predicted that the activity of one variant could be improved by l-3,4-dihydroxyphenylalanine (l-DOPA) administration; this hypothesis was corroborated in the patient-derived neuronal model, where l-DOPA treatment leads to amelioration of dopamine metabolites. Our study has shown that patient-derived disease modelling provides further insight into the neurodevelopmental sequelae of AADC deficiency, as well as a robust platform to investigate and develop personalized therapeutic approaches.
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Affiliation(s)
- Giada Rossignoli
- Developmental Neurosciences, GOS Institute of Child Health, University College London, London WC1N 1EH, UK
- Biological Chemistry, NBM Department, University of Verona, 37134 Verona, Italy
| | - Karolin Krämer
- Developmental Neurosciences, GOS Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Eleonora Lugarà
- Clinical and Experimental Epilepsy, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Haya Alrashidi
- Genetics and Genomic Medicine, GOS Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Simon Pope
- Neurometabolic Unit, National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
| | | | - Katy Barwick
- Developmental Neurosciences, GOS Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Giovanni Bisello
- Biological Chemistry, NBM Department, University of Verona, 37134 Verona, Italy
| | - Joanne Ng
- Developmental Neurosciences, GOS Institute of Child Health, University College London, London WC1N 1EH, UK
- Gene Transfer Technology Group, EGA-Institute for Women's Health, University College London, London WC1E 6HU, UK
| | - John Counsell
- Developmental Neurosciences, GOS Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Gabriele Lignani
- Clinical and Experimental Epilepsy, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Simon J R Heales
- Neurometabolic Unit, National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
- Centre for Inborn Errors of Metabolism, GOS Institute of Child Health, UniversCity College London, London WC1N 1EH, UK
| | - Mariarita Bertoldi
- Biological Chemistry, NBM Department, University of Verona, 37134 Verona, Italy
- Correspondence may also be addressed to: Prof Mariarita Bertoldi Department of Neuroscience, Biomedicine and Movement Sciences Biological Chemistry Section, Room 1.24 Strada le Grazie 8, 37134 Verona, Italy E-mail:
| | - Serena Barral
- Developmental Neurosciences, GOS Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Manju A Kurian
- Developmental Neurosciences, GOS Institute of Child Health, University College London, London WC1N 1EH, UK
- Department of Neurology, Great Ormond Street Hospital, London WC1N 3JH, UK
- Correspondence to: Prof Manju Kurian Zayed Centre for Research UCL Great Ormond Street Institute of Child Health 20 Guilford St, London WC1N 1DZ, UK E-mail:
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Le EPV, Rundo L, Tarkin JM, Evans NR, Chowdhury MM, Coughlin PA, Pavey H, Wall C, Zaccagna F, Gallagher FA, Huang Y, Sriranjan R, Le A, Weir-McCall JR, Roberts M, Gilbert FJ, Warburton EA, Schönlieb CB, Sala E, Rudd JHF. Assessing robustness of carotid artery CT angiography radiomics in the identification of culprit lesions in cerebrovascular events. Sci Rep 2021; 11:3499. [PMID: 33568735 PMCID: PMC7876096 DOI: 10.1038/s41598-021-82760-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/21/2021] [Indexed: 02/02/2023] Open
Abstract
Radiomics, quantitative feature extraction from radiological images, can improve disease diagnosis and prognostication. However, radiomic features are susceptible to image acquisition and segmentation variability. Ideally, only features robust to these variations would be incorporated into predictive models, for good generalisability. We extracted 93 radiomic features from carotid artery computed tomography angiograms of 41 patients with cerebrovascular events. We tested feature robustness to region-of-interest perturbations, image pre-processing settings and quantisation methods using both single- and multi-slice approaches. We assessed the ability of the most robust features to identify culprit and non-culprit arteries using several machine learning algorithms and report the average area under the curve (AUC) from five-fold cross validation. Multi-slice features were superior to single for producing robust radiomic features (67 vs. 61). The optimal image quantisation method used bin widths of 25 or 30. Incorporating our top 10 non-redundant robust radiomics features into ElasticNet achieved an AUC of 0.73 and accuracy of 69% (compared to carotid calcification alone [AUC: 0.44, accuracy: 46%]). Our results provide key information for introducing carotid CT radiomics into clinical practice. If validated prospectively, our robust carotid radiomic set could improve stroke prediction and target therapies to those at highest risk.
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Affiliation(s)
| | - Leonardo Rundo
- Department of Radiology, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
| | - Jason M Tarkin
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nicholas R Evans
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Mohammed M Chowdhury
- Division of Vascular Surgery, Department of Surgery, University of Cambridge, Cambridge, UK
| | - Patrick A Coughlin
- Division of Vascular Surgery, Department of Surgery, University of Cambridge, Cambridge, UK
| | - Holly Pavey
- Division of Experimental Medicine and Immunotherapeutics, University of Cambridge, Cambridge, UK
| | - Chris Wall
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Fulvio Zaccagna
- Department of Radiology, University of Cambridge, Cambridge, UK
- Department of Medical Imaging, University of Toronto, Toronto, ON, Canada
| | | | - Yuan Huang
- Department of Radiology, University of Cambridge, Cambridge, UK
- EPSRC Centre for Mathematical Imaging in Healthcare, University of Cambridge, Cambridge, UK
| | | | - Anthony Le
- School of Medicine, University of Leeds, Leeds, UK
| | | | - Michael Roberts
- EPSRC Centre for Mathematical Imaging in Healthcare, University of Cambridge, Cambridge, UK
- Oncology R&D, AstraZeneca, Cambridge, UK
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
| | - Fiona J Gilbert
- Department of Radiology, University of Cambridge, Cambridge, UK
| | | | - Carola-Bibiane Schönlieb
- EPSRC Centre for Mathematical Imaging in Healthcare, University of Cambridge, Cambridge, UK
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
| | - Evis Sala
- Department of Radiology, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
| | - James H F Rudd
- Department of Medicine, University of Cambridge, Cambridge, UK.
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