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Gautam C, Mishra PK, Tiwari A, Richhariya B, Pandey HM, Wang S, Tanveer M. Minimum variance-embedded deep kernel regularized least squares method for one-class classification and its applications to biomedical data. Neural Netw 2020; 123:191-216. [DOI: 10.1016/j.neunet.2019.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 11/20/2019] [Accepted: 12/01/2019] [Indexed: 10/25/2022]
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Nguyen D, Uhlmann V, Planchette AL, Marchand PJ, Van De Ville D, Lasser T, Radenovic A. Supervised learning to quantify amyloidosis in whole brains of an Alzheimer's disease mouse model acquired with optical projection tomography. BIOMEDICAL OPTICS EXPRESS 2019; 10:3041-3060. [PMID: 31259073 PMCID: PMC6583328 DOI: 10.1364/boe.10.003041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/19/2019] [Accepted: 05/19/2019] [Indexed: 05/14/2023]
Abstract
Alzheimer's disease (AD) is characterized by amyloidosis of brain tissues. This phenomenon is studied with genetically-modified mouse models. We propose a method to quantify amyloidosis in whole 5xFAD mouse brains, a model of AD. We use optical projection tomography (OPT) and a random forest voxel classifier to segment and measure amyloid plaques. We validate our method in a preliminary cross-sectional study, where we measure 6136 ± 1637, 8477 ± 3438, and 17267 ± 4241 plaques (AVG ± SD) at 11, 17, and 31 weeks. Overall, this method can be used in the evaluation of new treatments against AD.
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Affiliation(s)
- David Nguyen
- Laboratory of Nanoscale Biology, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
- Medical Image Processing Lab, École Polytechnique Fédérale de Lausanne, Genève, Genève,
Switzerland
- Laboratoire d’Optique Biomédicale, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
| | - Virginie Uhlmann
- Biomedical Imaging Group, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
- European Bioinformatics Institute, EMBL-EBI, Cambridge,
United Kingdom
| | - Arielle L. Planchette
- Laboratory of Nanoscale Biology, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
- Laboratoire d’Optique Biomédicale, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
| | - Paul J. Marchand
- Laboratoire d’Optique Biomédicale, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
| | - Dimitri Van De Ville
- Medical Image Processing Lab, École Polytechnique Fédérale de Lausanne, Genève, Genève,
Switzerland
- Department of Radiology and Medical Informatics, University of Geneva, Genève, Genève,
Switzerland
| | - Theo Lasser
- Laboratoire d’Optique Biomédicale, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
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Berthon B, Marshall C, Evans M, Spezi E. ATLAAS: an automatic decision tree-based learning algorithm for advanced image segmentation in positron emission tomography. Phys Med Biol 2016; 61:4855-69. [PMID: 27273293 DOI: 10.1088/0031-9155/61/13/4855] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Accurate and reliable tumour delineation on positron emission tomography (PET) is crucial for radiotherapy treatment planning. PET automatic segmentation (PET-AS) eliminates intra- and interobserver variability, but there is currently no consensus on the optimal method to use, as different algorithms appear to perform better for different types of tumours. This work aimed to develop a predictive segmentation model, trained to automatically select and apply the best PET-AS method, according to the tumour characteristics. ATLAAS, the automatic decision tree-based learning algorithm for advanced segmentation is based on supervised machine learning using decision trees. The model includes nine PET-AS methods and was trained on a 100 PET scans with known true contour. A decision tree was built for each PET-AS algorithm to predict its accuracy, quantified using the Dice similarity coefficient (DSC), according to the tumour volume, tumour peak to background SUV ratio and a regional texture metric. The performance of ATLAAS was evaluated for 85 PET scans obtained from fillable and printed subresolution sandwich phantoms. ATLAAS showed excellent accuracy across a wide range of phantom data and predicted the best or near-best segmentation algorithm in 93% of cases. ATLAAS outperformed all single PET-AS methods on fillable phantom data with a DSC of 0.881, while the DSC for H&N phantom data was 0.819. DSCs higher than 0.650 were achieved in all cases. ATLAAS is an advanced automatic image segmentation algorithm based on decision tree predictive modelling, which can be trained on images with known true contour, to predict the best PET-AS method when the true contour is unknown. ATLAAS provides robust and accurate image segmentation with potential applications to radiation oncology.
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Affiliation(s)
- Beatrice Berthon
- Wales Research & Diagnostic PET Imaging Centre, Cardiff University, CF14 4XN, Cardiff, UK
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Santin MD, Vandenberghe ME, Herard AS, Pradier L, Cohen C, Debeir T, Delzescaux T, Rooney T, Dhenain M. In Vivo Detection of Amyloid Plaques by Gadolinium-Stained MRI Can Be Used to Demonstrate the Efficacy of an Anti-amyloid Immunotherapy. Front Aging Neurosci 2016; 8:55. [PMID: 27047372 PMCID: PMC4802995 DOI: 10.3389/fnagi.2016.00055] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/08/2016] [Indexed: 01/05/2023] Open
Abstract
Extracellular deposition of β amyloid plaques is an early event associated to Alzheimer’s disease. Here, we have used in vivo gadolinium-stained high resolution (29∗29∗117 μm3) magnetic resonance imaging (MRI) to follow-up in a longitudinal way individual amyloid plaques in APP/PS1 mice and evaluate the efficacy of a new immunotherapy (SAR255952) directed against protofibrillar and fibrillary forms of Aβ. APP/PS1 mice were treated for 5 months between the age of 3.5 and 8.5 months. SAR255952 reduced amyloid load in 8.5-months-old animals, but not in 5.5-months animals compared to mice treated with a control antibody (DM4). Histological evaluation confirmed the reduction of amyloid load and revealed a lower density of amyloid plaques in 8.5-months SAR255952-treated animals. The longitudinal follow-up of individual amyloid plaques by MRI revealed that plaques that were visible at 5.5 months were still visible at 8.5 months in both SAR255952 and DM4-treated mice. This suggests that the amyloid load reduction induced by SAR255952 is related to a slowing down in the formation of new plaques rather than to the clearance of already formed plaques.
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Affiliation(s)
- Mathieu D Santin
- Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, UMR 9199, Neurodegenerative Diseases LaboratoryFontenay-aux-Roses, France; Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction de la Recherche Fondamentale, Institut d'Imagerie Biomédicale, MIRCenFontenay-aux-Roses, France
| | - Michel E Vandenberghe
- Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, UMR 9199, Neurodegenerative Diseases LaboratoryFontenay-aux-Roses, France; Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction de la Recherche Fondamentale, Institut d'Imagerie Biomédicale, MIRCenFontenay-aux-Roses, France
| | - Anne-Sophie Herard
- Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, UMR 9199, Neurodegenerative Diseases LaboratoryFontenay-aux-Roses, France; Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction de la Recherche Fondamentale, Institut d'Imagerie Biomédicale, MIRCenFontenay-aux-Roses, France
| | - Laurent Pradier
- Sanofi, Neurodegeneration and Pain Unit Chilly-Mazarin, France
| | - Caroline Cohen
- Sanofi, Neurodegeneration and Pain Unit Chilly-Mazarin, France
| | | | - Thierry Delzescaux
- Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, UMR 9199, Neurodegenerative Diseases LaboratoryFontenay-aux-Roses, France; Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction de la Recherche Fondamentale, Institut d'Imagerie Biomédicale, MIRCenFontenay-aux-Roses, France
| | - Thomas Rooney
- Sanofi, Neurodegeneration and Pain Unit Chilly-Mazarin, France
| | - Marc Dhenain
- Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, UMR 9199, Neurodegenerative Diseases LaboratoryFontenay-aux-Roses, France; Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction de la Recherche Fondamentale, Institut d'Imagerie Biomédicale, MIRCenFontenay-aux-Roses, France
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Lin L, Fu Z, Xu X, Wu S. Mouse brain magnetic resonance microscopy: Applications in Alzheimer disease. Microsc Res Tech 2015; 78:416-24. [PMID: 25810274 DOI: 10.1002/jemt.22489] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/23/2015] [Indexed: 01/26/2023]
Abstract
Over the past two decades, various Alzheimer's disease (AD) trangenetic mice models harboring genes with mutation known to cause familial AD have been created. Today, high-resolution magnetic resonance microscopy (MRM) technology is being widely used in the study of AD mouse models. It has greatly facilitated and advanced our knowledge of AD. In this review, most of the attention is paid to fundamental of MRM, the construction of standard mouse MRM brain template and atlas, the detection of amyloid plaques, following up on brain atrophy and the future applications of MRM in transgenic AD mice. It is believed that future testing of potential drugs in mouse models with MRM will greatly improve the predictability of drug effect in preclinical trials.
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Affiliation(s)
- Lan Lin
- Biomedical Engineering Department, College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
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