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Mass Spectrometry Imaging and Integration with Other Imaging Modalities for Greater Molecular Understanding of Biological Tissues
Over the last two decades, mass spectrometry imaging (MSI) has been increasingly employed to investigate the spatial distribution of a wide variety of molecules in complex biological samples. MSI has demonstrated its potential in numerous applications from drug discovery, disease state evaluation through proteomic and/or metabolomic studies. Significant technological and methodological advancements have addressed natural limitations of the techniques, i.e., increased spatial resolution, increased detection sensitivity especially for large molecules, higher throughput analysis and data management. One of the next major evolutions of MSI is linked to the introduction of imaging mass cytometry (IMC). IMC is a multiplexed method for tissue phenotyping, imaging signalling pathway or cell marker assessment, at sub-cellular resolution (1 μm). It uses MSI to simultaneously detect and quantify up to 30 different antibodies within a tissue section. The combination of MSI with other molecular imaging techniques can also provide highly relevant complementary information to explore new scientific fields. Traditionally, classical histology (especially haematoxylin and eosin–stained sections) is overlaid with molecular profiles obtained by MSI. Thus, MSI-based molecular histology provides a snapshot of a tissue microenvironment and enables the correlation of drugs, metabolites, lipids, peptides or proteins with histological/pathological features or tissue substructures. Recently, many examples combining MSI with other imaging modalities such as fluorescence, confocal Raman spectroscopy and MRI have emerged. For instance, brain pathophysiology has been studied using both MRI and MSI, establishing correlations between in and ex vivo molecular imaging techniques. Endogenous metabolite and small peptide modulation were evaluated depending on disease state. Here, we review advanced ‘hot topics’ in MSI development and explore the combination of MSI with established molecular imaging techniques to improve our understanding of biological and pathophysiological processes.
Journal Article
A multi-model deep convolutional neural network for automatic hippocampus segmentation and classification in Alzheimer’s disease
Alzheimer’s disease (AD) is a progressive and irreversible brain degenerative disorder. Mild cognitive impairment (MCI) is a clinical precursor of AD. Although some treatments can delay its progression, no effective cures are available for AD. Accurate early-stage diagnosis of AD is vital for the prevention and intervention of the disease progression. Hippocampus is one of the first affected brain regions in AD. To help AD diagnosis, the shape and volume of the hippocampus are often measured using structural magnetic resonance imaging (MRI). However, these features encode limited information and may suffer from segmentation errors. Additionally, the extraction of these features is independent of the classification model, which could result in sub-optimal performance. In this study, we propose a multi-model deep learning framework based on convolutional neural network (CNN) for joint automatic hippocampal segmentation and AD classification using structural MRI data. Firstly, a multi-task deep CNN model is constructed for jointly learning hippocampal segmentation and disease classification. Then, we construct a 3D Densely Connected Convolutional Networks (3D DenseNet) to learn features of the 3D patches extracted based on the hippocampal segmentation results for the classification task. Finally, the learned features from the multi-task CNN and DenseNet models are combined to classify disease status. Our method is evaluated on the baseline T1-weighted structural MRI data collected from 97 AD, 233 MCI, 119 Normal Control (NC) subjects in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database. The proposed method achieves a dice similarity coefficient of 87.0% for hippocampal segmentation. In addition, the proposed method achieves an accuracy of 88.9% and an AUC (area under the ROC curve) of 92.5% for classifying AD vs. NC subjects, and an accuracy of 76.2% and an AUC of 77.5% for classifying MCI vs. NC subjects. Our empirical study also demonstrates that the proposed multi-model method outperforms the single-model methods and several other competing methods.
Journal Article
Deep learning in biomedical and health informatics : current applications and possibilities
\"This book provides a proficient guide on the relationship between AI and healthcare and how AI is changing all aspects of the health care industry. It also covers how deep learning will help in diagnosis and prediction of disease spread\"-- Provided by publisher.
Book
European society of urogenital radiology (ESUR) guidelines: MR imaging of pelvic endometriosis
Endometriosis is a common gynaecological condition of unknown aetiology that primarily affects women of reproductive age. The accepted first-line imaging modality is pelvic ultrasound. However, magnetic resonance imaging (MRI) is increasingly performed as an additional investigation in complex cases and for surgical planning. There is currently no international consensus regarding patient preparation, MRI protocols or reporting criteria. Our aim was to develop clinical guidelines for MRI evaluation of pelvic endometriosis based on literature evidence and consensus expert opinion. This work was performed by a group of radiologists from the European Society of Urogenital Radiology (ESUR), experts in gynaecological imaging and a gynaecologist expert in methodology. The group discussed indications for MRI, technical requirements, patient preparation, MRI protocols and criteria for the diagnosis of pelvic endometriosis on MRI. The expert panel proposed a final recommendation for each criterion using Oxford Centre for Evidence Based Medicine (OCEBM) 2011 levels of evidence.
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This report provides guidelines for MRI in endometriosis
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Minimal and optimal MRI acquisition protocols are provided
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Recommendations are proposed for patient preparation
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best MRI sequences and reporting criteria
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Journal Article
Image processing and Quality Control for the first 10,000 brain imaging datasets from UK Biobank
UK Biobank is a large-scale prospective epidemiological study with all data accessible to researchers worldwide. It is currently in the process of bringing back 100,000 of the original participants for brain, heart and body MRI, carotid ultrasound and low-dose bone/fat x-ray. The brain imaging component covers 6 modalities (T1, T2 FLAIR, susceptibility weighted MRI, Resting fMRI, Task fMRI and Diffusion MRI). Raw and processed data from the first 10,000 imaged subjects has recently been released for general research access. To help convert this data into useful summary information we have developed an automated processing and QC (Quality Control) pipeline that is available for use by other researchers. In this paper we describe the pipeline in detail, following a brief overview of UK Biobank brain imaging and the acquisition protocol. We also describe several quantitative investigations carried out as part of the development of both the imaging protocol and the processing pipeline.
Journal Article
Integrated approach of federated learning with transfer learning for classification and diagnosis of brain tumor
Brain tumor classification using MRI images is a crucial yet challenging task in medical imaging. Accurate diagnosis is vital for effective treatment planning but is often hindered by the complex nature of tumor morphology and variations in imaging. Traditional methodologies primarily rely on manual interpretation of MRI images, supplemented by conventional machine learning techniques. These approaches often lack the robustness and scalability needed for precise and automated tumor classification. The major limitations include a high degree of manual intervention, potential for human error, limited ability to handle large datasets, and lack of generalizability to diverse tumor types and imaging conditions.To address these challenges, we propose a federated learning-based deep learning model that leverages the power of Convolutional Neural Networks (CNN) for automated and accurate brain tumor classification. This innovative approach not only emphasizes the use of a modified VGG16 architecture optimized for brain MRI images but also highlights the significance of federated learning and transfer learning in the medical imaging domain. Federated learning enables decentralized model training across multiple clients without compromising data privacy, addressing the critical need for confidentiality in medical data handling. This model architecture benefits from the transfer learning technique by utilizing a pre-trained CNN, which significantly enhances its ability to classify brain tumors accurately by leveraging knowledge gained from vast and diverse datasets.Our model is trained on a diverse dataset combining figshare, SARTAJ, and Br35H datasets, employing a federated learning approach for decentralized, privacy-preserving model training. The adoption of transfer learning further bolsters the model’s performance, making it adept at handling the intricate variations in MRI images associated with different types of brain tumors. The model demonstrates high precision (0.99 for glioma, 0.95 for meningioma, 1.00 for no tumor, and 0.98 for pituitary), recall, and F1-scores in classification, outperforming existing methods. The overall accuracy stands at 98%, showcasing the model’s efficacy in classifying various tumor types accurately, thus highlighting the transformative potential of federated learning and transfer learning in enhancing brain tumor classification using MRI images.
Journal Article