International challenges have become the standard for validation of biomedical image analysis methods. Given their scientific impact, it is surprising that a critical analysis of common practices related to the organization of challenges has not yet been performed. In this paper, we present a comprehensive analysis of biomedical image analysis challenges conducted up to now. We demonstrate the importance of challenges and show that the lack of quality control has critical consequences. First, reproducibility and interpretation of the results is often hampered as only a fraction of relevant information is typically provided. Second, the rank of an algorithm is generally not robust to a number of variables such as the test data used for validation, the ranking scheme applied and the observers that make the reference annotations. To overcome these problems, we recommend best practice guidelines and define open research questions to be addressed in the future.

https://hal.archives-ouvertes.fr/hal-01958848/document

Why rankings of biomedical image analysis competitions should be interpreted with care

Deep learning has become the most widely used approach for cardiac image segmentation in recent years. In this paper, we provide a review of over 100 cardiac image segmentation papers using deep learning, which covers common imaging modalities including magnetic resonance imaging (MRI), computed tomography (CT), and ultrasound and major anatomical structures of interest (ventricles, atria, and vessels). In addition, a summary of publicly available cardiac image datasets and code repositories are included to provide a base for encouraging reproducible research. Finally, we discuss the challenges and limitations with current deep learning-based approaches (scarcity of labels, model generalizability across different domains, interpretability) and suggest potential directions for future research.

/pdf/deep-learning-for-cardiac-image-segmentation-a-review-1xcz2e1pso.pdf

Deep Learning for Cardiac Image Segmentation: A Review.

Atrial fibrillation (AF)-the most common arrhythmia-significantly increases the risk of stroke and heart failure. Although catheter ablation can restore normal heart rhythms, patients with persistent AF who develop atrial fibrosis often undergo multiple failed ablations, and thus increased procedural risks. Here, we present personalized computational modelling for the reliable predetermination of ablation targets, which are then used to guide the ablation procedure in patients with persistent AF and atrial fibrosis. First, we show that a computational model of the atria of patients identifies fibrotic tissue that, if ablated, will not sustain AF. Then, we report the results of integrating the target ablation sites in a clinical mapping system and testing its feasibility in ten patients with persistent AF. The computational prediction of ablation targets avoids lengthy electrical mapping and could improve the accuracy and efficacy of targeted AF ablation in patients while eliminating the need for repeat procedures.

Computationally guided personalized targeted ablation of persistent atrial fibrillation.

Non-invasive imaging plays a critical role in managing patients with cardiovascular disease. Although subjective visual interpretation remains the clinical mainstay, quantitative analysis facilitates objective, evidence-based management, and advances in clinical research. This has driven developments in computing and software tools aimed at achieving fully automated image processing and quantitative analysis. In parallel, machine learning techniques have been used to rapidly integrate large amounts of clinical and quantitative imaging data to provide highly personalized individual patient-based conclusions. Areas covered: This review summarizes recent advances in automated quantitative imaging in cardiology and describes the latest techniques which incorporate machine learning principles. The review focuses on the cardiac imaging techniques which are in wide clinical use. It also discusses key issues and obstacles for these tools to become utilized in mainstream clinical practice. Expert commentary: Fully-automated processing and high-level computer interpretation of cardiac imaging are becoming a reality. Application of machine learning to the vast amounts of quantitative data generated per scan and integration with clinical data also facilitates a move to more patient-specific interpretation. These developments are unlikely to replace interpreting physicians but will provide them with highly accurate tools to detect disease, risk-stratify, and optimize patient-specific treatment. However, with each technological advance, we move further from human dependence and closer to fully-automated machine interpretation.

/pdf/cardiac-imaging-working-towards-fully-automated-machine-2avtnrzu9x.pdf

Cardiac imaging: working towards fully-automated machine analysis & interpretation.

The aim of this paper is to investigate the use of fully convolutional neural networks (FCNNs) to segment scar tissue in the left ventricle from cardiac magnetic resonance with late gadolinium enhancement (CMR-LGE) images. A successful FCNN in the literature (the ENet) was modified and trained to provide scar-tissue segmentation. Two segmentation protocols (Protocol 1 and Protocol 2) were investigated, the latter limiting the scar-segmentation search area to the left ventricular myocardial tissue region. CMR-LGE from 30 patients with ischemic-heart disease were retrospectively analyzed, for a total of 250 images, presenting high variability in terms of scar dimension and location. Segmentation results were assessed against manual scar-tissue tracing using one-patient-out cross validation. Protocol 2 outperformed Protocol 1 significantly (p value < 0.05), with median sensitivity and Dice similarity coefficient equal to 88.07% [inter-quartile range (IQR) 18.84%] and 71.25% (IQR 31.82%), respectively. Both segmentation protocols were able to detect scar tissues in the CMR-LGE images but higher performance was achieved when limiting the search area to the myocardial region. The findings of this paper represent an encouraging starting point for the use of FCNNs for the segmentation of nonviable scar tissue from CMR-LGE images.

/pdf/development-and-testing-of-a-deep-learning-based-strategy-ryram03z0a.pdf

Development and testing of a deep learning-based strategy for scar segmentation on CMR-LGE images

https://spiral.imperial.ac.uk/bitstream/10044/1/30737/7/1-s2.0-S1361841516000050-main.pdf

Evaluation of state-of-the-art segmentation algorithms for left ventricle infarct from late Gadolinium enhancement MR images

We have developed a system for computer-assisted surgical planning of tracheal surgeries. The system allows to plan the intervention based on CT images of the patient, and includes a virtual database of commercially available prostheses. Automatic segmentation of the trachea and apparent pathological structures is obtained using a modified region growing algorithm. A method for automatic adaptation of a finite element mesh allows to build a patient-specific biomechanical model for simulation of the expected performance of the implant under physiological movement (swallowing, sneezing). Laboratory experiments were performed to characterise the tissues present in the trachea, and movement models were obtained from fluoroscopic images of a patient. Results are reported on the planning and biomechanical simulation of two patients that underwent surgery at our hospital.

/pdf/surgical-planning-and-patient-specific-biomechanical-b5bey58rvq.pdf

Laura Lara Rodríguez

Papers

Evaluation of state-of-the-art segmentation algorithms for left ventricle infarct from late Gadolinium enhancement MR images

Surgical Planning and Patient-Specific Biomechanical Simulation for Tracheal Endoprostheses Interventions