Feature Tracking Cardiac Magnetic Resonance via Deep Learning and Spline Optimization

Feature tracking Cardiac Magnetic Resonance (CMR) has recently emerged as an area of interest for quantification of regional cardiac function from balanced, steady state free precession (SSFP) cine sequences. However, currently available techniques lack full automation, limiting reproducibility. We propose a fully automated technique whereby a CMR image sequence is first segmented with a deep, fully convolutional neural network (CNN) architecture, and quadratic basis splines are fitted simultaneously across all cardiac frames using least squares optimization. Experiments are performed using data from 42 patients with hypertrophic cardiomyopathy (HCM) and 21 healthy control subjects. In terms of segmentation, we compared state-of-the-art CNN frameworks, U-Net and dilated convolution architectures, with and without temporal context, using cross validation with three folds. Performance relative to expert manual segmentation was similar across all networks: pixel accuracy was ~97%, intersection-over-union (IoU) across all classes was ~87%, and IoU across foreground classes only was ~85%. Endocardial left ventricular circumferential strain calculated from the proposed pipeline was significantly different in control and disease subjects (-25.3% vs -29.1%, p = 0.006), in agreement with the current clinical literature.Comment: Accepted to Functional Imaging and Modeling of the Heart (FIMH) 201

UPI-Net: Semantic Contour Detection in Placental Ultrasound

Semantic contour detection is a challenging problem that is often met in medical imaging, of which placental image analysis is a particular example. In this paper, we investigate utero-placental interface (UPI) detection in 2D placental ultrasound images by formulating it as a semantic contour detection problem. As opposed to natural images, placental ultrasound images contain specific anatomical structures thus have unique geometry. We argue it would be beneficial for UPI detectors to incorporate global context modelling in order to reduce unwanted false positive UPI predictions. Our approach, namely UPI-Net, aims to capture long-range dependencies in placenta geometry through lightweight global context modelling and effective multi-scale feature aggregation. We perform a subject-level 10-fold nested cross-validation on a placental ultrasound database (4,871 images with labelled UPI from 49 scans). Experimental results demonstrate that, without introducing considerable computational overhead, UPI-Net yields the highest performance in terms of standard contour detection metrics, compared to other competitive benchmarks.Comment: 9 pages, 8 figures, accepted at Visual Recognition for Medical Images (VRMI), ICCV 201

Unpaired mesh-to-image translation for 3D fluorescent microscopy images of neurons

While Generative Adversarial Networks (GANs) can now reliably produce realistic images in a multitude of imaging domains, they are ill-equipped to model thin, stochastic textures present in many large 3D fluorescent microscopy (FM) images acquired in biological research. This is especially problematic in neuroscience where the lack of ground truth data impedes the development of automated image analysis algorithms for neurons and neural populations. We therefore propose an unpaired mesh-to-image translation methodology for generating volumetric FM images of neurons from paired ground truths. We start by learning unique FM styles efficiently through a Gramian-based discriminator. Then, we stylize 3D voxelized meshes of previously reconstructed neurons by successively generating slices. As a result, we effectively create a synthetic microscope and can acquire realistic FM images of neurons with control over the image content and imaging configurations. We demonstrate the feasibility of our architecture and its superior performance compared to state-of-the-art image translation architectures through a variety of texture-based metrics, unsupervised segmentation accuracy, and an expert opinion test. In this study, we use 2 synthetic FM datasets and 2 newly acquired FM datasets of retinal neurons

Rethinking Semi-Supervised Federated Learning: How to co-train fully-labeled and fully-unlabeled client imaging data

The most challenging, yet practical, setting of semi-supervised federated learning (SSFL) is where a few clients have fully labeled data whereas the other clients have fully unlabeled data. This is particularly common in healthcare settings where collaborating partners (typically hospitals) may have images but not annotations. The bottleneck in this setting is the joint training of labeled and unlabeled clients as the objective function for each client varies based on the availability of labels. This paper investigates an alternative way for effective training with labeled and unlabeled clients in a federated setting. We propose a novel learning scheme specifically designed for SSFL which we call Isolated Federated Learning (IsoFed) that circumvents the problem by avoiding simple averaging of supervised and semi-supervised models together. In particular, our training approach consists of two parts - (a) isolated aggregation of labeled and unlabeled client models, and (b) local self-supervised pretraining of isolated global models in all clients. We evaluate our model performance on medical image datasets of four different modalities publicly available within the biomedical image classification benchmark MedMNIST. We further vary the proportion of labeled clients and the degree of heterogeneity to demonstrate the effectiveness of the proposed method under varied experimental settings.Comment: Published in MICCAI 2023 with early acceptance and selected as 1 of the top 20 poster highlights under the category: Which work has the potential to impact other applications of AI and C

Effects of Surface Morphology on the Anchoring and Electrooptical Dynamics of Confined Nanoscale Liquid Crystalline Films

The orientation and dynamics of two 40-nm thick films of 4-n-pentyl-4‘-cyanobiphenyl (5CB), a nematic liquid crystal, have been studied using step-scan Fourier transform infrared spectroscopy (FTIR). The films are confined in nanocavities bounded by an interdigitated electrode array (IDA) patterned on a zinc selenide (ZnSe) substrate. The effects of the ZnSe surface morphology (specifically, two variations of nanometer-scale corrugations obtained by mechanical polishing) on the initial ordering and reorientation dynamics of the electric-field-induced Freedericksz transition are presented here. The interaction of the 5CB with ZnSe surfaces bearing a spicular corrugation induces a homeotropic (surface normal) alignment of the film confined in the cavity. Alternately, when ZnSe is polished to generate fine grooves along the surface, a planar alignment is promoted in the liquid crystalline film. Time-resolved FTIR studies that enable the direct measurement of the rate constants for the electric-field-induced orientation and thermal relaxation reveal that the dynamic transitions of the two film structures are significantly different. These measurements quantitatively demonstrate the strong effects of surface morphology on the anchoring, order, and dynamics of liquid crystalline thin films

Explaining Explainability: Understanding Concept Activation Vectors

Recent interpretability methods propose using concept-based explanations to translate the internal representations of deep learning models into a language that humans are familiar with: concepts. This requires understanding which concepts are present in the representation space of a neural network. One popular method for finding concepts is Concept Activation Vectors (CAVs), which are learnt using a probe dataset of concept exemplars. In this work, we investigate three properties of CAVs. CAVs may be: (1) inconsistent between layers, (2) entangled with different concepts, and (3) spatially dependent. Each property provides both challenges and opportunities in interpreting models. We introduce tools designed to detect the presence of these properties, provide insight into how they affect the derived explanations, and provide recommendations to minimise their impact. Understanding these properties can be used to our advantage. For example, we introduce spatially dependent CAVs to test if a model is translation invariant with respect to a specific concept and class. Our experiments are performed on ImageNet and a new synthetic dataset, Elements. Elements is designed to capture a known ground truth relationship between concepts and classes. We release this dataset to facilitate further research in understanding and evaluating interpretability methods.Comment: (54 pages, 39 figures

Cross-Task Representation Learning for Anatomical Landmark Detection

Recently, there is an increasing demand for automatically detecting anatomical landmarks which provide rich structural information to facilitate subsequent medical image analysis. Current methods related to this task often leverage the power of deep neural networks, while a major challenge in fine tuning such models in medical applications arises from insufficient number of labeled samples. To address this, we propose to regularize the knowledge transfer across source and target tasks through cross-task representation learning. The proposed method is demonstrated for extracting facial anatomical landmarks which facilitate the diagnosis of fetal alcohol syndrome. The source and target tasks in this work are face recognition and landmark detection, respectively. The main idea of the proposed method is to retain the feature representations of the source model on the target task data, and to leverage them as an additional source of supervisory signals for regularizing the target model learning, thereby improving its performance under limited training samples. Concretely, we present two approaches for the proposed representation learning by constraining either final or intermediate model features on the target model. Experimental results on a clinical face image dataset demonstrate that the proposed approach works well with few labeled data, and outperforms other compared approaches.Comment: MICCAI-MLMI 202

Skill, or style? Classification of fetal sonography eye-tracking data

We present a method for classifying human skill at fetal ultrasound scanning from eye-tracking and pupillary data of sonographers. Human skill characterization for this clinical task typically creates groupings of clinician skills such as expert and beginner based on the number of years of professional experience; experts typically have more than 10 years and beginners between 0-5 years. In some cases, they also include trainees who are not yet fully-qualified professionals. Prior work has considered eye movements that necessitates separating eye-tracking data into eye movements, such as fixations and saccades. Our method does not use prior assumptions about the relationship between years of experience and does not require the separation of eye-tracking data. Our best performing skill classification model achieves an F1 score of 98% and 70% for expert and trainee classes respectively. We also show that years of experience as a direct measure of skill, is significantly correlated to the expertise of a sonographer

Intraoperative Organ Motion Models with an Ensemble of Conditional Generative Adversarial Networks

In this paper, we describe how a patient-specific, ultrasound-probe-induced prostate motion model can be directly generated from a single preoperative MR image. Our motion model allows for sampling from the conditional distribution of dense displacement fields, is encoded by a generative neural network conditioned on a medical image, and accepts random noise as additional input. The generative network is trained by a minimax optimisation with a second discriminative neural network, tasked to distinguish generated samples from training motion data. In this work, we propose that 1) jointly optimising a third conditioning neural network that pre-processes the input image, can effectively extract patient-specific features for conditioning; and 2) combining multiple generative models trained separately with heuristically pre-disjointed training data sets can adequately mitigate the problem of mode collapse. Trained with diagnostic T2-weighted MR images from 143 real patients and 73,216 3D dense displacement fields from finite element simulations of intraoperative prostate motion due to transrectal ultrasound probe pressure, the proposed models produced physically-plausible patient-specific motion of prostate glands. The ability to capture biomechanically simulated motion was evaluated using two errors representing generalisability and specificity of the model. The median values, calculated from a 10-fold cross-validation, were 2.8+/-0.3 mm and 1.7+/-0.1 mm, respectively. We conclude that the introduced approach demonstrates the feasibility of applying state-of-the-art machine learning algorithms to generate organ motion models from patient images, and shows significant promise for future research.Comment: Accepted to MICCAI 201