arXiv subjects

Marius Staring

Publications and source records attributed to Marius Staring.

At least 37 records · Page 2Linked to original sources

arXiv2024

Efficient MedSAMs: Segment Anything in Medical Images on Laptop

Promptable segmentation foundation models have emerged as a transformative approach to addressing the diverse needs in medical images, but most existing models require expensive computing, posing a big barrier to their adoption in clinical practice. In this work, we organized the first international competition dedicated to promptable medical image segmentation, featuring a large-scale dataset spanning nine common imaging modalities from over 20 different institutions. The top teams developed lightweight segmentation foundation models and implemented an efficient inference pipeline that substantially reduced computational requirements while maintaining state-of-the-art segmentation accuracy. Moreover, the post-challenge phase advanced the algorithms through the design of performance booster and reproducibility tasks, resulting in improved algorithms and validated reproducibility of the winning solution. Furthermore, the best-performing algorithms have been incorporated into the open-source software with a user-friendly interface to facilitate clinical adoption. The data and code are publicly available to foster the further development of medical image segmentation foundation models and pave the way for impactful real-world applications.

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arXiv2024

Swin-LiteMedSAM: A Lightweight Box-Based Segment Anything Model for Large-Scale Medical Image Datasets

Medical imaging is essential for the diagnosis and treatment of diseases, with medical image segmentation as a subtask receiving high attention. However, automatic medical image segmentation models are typically task-specific and struggle to handle multiple scenarios, such as different imaging modalities and regions of interest. With the introduction of the Segment Anything Model (SAM), training a universal model for various clinical scenarios has become feasible. Recently, several Medical SAM (MedSAM) methods have been proposed, but these models often rely on heavy image encoders to achieve high performance, which may not be practical for real-world applications due to their high computational demands and slow inference speed. To address this issue, a lightweight version of the MedSAM (LiteMedSAM) can provide a viable solution, achieving high performance while requiring fewer resources and less time. In this work, we introduce Swin-LiteMedSAM, a new variant of LiteMedSAM. This model integrates the tiny Swin Transformer as the image encoder, incorporates multiple types of prompts, including box-based points and scribble generated from a given bounding box, and establishes skip connections between the image encoder and the mask decoder. In the \textit{Segment Anything in Medical Images on Laptop} challenge (CVPR 2024), our approach strikes a good balance between segmentation performance and speed, demonstrating significantly improved overall results across multiple modalities compared to the LiteMedSAM baseline provided by the challenge organizers. Our proposed model achieved a DSC score of \textbf{0.8678} and an NSD score of \textbf{0.8844} on the validation set. On the final test set, it attained a DSC score of \textbf{0.8193} and an NSD score of \textbf{0.8461}, securing fourth place in the challenge.

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arXiv2024

Improving Uncertainty-Error Correspondence in Deep Bayesian Medical Image Segmentation

Increased usage of automated tools like deep learning in medical image segmentation has alleviated the bottleneck of manual contouring. This has shifted manual labour to quality assessment (QA) of automated contours which involves detecting errors and correcting them. A potential solution to semi-automated QA is to use deep Bayesian uncertainty to recommend potentially erroneous regions, thus reducing time spent on error detection. Previous work has investigated the correspondence between uncertainty and error, however, no work has been done on improving the "utility" of Bayesian uncertainty maps such that it is only present in inaccurate regions and not in the accurate ones. Our work trains the FlipOut model with the Accuracy-vs-Uncertainty (AvU) loss which promotes uncertainty to be present only in inaccurate regions. We apply this method on datasets of two radiotherapy body sites, c.f. head-and-neck CT and prostate MR scans. Uncertainty heatmaps (i.e. predictive entropy) are evaluated against voxel inaccuracies using Receiver Operating Characteristic (ROC) and Precision-Recall (PR) curves. Numerical results show that when compared to the Bayesian baseline the proposed method successfully suppresses uncertainty for accurate voxels, with similar presence of uncertainty for inaccurate voxels. Code to reproduce experiments is available at https://github.com/prerakmody/bayesuncertainty-error-correspondence

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arXiv2024

Vestibular schwannoma growth prediction from longitudinal MRI by time conditioned neural fields

Vestibular schwannomas (VS) are benign tumors that are generally managed by active surveillance with MRI examination. To further assist clinical decision-making and avoid overtreatment, an accurate prediction of tumor growth based on longitudinal imaging is highly desirable. In this paper, we introduce DeepGrowth, a deep learning method that incorporates neural fields and recurrent neural networks for prospective tumor growth prediction. In the proposed method, each tumor is represented as a signed distance function (SDF) conditioned on a low-dimensional latent code. Unlike previous studies that perform tumor shape prediction directly in the image space, we predict the latent codes instead and then reconstruct future shapes from it. To deal with irregular time intervals, we introduce a time-conditioned recurrent module based on a ConvLSTM and a novel temporal encoding strategy, which enables the proposed model to output varying tumor shapes over time. The experiments on an in-house longitudinal VS dataset showed that the proposed model significantly improved the performance ($\ge 1.6\%$ Dice score and $\ge0.20$ mm 95\% Hausdorff distance), in particular for top 20\% tumors that grow or shrink the most ($\ge 4.6\%$ Dice score and $\ge 0.73$ mm 95\% Hausdorff distance). Our code is available at ~\burl{https://github.com/cyjdswx/DeepGrowth}

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arXiv2024

CoNeS: Conditional neural fields with shift modulation for multi-sequence MRI translation

Multi-sequence magnetic resonance imaging (MRI) has found wide applications in both modern clinical studies and deep learning research. However, in clinical practice, it frequently occurs that one or more of the MRI sequences are missing due to different image acquisition protocols or contrast agent contraindications of patients, limiting the utilization of deep learning models trained on multi-sequence data. One promising approach is to leverage generative models to synthesize the missing sequences, which can serve as a surrogate acquisition. State-of-the-art methods tackling this problem are based on convolutional neural networks (CNN) which usually suffer from spectral biases, resulting in poor reconstruction of high-frequency fine details. In this paper, we propose Conditional Neural fields with Shift modulation (CoNeS), a model that takes voxel coordinates as input and learns a representation of the target images for multi-sequence MRI translation. The proposed model uses a multi-layer perceptron (MLP) instead of a CNN as the decoder for pixel-to-pixel mapping. Hence, each target image is represented as a neural field that is conditioned on the source image via shift modulation with a learned latent code. Experiments on BraTS 2018 and an in-house clinical dataset of vestibular schwannoma patients showed that the proposed method outperformed state-of-the-art methods for multi-sequence MRI translation both visually and quantitatively. Moreover, we conducted spectral analysis, showing that CoNeS was able to overcome the spectral bias issue common in conventional CNN models. To further evaluate the usage of synthesized images in clinical downstream tasks, we tested a segmentation network using the synthesized images at inference.

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arXiv2024

Seg-metrics: a Python package to compute segmentation metrics

In response to a concerning trend of selectively emphasizing metrics in medical image segmentation (MIS) studies, we introduce \texttt{seg-metrics}, an open-source Python package for standardized MIS model evaluation. Unlike existing packages, \texttt{seg-metrics} offers user-friendly interfaces for various overlap-based and distance-based metrics, providing a comprehensive solution. \texttt{seg-metrics} supports multiple file formats and is easily installable through the Python Package Index (PyPI). With a focus on speed and convenience, \texttt{seg-metrics} stands as a valuable tool for efficient MIS model assessment.

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arXiv2023

Local Implicit Neural Representations for Multi-Sequence MRI Translation

In radiological practice, multi-sequence MRI is routinely acquired to characterize anatomy and tissue. However, due to the heterogeneity of imaging protocols and contra-indications to contrast agents, some MRI sequences, e.g. contrast-enhanced T1-weighted image (T1ce), may not be acquired. This creates difficulties for large-scale clinical studies for which heterogeneous datasets are aggregated. Modern deep learning techniques have demonstrated the capability of synthesizing missing sequences from existing sequences, through learning from an extensive multi-sequence MRI dataset. In this paper, we propose a novel MR image translation solution based on local implicit neural representations. We split the available MRI sequences into local patches and assign to each patch a local multi-layer perceptron (MLP) that represents a patch in the T1ce. The parameters of these local MLPs are generated by a hypernetwork based on image features. Experimental results and ablation studies on the BraTS challenge dataset showed that the local MLPs are critical for recovering fine image and tumor details, as they allow for local specialization that is highly important for accurate image translation. Compared to a classical pix2pix model, the proposed method demonstrated visual improvement and significantly improved quantitative scores (MSE 0.86 x 10^-3 vs. 1.02 x 10^-3 and SSIM 94.9 vs 94.3)

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arXiv2023

Joint optimization of a $β$-VAE for ECG task-specific feature extraction

Electrocardiography is the most common method to investigate the condition of the heart through the observation of cardiac rhythm and electrical activity, for both diagnosis and monitoring purposes. Analysis of electrocardiograms (ECGs) is commonly performed through the investigation of specific patterns, which are visually recognizable by trained physicians and are known to reflect cardiac (dis)function. In this work we study the use of $β$-variational autoencoders (VAEs) as an explainable feature extractor, and improve on its predictive capacities by jointly optimizing signal reconstruction and cardiac function prediction. The extracted features are then used for cardiac function prediction using logistic regression. The method is trained and tested on data from 7255 patients, who were treated for acute coronary syndrome at the Leiden University Medical Center between 2010 and 2021. The results show that our method significantly improved prediction and explainability compared to a vanilla $β$-VAE, while still yielding similar reconstruction performance.

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arXiv2022

Report on AI-Infused Contouring Workflows for Adaptive Proton Therapy in the Head and Neck

Delineation of tumors and organs-at-risk permits detecting and correcting changes in the patients' anatomy throughout the treatment, making it a core step of adaptive proton therapy (APT). Although AI-based auto-contouring technologies have sped up this process, the time needed to perform the quality assessment (QA) of the generated contours remains a bottleneck, taking clinicians between several minutes up to an hour to complete. This paper introduces a fast contouring workflow suitable for time-critical APT, enabling detection of anatomical changes in shorter time frames and with a lower demand of clinical resources. The proposed AI-infused workflow follows two principles uncovered after reviewing the APT literature and conducting several interviews and an observational study in two radiotherapy centers in the Netherlands. First, enable targeted inspection of the generated contours by leveraging AI uncertainty and clinically-relevant features such as the proximity of the organs-at-risk to the tumor. Second, minimize the number of interactions needed to edit faulty delineations with redundancy-aware editing tools that provide the user a sense of predictability and control. We use a proof of concept that we validated with clinicians to demonstrate how current and upcoming AI capabilities support the workflow and how it would fit into clinical practice.

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arXiv2022

Comparing Bayesian Models for Organ Contouring in Head and Neck Radiotherapy

Deep learning models for organ contouring in radiotherapy are poised for clinical usage, but currently, there exist few tools for automated quality assessment (QA) of the predicted contours. Using Bayesian models and their associated uncertainty, one can potentially automate the process of detecting inaccurate predictions. We investigate two Bayesian models for auto-contouring, DropOut and FlipOut, using a quantitative measure - expected calibration error (ECE) and a qualitative measure - region-based accuracy-vs-uncertainty (R-AvU) graphs. It is well understood that a model should have low ECE to be considered trustworthy. However, in a QA context, a model should also have high uncertainty in inaccurate regions and low uncertainty in accurate regions. Such behaviour could direct visual attention of expert users to potentially inaccurate regions, leading to a speed up in the QA process. Using R-AvU graphs, we qualitatively compare the behaviour of different models in accurate and inaccurate regions. Experiments are conducted on the MICCAI2015 Head and Neck Segmentation Challenge and on the DeepMindTCIA CT dataset using three models: DropOut-DICE, Dropout-CE (Cross Entropy) and FlipOut-CE. Quantitative results show that DropOut-DICE has the highest ECE, while Dropout-CE and FlipOut-CE have the lowest ECE. To better understand the difference between DropOut-CE and FlipOut-CE, we use the R-AvU graph which shows that FlipOut-CE has better uncertainty coverage in inaccurate regions than DropOut-CE. Such a combination of quantitative and qualitative metrics explores a new approach that helps to select which model can be deployed as a QA tool in clinical settings.

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arXiv2021

Prediction of Lung CT Scores of Systemic Sclerosis by Cascaded Regression Neural Networks

Visually scoring lung involvement in systemic sclerosis from CT scans plays an important role in monitoring progression, but its labor intensiveness hinders practical application. We proposed, therefore, an automatic scoring framework that consists of two cascaded deep regression neural networks. The first (3D) network aims to predict the craniocaudal position of five anatomically defined scoring levels on the 3D CT scans. The second (2D) network receives the resulting 2D axial slices and predicts the scores. We used 227 3D CT scans to train and validate the first network, and the resulting 1135 axial slices were used in the second network. Two experts scored independently a subset of data to obtain intra- and interobserver variabilities and the ground truth for all data was obtained in consensus. To alleviate the unbalance in training labels in the second network, we introduced a sampling technique and to increase the diversity of the training samples synthetic data was generated, mimicking ground glass and reticulation patterns. The 4-fold cross validation showed that our proposed network achieved an average MAE of 5.90, 4.66 and 4.49, weighted kappa of 0.66, 0.58 and 0.65 for total score (TOT), ground glass (GG) and reticular pattern (RET), respectively. Our network performed slightly worse than the best experts on TOT and GG prediction but it has competitive performance on RET prediction and has the potential to be an objective alternative for the visual scoring of SSc in CT thorax studies.

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arXiv2021

Joint Registration and Segmentation via Multi-Task Learning for Adaptive Radiotherapy of Prostate Cancer

Medical image registration and segmentation are two of the most frequent tasks in medical image analysis. As these tasks are complementary and correlated, it would be beneficial to apply them simultaneously in a joint manner. In this paper, we formulate registration and segmentation as a joint problem via a Multi-Task Learning (MTL) setting, allowing these tasks to leverage their strengths and mitigate their weaknesses through the sharing of beneficial information. We propose to merge these tasks not only on the loss level, but on the architectural level as well. We studied this approach in the context of adaptive image-guided radiotherapy for prostate cancer, where planning and follow-up CT images as well as their corresponding contours are available for training. The study involves two datasets from different manufacturers and institutes. The first dataset was divided into training (12 patients) and validation (6 patients), and was used to optimize and validate the methodology, while the second dataset (14 patients) was used as an independent test set. We carried out an extensive quantitative comparison between the quality of the automatically generated contours from different network architectures as well as loss weighting methods. Moreover, we evaluated the quality of the generated deformation vector field (DVF). We show that MTL algorithms outperform their Single-Task Learning (STL) counterparts and achieve better generalization on the independent test set. The best algorithm achieved a mean surface distance of $1.06 \pm 0.3$ mm, $1.27 \pm 0.4$ mm, $0.91 \pm 0.4$ mm, and $1.76 \pm 0.8$ mm on the validation set for the prostate, seminal vesicles, bladder, and rectum, respectively. The high accuracy of the proposed method combined with the fast inference speed, makes it a promising method for automatic re-contouring of follow-up scans for adaptive radiotherapy.

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arXiv2021

Multi-task Semi-supervised Learning for Pulmonary Lobe Segmentation

Pulmonary lobe segmentation is an important preprocessing task for the analysis of lung diseases. Traditional methods relying on fissure detection or other anatomical features, such as the distribution of pulmonary vessels and airways, could provide reasonably accurate lobe segmentations. Deep learning based methods can outperform these traditional approaches, but require large datasets. Deep multi-task learning is expected to utilize labels of multiple different structures. However, commonly such labels are distributed over multiple datasets. In this paper, we proposed a multi-task semi-supervised model that can leverage information of multiple structures from unannotated datasets and datasets annotated with different structures. A focused alternating training strategy is presented to balance the different tasks. We evaluated the trained model on an external independent CT dataset. The results show that our model significantly outperforms single-task alternatives, improving the mean surface distance from 7.174 mm to 4.196 mm. We also demonstrated that our approach is successful for different network architectures as backbones.

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arXiv2021

Esophageal Tumor Segmentation in CT Images using Dilated Dense Attention Unet (DDAUnet)

Manual or automatic delineation of the esophageal tumor in CT images is known to be very challenging. This is due to the low contrast between the tumor and adjacent tissues, the anatomical variation of the esophagus, as well as the occasional presence of foreign bodies (e.g. feeding tubes). Physicians therefore usually exploit additional knowledge such as endoscopic findings, clinical history, additional imaging modalities like PET scans. Achieving his additional information is time-consuming, while the results are error-prone and might lead to non-deterministic results. In this paper we aim to investigate if and to what extent a simplified clinical workflow based on CT alone, allows one to automatically segment the esophageal tumor with sufficient quality. For this purpose, we present a fully automatic end-to-end esophageal tumor segmentation method based on convolutional neural networks (CNNs). The proposed network, called Dilated Dense Attention Unet (DDAUnet), leverages spatial and channel attention gates in each dense block to selectively concentrate on determinant feature maps and regions. Dilated convolutional layers are used to manage GPU memory and increase the network receptive field. We collected a dataset of 792 scans from 288 distinct patients including varying anatomies with \mbox{air pockets}, feeding tubes and proximal tumors. Repeatability and reproducibility studies were conducted for three distinct splits of training and validation sets. The proposed network achieved a $\mathrm{DSC}$ value of $0.79 \pm 0.20$, a mean surface distance of $5.4 \pm 20.2mm$ and $95\%$ Hausdorff distance of $14.7 \pm 25.0mm$ for 287 test scans, demonstrating promising results with a simplified clinical workflow based on CT alone. Our code is publicly available via \url{https://github.com/yousefis/DenseUnet_Esophagus_Segmentation}.

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arXiv2021

ASL to PET Translation by a Semi-supervised Residual-based Attention-guided Convolutional Neural Network

Positron Emission Tomography (PET) is an imaging method that can assess physiological function rather than structural disturbances by measuring cerebral perfusion or glucose consumption. However, this imaging technique relies on injection of radioactive tracers and is expensive. On the contrary, Arterial Spin Labeling (ASL) MRI is a non-invasive, non-radioactive, and relatively cheap imaging technique for brain hemodynamic measurements, which allows quantification to some extent. In this paper we propose a convolutional neural network (CNN) based model for translating ASL to PET images, which could benefit patients as well as the healthcare system in terms of expenses and adverse side effects. However, acquiring a sufficient number of paired ASL-PET scans for training a CNN is prohibitive for many reasons. To tackle this problem, we present a new semi-supervised multitask CNN which is trained on both paired data, i.e. ASL and PET scans, and unpaired data, i.e. only ASL scans, which alleviates the problem of training a network on limited paired data. Moreover, we present a new residual-based-attention guided mechanism to improve the contextual features during the training process. Also, we show that incorporating T1-weighted scans as an input, due to its high resolution and availability of anatomical information, improves the results. We performed a two-stage evaluation based on quantitative image metrics by conducting a 7-fold cross validation followed by a double-blind observer study. The proposed network achieved structural similarity index measure (SSIM), mean squared error (MSE) and peak signal-to-noise ratio (PSNR) values of $0.85\pm0.08$, $0.01\pm0.01$, and $21.8\pm4.5$ respectively, for translating from 2D ASL and T1-weighted images to PET data. The proposed model is publicly available via https://github.com/yousefis/ASL2PET.

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arXiv2020

An Adaptive Intelligence Algorithm for Undersampled Knee MRI Reconstruction

Adaptive intelligence aims at empowering machine learning techniques with the additional use of domain knowledge. In this work, we present the application of adaptive intelligence to accelerate MR acquisition. Starting from undersampled k-space data, an iterative learning-based reconstruction scheme inspired by compressed sensing theory is used to reconstruct the images. We adopt deep neural networks to refine and correct prior reconstruction assumptions given the training data. The network was trained and tested on a knee MRI dataset from the 2019 fastMRI challenge organized by Facebook AI Research and NYU Langone Health. All submissions to the challenge were initially ranked based on similarity with a known groundtruth, after which the top 4 submissions were evaluated radiologically. Our method was evaluated by the fastMRI organizers on an independent challenge dataset. It ranked #1, shared #1, and #3 on respectively the 8x accelerated multi-coil, the 4x multi-coil, and the 4x single-coil track. This demonstrates the superior performance and wide applicability of the method.

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arXiv2020

A Cross-Stitch Architecture for Joint Registration and Segmentation in Adaptive Radiotherapy

Recently, joint registration and segmentation has been formulated in a deep learning setting, by the definition of joint loss functions. In this work, we investigate joining these tasks at the architectural level. We propose a registration network that integrates segmentation propagation between images, and a segmentation network to predict the segmentation directly. These networks are connected into a single joint architecture via so-called cross-stitch units, allowing information to be exchanged between the tasks in a learnable manner. The proposed method is evaluated in the context of adaptive image-guided radiotherapy, using daily prostate CT imaging. Two datasets from different institutes and manufacturers were involved in the study. The first dataset was used for training (12 patients) and validation (6 patients), while the second dataset was used as an independent test set (14 patients). In terms of mean surface distance, our approach achieved $1.06 \pm 0.3$ mm, $0.91 \pm 0.4$ mm, $1.27 \pm 0.4$ mm, and $1.76 \pm 0.8$ mm on the validation set and $1.82 \pm 2.4$ mm, $2.45 \pm 2.4$ mm, $2.45 \pm 5.0$ mm, and $2.57 \pm 2.3$ mm on the test set for the prostate, bladder, seminal vesicles, and rectum, respectively. The proposed multi-task network outperformed single-task networks, as well as a network only joined through the loss function, thus demonstrating the capability to leverage the individual strengths of the segmentation and registration tasks. The obtained performance as well as the inference speed make this a promising candidate for daily re-contouring in adaptive radiotherapy, potentially reducing treatment-related side effects and improving quality-of-life after treatment.

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arXiv2020

Patient-Specific Finetuning of Deep Learning Models for Adaptive Radiotherapy in Prostate CT

Contouring of the target volume and Organs-At-Risk (OARs) is a crucial step in radiotherapy treatment planning. In an adaptive radiotherapy setting, updated contours need to be generated based on daily imaging. In this work, we leverage personalized anatomical knowledge accumulated over the treatment sessions, to improve the segmentation accuracy of a pre-trained Convolution Neural Network (CNN), for a specific patient. We investigate a transfer learning approach, fine-tuning the baseline CNN model to a specific patient, based on imaging acquired in earlier treatment fractions. The baseline CNN model is trained on a prostate CT dataset from one hospital of 379 patients. This model is then fine-tuned and tested on an independent dataset of another hospital of 18 patients, each having 7 to 10 daily CT scans. For the prostate, seminal vesicles, bladder and rectum, the model fine-tuned on each specific patient achieved a Mean Surface Distance (MSD) of $1.64 \pm 0.43$ mm, $2.38 \pm 2.76$ mm, $2.30 \pm 0.96$ mm, and $1.24 \pm 0.89$ mm, respectively, which was significantly better than the baseline model. The proposed personalized model adaptation is therefore very promising for clinical implementation in the context of adaptive radiotherapy of prostate cancer.

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