•Deep learning allows automatic segmentation of brain tissues and ischemic lesions in MRI scans of patients affected by perinatal arterial stroke.•Qualitative evaluation of the automatic ...segmentations showed that in 85% of MRIs acquired after the stroke onset and in 91% of MRIs acquired at 3-moths follow-up were clinically useable after no or minor correction.•Automatic segmentation method may allow evaluation of the brain development and efficacy of stroke treatment in large scale studies.
Perinatal arterial ischemic stroke (PAIS) is associated with adverse neurological outcomes. Quantification of ischemic lesions and consequent brain development in newborn infants relies on labor-intensive manual assessment of brain tissues and ischemic lesions. Hence, we propose an automatic method utilizing convolutional neural networks (CNNs) to segment brain tissues and ischemic lesions in MRI scans of infants suffering from PAIS.
This single-center retrospective study included 115 patients with PAIS that underwent MRI after the stroke onset (baseline) and after three months (follow-up). Nine baseline and 12 follow-up MRI scans were manually annotated to provide reference segmentations (white matter, gray matter, basal ganglia and thalami, brainstem, ventricles, extra-ventricular cerebrospinal fluid, and cerebellum, and additionally on the baseline scans the ischemic lesions). Two CNNs were trained to perform automatic segmentation on the baseline and follow-up MRIs, respectively. Automatic segmentations were quantitatively evaluated using the Dice coefficient (DC) and the mean surface distance (MSD). Volumetric agreement between segmentations that were manually and automatically obtained was computed. Moreover, the scan quality and automatic segmentations were qualitatively evaluated in a larger set of MRIs without manual annotation by two experts. In addition, the scan quality was qualitatively evaluated in these scans to establish its impact on the automatic segmentation performance.
Automatic brain tissue segmentation led to a DC and MSD between 0.78–0.92 and 0.18–1.08 mm for baseline, and between 0.88–0.95 and 0.10–0.58 mm for follow-up scans, respectively. For the ischemic lesions at baseline the DC and MSD were between 0.72–0.86 and 1.23–2.18 mm, respectively. Volumetric measurements indicated limited oversegmentation of the extra-ventricular cerebrospinal fluid in both the follow-up and baseline scans, oversegmentation of the ischemic lesions in the left hemisphere, and undersegmentation of the ischemic lesions in the right hemisphere. In scans without imaging artifacts, brain tissue segmentation was graded as excellent in more than 85% and 91% of cases, respectively for the baseline and follow-up scans. For the ischemic lesions at baseline, this was in 61% of cases.
Automatic segmentation of brain tissue and ischemic lesions in MRI scans of patients with PAIS is feasible. The method may allow evaluation of the brain development and efficacy of treatment in large datasets.
•Automatic intracranial volume segmentation.•Fetal and neonatal MRI.•Deep learning.
MR images of infants and fetuses allow non-invasive analysis of the brain. Quantitative analysis of brain ...development requires automatic brain tissue segmentation that is typically preceded by segmentation of the intracranial volume (ICV). Fast changes in the size and morphology of the developing brain, motion artifacts, and large variation in the field of view make ICV segmentation a challenging task.
We propose an automatic method for segmentation of the ICV in fetal and neonatal MRI scans. The method was developed and tested with a diverse set of scans regarding image acquisition parameters (i.e. field strength, image acquisition plane, image resolution), infant age (23–45 weeks post menstrual age), and pathology (posthaemorrhagic ventricular dilatation, stroke, asphyxia, and Down syndrome). The results demonstrate that the method achieves accurate segmentation with a Dice coefficient (DC) ranging from 0.98 to 0.99 in neonatal and fetal scans regardless of image acquisition parameters or patient characteristics. Hence, the algorithm provides a generic tool for segmentation of the ICV that may be used as a preprocessing step for brain tissue segmentation in fetal and neonatal brain MR scans.
In patients with obstructive coronary artery disease, the functional significance of a coronary artery stenosis needs to be determined to guide treatment. This is typically established through ...fractional flow reserve (FFR) measurement, performed during invasive coronary angiography (ICA). We present a method for automatic and non-invasive detection of patients requiring ICA, employing deep unsupervised analysis of complete coronary arteries in cardiac CT angiography (CCTA) images. We retrospectively collected CCTA scans of 187 patients, 137 of them underwent invasive FFR measurement in 192 different coronary arteries. These FFR measurements served as a reference standard for the functional significance of the coronary stenosis. The centerlines of the coronary arteries were extracted and used to reconstruct straightened multi-planar reformatted (MPR) volumes. To automatically identify arteries with functionally significant stenosis that require ICA, each MPR volume was encoded into a fixed number of encodings using two disjoint 3D and 1D convolutional autoencoders performing spatial and sequential encodings, respectively. Thereafter, these encodings were employed to classify arteries using a support vector machine classifier. The detection of coronary arteries requiring invasive evaluation, evaluated using repeated cross-validation experiments, resulted in an area under the receiver operating characteristic curve of 0.81 ± 0.02 on the artery-level, and 0.87 ± 0.02 on the patient-level. The results demonstrate the feasibility of automatic non-invasive detection of patients that require ICA and possibly subsequent coronary artery intervention. This could potentially reduce the number of patients that unnecessarily undergo ICA.
To compare the effect of early and late intervention for posthemorrhagic ventricular dilatation on additional brain injury and ventricular volume using term-equivalent age-MRI.
In the Early vs Late ...Ventricular Intervention Study (ELVIS) trial, 126 preterm infants ≤34 weeks of gestation with posthemorrhagic ventricular dilatation were randomized to low-threshold (ventricular index >p97 and anterior horn width >6 mm) or high-threshold (ventricular index >p97 + 4 mm and anterior horn width >10 mm) groups. In 88 of those (80%) with a term-equivalent age-MRI, the Kidokoro Global Brain Abnormality Score and the frontal and occipital horn ratio were measured. Automatic segmentation was used for volumetric analysis.
The total Kidokoro score of the infants in the low-threshold group (n = 44) was lower than in the high-threshold group (n = 44; median, 8 IQR, 5-12 vs median 12 IQR, 9-17, respectively; P < .001). More infants in the low-threshold group had a normal or mildly increased score vs more infants in the high-threshold group with a moderately or severely increased score (46% vs 11% and 89% vs 54%, respectively; P = .002). The frontal and occipital horn ratio was lower in the low-threshold group (median, 0.42 IQR, 0.34-0.63) than the high-threshold group (median 0.48 IQR, 0.37-0.68, respectively; P = .001). Ventricular cerebrospinal fluid volumes could be calculated in 47 infants and were smaller in the low-threshold group (P = .03).
More brain injury and larger ventricular volumes were demonstrated in the high vs the low-threshold group. These results support the positive effects of early intervention for posthemorrhagic ventricular dilatation.
ISRCTN43171322.
Deep learning algorithms, often critiqued for their 'black box' nature, traditionally fall short in providing the necessary transparency for trusted clinical use. This challenge is particularly ...evident when such models are deployed in local hospitals, encountering out-of-domain distributions due to varying imaging techniques and patient-specific pathologies. Yet, this limitation offers a unique avenue for continual learning. The Uncertainty-Guided Annotation (UGA) framework introduces a human-in-the-loop approach, enabling AI to convey its uncertainties to clinicians, effectively acting as an automated quality control mechanism. UGA eases this interaction by quantifying uncertainty at the pixel level, thereby revealing the model's limitations and opening the door for clinician-guided corrections. We evaluated UGA on the Camelyon dataset for lymph node metastasis segmentation which revealed that UGA improved the Dice coefficient (DC), from 0.66 to 0.76 by adding 5 patches, and further to 0.84 with 10 patches. To foster broader application and community contribution, we have made our code accessible at
In digital pathology, different staining procedures and scanners cause substantial color variations in whole-slide images (WSIs), especially across different laboratories. These color shifts result ...in a poor generalization of deep learning-based methods from the training domain to external pathology data. To increase test performance, stain normalization techniques are used to reduce the variance between training and test domain. Alternatively, color augmentation can be applied during training leading to a more robust model without the extra step of color normalization at test time. We propose a novel color augmentation technique, HistAuGAN, that can simulate a wide variety of realistic histology stain colors, thus making neural networks stain-invariant when applied during training. Based on a generative adversarial network (GAN) for image-to-image translation, our model disentangles the content of the image, i.e., the morphological tissue structure, from the stain color attributes. It can be trained on multiple domains and, therefore, learns to cover different stain colors as well as other domain-specific variations introduced in the slide preparation and imaging process. We demonstrate that HistAuGAN outperforms conventional color augmentation techniques on a classification task on the publicly available dataset Camelyon17 and show that it is able to mitigate present batch effects.
In patients with obstructive coronary artery disease, the functional significance of a coronary artery stenosis needs to be determined to guide treatment. This is typically established through ...fractional flow reserve (FFR) measurement, performed during invasive coronary angiography (ICA). We present a method for automatic and non-invasive detection of patients requiring ICA, employing deep unsupervised analysis of complete coronary arteries in cardiac CT angiography (CCTA) images. We retrospectively collected CCTA scans of 187 patients, 137 of them underwent invasive FFR measurement in 192 different coronary arteries. These FFR measurements served as a reference standard for the functional significance of the coronary stenosis. The centerlines of the coronary arteries were extracted and used to reconstruct straightened multi-planar reformatted (MPR) volumes. To automatically identify arteries with functionally significant stenosis that require ICA, each MPR volume was encoded into a fixed number of encodings using two disjoint 3D and 1D convolutional autoencoders performing spatial and sequential encodings, respectively. Thereafter, these encodings were employed to classify arteries using a support vector machine classifier. The detection of coronary arteries requiring invasive evaluation, evaluated using repeated cross-validation experiments, resulted in an area under the receiver operating characteristic curve of \(0.81 \pm 0.02\) on the artery-level, and \(0.87 \pm 0.02\) on the patient-level. The results demonstrate the feasibility of automatic non-invasive detection of patients that require ICA and possibly subsequent coronary artery intervention. This could potentially reduce the number of patients that unnecessarily undergo ICA.
Treatment of patients with obstructive coronary artery disease is guided by the functional significance of a coronary artery stenosis. Fractional flow reserve (FFR), measured during invasive coronary ...angiography (ICA), is considered the gold standard to define the functional significance of a coronary stenosis. Here, we present a method for non-invasive detection of patients with functionally significant coronary artery stenosis, combining analysis of the coronary artery tree and the left ventricular (LV) myocardium in cardiac CT angiography (CCTA) images. We retrospectively collected CCTA scans of 126 patients who underwent invasive FFR measurements, to determine the functional significance of coronary stenoses. We combine our previous works for the analysis of the complete coronary artery tree and the LV myocardium: Coronary arteries are encoded by two disjoint convolutional autoencoders (CAEs) and the LV myocardium is characterized by a convolutional neural network (CNN) and a CAE. Thereafter, using the extracted encodings of all coronary arteries and the LV myocardium, patients are classified according to the presence of functionally significant stenosis, as defined by the invasively measured FFR. To handle the varying number of coronary arteries in a patient, the classification is formulated as a multiple instance learning problem and is performed using an attention-based neural network. Cross-validation experiments resulted in an average area under the receiver operating characteristic curve of \(0.74 \pm 0.01\), and showed that the proposed combined analysis outperformed the analysis of the coronary arteries or the LV myocardium only. The results demonstrate the feasibility of combining the analyses of the complete coronary artery tree and the LV myocardium in CCTA images for the detection of patients with functionally significant stenosis in coronary arteries.
Recent advances in artificial intelligence (AI) have revolutionized computational pathology (CPath), particularly through deep learning (DL) and convolutional neural networks (CNNs). In a recent ...study, Vorontsov et al. introduced Virchow, a new foundation model (FM) for CPath, which has shown promising results in cancer detection and biomarker prediction.
Recent advances in artificial intelligence (AI) have revolutionized computational pathology (CPath), particularly through deep learning (DL) and convolutional neural networks (CNNs). In a recent study, Vorontsov et al. introduced Virchow, a new foundation model (FM) for CPath, which has shown promising results in cancer detection and biomarker prediction.
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