Hemorrhagic stroke lesion segmentation using a 3D U-Net with squeeze-and-excitation blocks

Multi-scale object equalization learning network for intracerebral hemorrhage region segmentation

Segmentation and the subsequent quantitative assessment of the target object in computed tomography (CT) images provide valuable information for the analysis of intracerebral hemorrhage (ICH) pathology. However, most existing methods lack a reasonable strategy to explore the discriminative semantics of multi-scale ICH regions, making it difficult to address the challenge of complex morphology in clinical data. In this paper, we propose a novel multi-scale object equalization learning network (MOEL-Net) for accurate ICH region segmentation. Specifically, we first introduce a shallow feature extraction module (SFEM) for obtaining shallow semantic representations to maintain sufficient and effective detailed location information. Then, a deep feature extraction module (DFEM) is leveraged to extract the deep semantic information of the ICH region from the combination of SFEM and original image features. To further achieve equalization learning in different scales of ICH regions, we introduce a multi-level semantic feature equalization fusion module (MSFEFM), which explores the equalized fusion features of the described objects with the assistance of shallow and deep semantic information provided by SFEM and DFEM. Driven by the above three designs, MOEL-Net shows a solid capacity to capture more discriminative features in various ICH region segmentation. To promote the research of clinical automatic ICH region segmentation, we collect two datasets, VMICH and FRICH (divided into Test A and Test B) for evaluation. Experimental results show that the proposed model achieves the Dice scores of 88.28%, 90.92%, and 90.95% on the VMICH, FRICH Test A, and Test B, respectively, which outperform fourteen competing methods.

Hematoma expansion prediction in intracerebral hemorrhage patients by using synthesized CT images in an end-to-end deep learning framework

Spontaneous intracerebral hemorrhage (ICH) is a type of stroke less prevalent than ischemic stroke but associated with high mortality rates. Hematoma expansion (HE) is an increase in the bleeding that affects 30%-38% of hemorrhagic stroke patients. It is observed within 24 h of onset and associated with patient worsening. Clinically it is relevant to detect the patients that will develop HE from their initial computed tomography (CT) scans which could improve patient management and treatment decisions. However, this is a significant challenge due to the predictive nature of the task and its low prevalence, which hinders the availability of large datasets with the required longitudinal information. In this work, we present an end-to-end deep learning framework capable of predicting which cases will exhibit HE using only the initial basal image. We introduce a deep learning framework based on the 2D EfficientNet B0 model to predict the occurrence of HE using initial non-contrasted CT scans and their corresponding lesion annotation as priors. We used an in-house acquired dataset of 122 ICH patients, including 35 HE cases, containing longitudinal CT scans with manual lesion annotations in both basal and follow-up (obtained within 24 h after the basal scan). Experiments were conducted using a 5-fold cross-validation strategy. We addressed the limited data problem by incorporating synthetic images into the training process. To the best of our knowledge, our approach is novel in the field of HE prediction, being the first to use image synthesis to enhance results. We studied different scenarios such as training only with the original scans, using standard image augmentation techniques, and using synthetic image generation. The best performance was achieved by adding five generated versions of each image, along with standard data augmentation, during the training process. This significantly improved (p=0.0003) the performance obtained with our baseline model using directly the original CT scans from an Accuracy of 0.56 to 0.84, F1-Score of 0.53 to 0.82, Sensitivity of 0.51 to 0.77, and Specificity of 0.60 to 0.91, respectively. The proposed approach shows promising results in predicting HE, especially with the inclusion of synthetically generated images. The obtained results highlight the significance of this research direction, which has the potential to improve the clinical management of patients with hemorrhagic stroke. The code is available at: https://github.com/NIC-VICOROB/HE-prediction-SynthCT.

Neuroimage analysis using artificial intelligence approaches: a systematic review

In the contemporary era, artificial intelligence (AI) has undergone a transformative evolution, exerting a profound influence on neuroimaging data analysis. This development has significantly elevated our comprehension of intricate brain functions. This study investigates the ramifications of employing AI techniques on neuroimaging data, with a specific objective to improve diagnostic capabilities and contribute to the overall progress of the field. A systematic search was conducted in prominent scientific databases, including PubMed, IEEE Xplore, and Scopus, meticulously curating 456 relevant articles on AI-driven neuroimaging analysis spanning from 2013 to 2023. To maintain rigor and credibility, stringent inclusion criteria, quality assessments, and precise data extraction protocols were consistently enforced throughout this review. Following a rigorous selection process, 104 studies were selected for review, focusing on diverse neuroimaging modalities with an emphasis on mental and neurological disorders. Among these, 19.2% addressed mental illness, and 80.7% focused on neurological disorders. It is found that the prevailing clinical tasks are disease classification (58.7%) and lesion segmentation (28.9%), whereas image reconstruction constituted 7.3%, and image regression and prediction tasks represented 9.6%. AI-driven neuroimaging analysis holds tremendous potential, transforming both research and clinical applications. Machine learning and deep learning algorithms outperform traditional methods, reshaping the field significantly.

Deep learning-assisted detection and segmentation of intracranial hemorrhage in noncontrast computed tomography scans of acute stroke patients: a systematic review and meta-analysis

BACKGROUND

Deep learning (DL)-assisted detection and segmentation of intracranial hemorrhage stroke in noncontrast computed tomography (NCCT) scans are well-established, but evidence on this topic is lacking.

MATERIALS AND METHODS

PubMed and Embase databases were searched from their inception to November 2023 to identify related studies. The primary outcomes included sensitivity, specificity, and the Dice Similarity Coefficient (DSC); while the secondary outcomes were positive predictive value (PPV), negative predictive value (NPV), precision, area under the receiver operating characteristic curve (AUROC), processing time, and volume of bleeding. Random-effect model and bivariate model were used to pooled independent effect size and diagnostic meta-analysis data, respectively.

RESULTS

A total of 36 original studies were included in this meta-analysis. Pooled results indicated that DL technologies have a comparable performance in intracranial hemorrhage detection and segmentation with high values of sensitivity (0.89, 95% CI: 0.88-0.90), specificity (0.91, 95% CI: 0.89-0.93), AUROC (0.94, 95% CI: 0.93-0.95), PPV (0.92, 95% CI: 0.91-0.93), NPV (0.94, 95% CI: 0.91-0.96), precision (0.83, 95% CI: 0.77-0.90), DSC (0.84, 95% CI: 0.82-0.87). There is no significant difference between manual labeling and DL technologies in hemorrhage quantification (MD 0.08, 95% CI: -5.45-5.60, P =0.98), but the latter takes less process time than manual labeling (WMD 2.26, 95% CI: 1.96-2.56, P =0.001).

CONCLUSION

This systematic review has identified a range of DL algorithms that the performance was comparable to experienced clinicians in hemorrhage lesions identification, segmentation, and quantification but with greater efficiency and reduced cost. It is highly emphasized that multicenter randomized controlled clinical trials will be needed to validate the performance of these tools in the future, paving the way for fast and efficient decision-making during clinical procedure in patients with acute hemorrhagic stroke.

Automatic segmentation of hemorrhagic transformation on follow-up non-contrast CT after acute ischemic stroke

Background

Hemorrhagic transformation (HT) following reperfusion therapies is a serious complication for patients with acute ischemic stroke. Segmentation and quantification of hemorrhage provides critical insights into patients' condition and aids in prognosis. This study aims to automatically segment hemorrhagic regions on follow-up non-contrast head CT (NCCT) for stroke patients treated with endovascular thrombectomy (EVT).

Methods

Patient data were collected from 10 stroke centers across two countries. We propose a semi-automated approach with adaptive thresholding methods, eliminating the need for extensive training data and reducing computational demands. We used Dice Similarity Coefficient (DSC) and Lin's Concordance Correlation Coefficient (Lin's CCC) to evaluate the performance of the algorithm.

Results

A total of 51 patients were included, with 28 Type 2 hemorrhagic infarction (HI2) cases and 23 parenchymal hematoma (PH) cases. The algorithm achieved a mean DSC of 0.66 ± 0.17. Notably, performance was superior for PH cases (mean DSC of 0.73 ± 0.14) compared to HI2 cases (mean DSC of 0.61 ± 0.18). Lin's CCC was 0.88 (95% CI 0.79-0.93), indicating a strong agreement between the algorithm's results and the ground truth. In addition, the algorithm demonstrated excellent processing time, with an average of 2.7 s for each patient case.

Conclusion

To our knowledge, this is the first study to perform automated segmentation of post-treatment hemorrhage for acute stroke patients and evaluate the performance based on the radiological severity of HT. This rapid and effective tool has the potential to assist with predicting prognosis in stroke patients with HT after EVT.

Diagnosis of Alzheimer's disease by joining dual attention CNN and MLP based on structural MRIs, clinical and genetic data

Alzheimer's disease (AD) is an irreversible central nervous degenerative disease, while mild cognitive impairment (MCI) is a precursor state of AD. Accurate early diagnosis of AD is conducive to the prevention and early intervention treatment of AD. Although some computational methods have been developed for AD diagnosis, most employ only neuroimaging, ignoring other data (e.g., genetic, clinical) that may have potential disease information. In addition, the results of some methods lack interpretability. In this work, we proposed a novel method (called DANMLP) of joining dual attention convolutional neural network (CNN) and multilayer perceptron (MLP) for computer-aided AD diagnosis by integrating multi-modality data of the structural magnetic resonance imaging (sMRI), clinical data (i.e., demographics, neuropsychology), and APOE genetic data. Our DANMLP consists of four primary components: (1) the Patch-CNN for extracting the image characteristics from each local patch, (2) the position self-attention block for capturing the dependencies between features within a patch, (3) the channel self-attention block for capturing dependencies of inter-patch features, (4) two MLP networks for extracting the clinical features and outputting the AD classification results, respectively. Compared with other state-of-the-art methods in the 5CV test, DANMLP achieves 93% and 82.4% classification accuracy for the AD vs. MCI and MCI vs. NC tasks on the ADNI database, which is 0.2%∼15.2% and 3.4%∼26.8% higher than that of other five methods, respectively. The individualized visualization of focal areas can also help clinicians in the early diagnosis of AD. These results indicate that DANMLP can be effectively used for diagnosing AD and MCI patients.

Assessment of the Extent of Intracerebral Hemorrhage Using 3D Modeling Technology

The second most common cause of stroke, accounting for 10% of hospital admissions, is intracerebral hemorrhage (ICH), and risk factors include diabetes, smoking, and hypertension. People with intracerebral bleeding experience symptoms that are related to the functions that are managed by the affected part of the brain. Having obtained 15 computed tomography (CT) scans from five patients with ICH, we decided to use three-dimensional (3D) modeling technology to estimate the bleeding volume. CT was performed on admission to hospital, and after one week and two weeks of treatment. We segmented the brain, ventricles, and hemorrhage using semi-automatic algorithms in Slicer 3D, then improved the obtained models in Blender. Moreover, the accuracy of the models was checked by comparing corresponding CT scans with 3D brain model cross-sections. The goal of the research was to examine the possibility of using 3D modeling technology to visualize intracerebral hemorrhage and assess its treatment.

Intracerebral hemorrhage CT scan image segmentation with HarDNet based transformer

Although previous studies conducted on the segmentation of hemorrhage images were based on the U-Net model, which comprises an encoder-decoder architecture, these models exhibit low parameter passing efficiency between the encoder and decoder, large model size, and slow speed. Therefore, to overcome these drawbacks, this study proposes TransHarDNet, an image segmentation model for the diagnosis of intracerebral hemorrhage in CT scan images of the brain. In this model, the HarDNet block is applied to the U-Net architecture, and the encoder and decoder are connected using a transformer block. As a result, the network complexity was reduced and the inference speed improved while maintaining the high performance compared to conventional models. Furthermore, the superiority of the proposed model was verified by using 82,636 CT scan images showing five different types of hemorrhages to train and test the model. Experimental results showed that the proposed model exhibited a Dice coefficient and IoU of 0.712 and 0.597, respectively, in a test set comprising 1200 images of hemorrhage, indicating better performance compared to typical segmentation models such as U-Net, U-Net++, SegNet, PSPNet, and HarDNet. Moreover, the inference time was 30.78 frames per second (FPS), which was faster than all en-coder-decoder-based models except HarDNet.

BBox-Guided Segmentor: Leveraging expert knowledge for accurate stroke lesion segmentation using weakly supervised bounding box prior

Stroke is one of the leading causes of death and disability in the world. Despite intensive research on automatic stroke lesion segmentation from non-invasive imaging modalities including diffusion-weighted imaging (DWI), challenges remain such as a lack of sufficient labeled data for training deep learning models and failure in detecting small lesions. In this paper, we propose BBox-Guided Segmentor, a method that significantly improves the accuracy of stroke lesion segmentation by leveraging expert knowledge. Specifically, our model uses a very coarse bounding box label provided by the expert and then performs accurate segmentation automatically. The small overhead of having the expert provide a rough bounding box leads to large performance improvement in segmentation, which is paramount to accurate stroke diagnosis. To train our model, we employ a weakly-supervised approach that uses a large number of weakly-labeled images with only bounding boxes and a small number of fully labeled images. The scarce fully labeled images are used to train a generator segmentation network, while adversarial training is used to leverage the large number of weakly-labeled images to provide additional learning signals. We evaluate our method extensively using a unique clinical dataset of 99 fully labeled cases (i.e., with full segmentation map labels) and 831 weakly labeled cases (i.e., with only bounding box labels), and the results demonstrate the superior performance of our approach over state-of-the-art stroke lesion segmentation models. We also achieve competitive performance as a SOTA fully supervised method using less than one-tenth of the complete labels. Our proposed approach has the potential to improve stroke diagnosis and treatment planning, which may lead to better patient outcomes.

RU-Net: skull stripping in rat brain MR images after ischemic stroke with rat U-Net

BACKGROUND

Experimental ischemic stroke models play a fundamental role in interpreting the mechanism of cerebral ischemia and appraising the development of pathological extent. An accurate and automatic skull stripping tool for rat brain image volumes with magnetic resonance imaging (MRI) are crucial in experimental stroke analysis. Due to the deficiency of reliable rat brain segmentation methods and motivated by the demand for preclinical studies, this paper develops a new skull stripping algorithm to extract the rat brain region in MR images after stroke, which is named Rat U-Net (RU-Net).

METHODS

Based on a U-shape like deep learning architecture, the proposed framework integrates batch normalization with the residual network to achieve efficient end-to-end segmentation. A pooling index transmission mechanism between the encoder and decoder is exploited to reinforce the spatial correlation. Two different modalities of diffusion-weighted imaging (DWI) and T2-weighted MRI (T2WI) corresponding to two in-house datasets with each consisting of 55 subjects were employed to evaluate the performance of the proposed RU-Net.

RESULTS

Extensive experiments indicated great segmentation accuracy across diversified rat brain MR images. It was suggested that our rat skull stripping network outperformed several state-of-the-art methods and achieved the highest average Dice scores of 98.04% (p < 0.001) and 97.67% (p < 0.001) in the DWI and T2WI image datasets, respectively.

CONCLUSION

The proposed RU-Net is believed to be potential for advancing preclinical stroke investigation and providing an efficient tool for pathological rat brain image extraction, where accurate segmentation of the rat brain region is fundamental.

An Efficient USE-Net Deep Learning Model for Cancer Detection

Breast cancer (BrCa) is the most common disease in women worldwide. Classifying the BrCa image is extremely important for finding BrCa at an earlier stage and monitoring BrCa during treatment. The computer-aided detection methods have been used to interpret BrCa and improve the detection of BrCa during the screening and treatment stages. However, if a new BrCa image is generated for the treatment, it will not classify correctly. The main objective of this research is to classify the BrCa images for newly generated images. The model performs preprocessing, segmentation, feature extraction, and classification. In preprocessing, a hybrid median filtering (HMF) is used to eliminate the noise in the images. The contrast of the images is enhanced using quadrant dynamic histogram equalization (QDHE). Then, ROI segmentation is performed using the USE-Net deep learning model. The CaffeNet model is used for feature extraction on the segmented images, and finally, classification is made using the improved random forest (IRF) with extreme gradient boosting (XGB). The model obtained 97.87% accuracy, 98.45% sensitivity, 95.24% specificity, 98.96% precision, and 98.70% f1-score for ultrasound images. The model gives 98.31% accuracy, 99.29% sensitivity, 90.20% specificity, 98.82% precision, and 99.05% f1-score for mammogram images.

Intracerebral Hemorrhage Segmentation on Noncontrast Computed Tomography Using a Masked Loss Function U-Net Approach

OBJECTIVE

Intracerebral hemorrhage (ICH) volume is a strong predictor of outcome in patients presenting with acute hemorrhagic stroke. It is necessary to segment the hematoma for ICH volume estimation and for computerized extraction of features, such as spot sign, texture parameters, or extravasated iodine content at dual-energy computed tomography. Manual and semiautomatic segmentation methods to delineate the hematoma are tedious, user dependent, and require trained personnel. This article presents a convolutional neural network to automatically delineate ICH from noncontrast computed tomography scans of the head.

METHODS

A model combining a U-Net architecture with a masked loss function was trained on standard noncontrast computed tomography images that were down sampled to 256 × 256 size. Data augmentation was applied to prevent overfitting, and the loss score was calculated using the soft Dice loss function. The Dice coefficient and the Hausdorff distance were computed to quantitatively evaluate the segmentation performance of the model, together with the sensitivity and specificity to determine the ICH detection accuracy.

RESULTS

The results demonstrate a median Dice coefficient of 75.9% and Hausdorff distance of 2.65 pixels in segmentation performance, with a detection sensitivity of 77.0% and specificity of 96.2%.

CONCLUSIONS

The proposed masked loss U-Net is accurate in the automatic segmentation of ICH. Future research should focus on increasing the detection sensitivity of the model and comparing its performance with other model architectures.

Artificial intelligence for localization of the acute ischemic stroke by non-contrast computed tomography

A non-contrast cranial computer tomography (ncCT) is often employed for the diagnosis of the early stage of the ischemic stroke. However, the number of false negatives is high. More accurate results are obtained by an MRI. However, the MRI is not available in every hospital. Moreover, even if it is available in the clinic for the routine tests, emergency often does not have it. Therefore, this paper proposes an end-to-end framework for detection and segmentation of the brain infarct on the ncCT. The computer tomography perfusion (CTp) is used as the ground truth. The proposed ensemble model employs three deep convolution neural networks (CNNs) to process three end-to-end feature maps and a hand-craft features characterized by specific contra-lateral features. To improve the accuracy of the detected infarct area, the spatial dependencies between neighboring slices are employed at the postprocessing step. The numerical experiments have been performed on 18 ncCT-CTp paired stroke cases (804 image-pairs). The leave-one-out approach is applied for evaluating the proposed method. The model achieves 91.16% accuracy, 65.15% precision, 77.44% recall, 69.97% F1 score, and 0.4536 IoU.

U-net Models Based on Computed Tomography Perfusion Predict Tissue Outcome in Patients with Different Reperfusion Patterns

Evaluation of cerebral perfusion is important for treatment selection in patients with acute large vessel occlusion (LVO). To assess ischemic core and tissue at risk more accurately, we developed a deep learning model named U-net using computed tomography perfusion (CTP) images. A total of 110 acute ischemic stroke patients undergoing endovascular treatment with major reperfusion (≥ 80%) or minimal reperfusion (≤ 20%) were included. Using baseline CTP, we developed two U-net models: one model in major reperfusion group to identify infarct core; the other in minimal reperfusion group to identify tissue at risk. The performance of fixed-thresholding methods was compared with that of U-net models. In the major reperfusion group, the model estimated infarct core with a Dice score coefficient (DSC) of 0.61 and an area under the curve (AUC) of 0.92, while fixed-thresholding methods had a DSC of 0.52. In the minimal reperfusion group, the model estimated tissue at risk with a DSC of 0.67 and an AUC of 0.93, while fixed-thresholding methods had a DSC of 0.51. In both groups, excellent volumetric consistency (intraclass correlation coefficient was 0.951 in major reperfusion and 0.746 in minimal reperfusion) was achieved between the estimated lesion and the actual lesion volume. Thus, in patients with anterior LVO, the CTP-based U-net models were able to identify infarct core and tissue at risk on baseline CTP superior to fixed-thresholding methods, providing individualized prediction of final lesion in patients with different reperfusion patterns.

Can Artificial Intelligence Be Applied to Diagnose Intracerebral Hemorrhage under the Background of the Fourth Industrial Revolution? A Novel Systemic Review and Meta-Analysis

Aim

We intended to provide the clinical evidence that artificial intelligence (AI) could be used to assist doctors in the diagnosis of intracerebral hemorrhage (ICH).

Methods

Studies published in 2021 were identified after the literature search of PubMed, Embase, and Cochrane. Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) was used to perform the quality assessment of studies. Data extraction of diagnosis effect included accuracy (ACC), sensitivity (SEN), specificity (SPE), positive predictive value (PPV), negative predictive value (NPV), area under curve (AUC), and Dice scores (Dices). The pooled effect with its 95% confidence interval (95%CI) was calculated by the random effects model. I-Square (I 2) was used to test heterogeneity. To check the stability of the overall results, sensitivity analysis was conducted by recalculating the pooled effect of the remaining studies after omitting the study with the highest quality or the random effects model was switched to the fixed effects model. Funnel plot was used to evaluate publication bias. To reduce heterogeneity, recalculating the pooled effect of the remaining studies after omitting the study with the lowest quality or perform subgroup analysis.

Results

Twenty-five diagnostic tests of ICH via AI and doctors with overall high quality were included. Pooled ACC, SEN, SPE, PPV, NPV, AUC, and Dices were 0.88 (0.83∼0.93), 0.85 (0.81∼0.89), 0.90 (0.88∼0.92), 0.80 (0.75∼0.85), 0.93 (0.91∼0.95), 0.84 (0.80∼0.89), and 0.90 (0.85∼0.95), respectively. There was no publication bias. All of results were stable as revealed by sensitivity analysis and were accordant as outcomes via subgroups analysis.

Conclusion

Under the background of the fourth industrial revolution, AI might be an effective and efficient tool to assist doctors in the clinical diagnosis of ICH.

Improvement of automatic ischemic stroke lesion segmentation in CT perfusion maps using a learned deep neural network

Acute ischemic stroke is one of the leading causes of death and long-term disability worldwide. It occurs when a blood clot blocks an artery that supplies blood to the brain tissue. Segmentation of acute ischemic stroke lesions plays a vital role to improve diagnosis, outcome assessment, and treatment planning. The current standard approach of ischemic stroke lesion segmentation is simply thresholding the Computed Tomography Perfusion (CTP) maps, i.e., quantitative feature maps created by summarizing CTP time sequence scans. However, this approach is not precise enough (its Dice similarity score is only around 50%) to be used in practice. Numerous machine learning-based techniques have recently been proposed to improve the accuracy of ischemic stroke lesion segmentation. Although they have achieved remarkable results, they still need to be improved before they can be used in actual practice. This paper presents a novel deep learning-based technique, MutiRes U-Net, for the segmentation of ischemic stroke lesions in CTP maps. MultiRes U-Net is a modified version of the original U-Net that is re-designed to be robust to segment the objects in different scales and unusual appearances. Additionally, in this paper, we propose to enrich the input CTP maps by using their contra-lateral and corresponding Tmax images. We evaluated the proposed method using the ISLES challenge 2018 dataset. As compared to the state-of-the-art methods, the results show an improvement in segmentation task accuracy. The dice similarity score (DSC) was 68%, the Jaccard score was 57.13%, and the mean absolute volume error was 22.62(ml).