Prostate Segmentation Research Articles

Impact of uncertainty quantification through conformal prediction on volume assessment from deep learning-based MRI prostate segmentation

ObjectivesTo estimate the uncertainty of a deep learning (DL)-based prostate segmentation algorithm through conformal prediction (CP) and to assess its effect on the calculation of the prostate volume (PV) in patients at risk of prostate cancer (PC).MethodsThree-hundred seventy-seven multi-center 3-Tesla axial T2-weighted exams from biopsied males (66.64 ±\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\pm$$\\end{document} 7.47 years) at risk of PC were retrospectively included in the study. Assessment of PV based on PI-RADS 2.1 ellipsoid formula (PVref\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${{{\\rm{PV}}}}_{{ref}}$$\\end{document}) was available for included patients. Prostate segmentations were obtained from a DL model and used to calculate the PV (PVDL\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${{{\\rm{PV}}}}_{{DL}}$$\\end{document}). CP was applied at a confidence level of 85% to flag unreliable pixel segmentations of the DL model. Subsequently, the PV (PVCP\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${{{\\rm{PV}}}}_{{CP}}$$\\end{document}) was calculated when disregarding uncertain pixel segmentations. Agreement between PVDL\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${{{\\rm{PV}}}}_{{DL}}$$\\end{document} and PVCP\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${{{\\rm{PV}}}}_{{CP}}$$\\end{document} was evaluated against the reference standard PVref\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${{{\\rm{PV}}}}_{{ref}}$$\\end{document}. Intraclass correlation coefficient (ICC) and Bland–Altman plots were used to assess the agreement. The relative volume difference (RVD) was used to evaluate the PV calculation accuracy, and the Wilcoxon Signed-Rank Test was used to assess statistical differences. A p-value < 0.05 was considered statistically significant.ResultsConformal prediction significantly reduced RVD when compared to the DL algorithm (RVD = − 2.81 ±\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\pm$$\\end{document} 8.85 and RVD = −8.01 ±\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\pm$$\\end{document} 11.50). PVCP\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${{{\\rm{PV}}}}_{{CP}}$$\\end{document} showed a significantly larger agreement than PVDL\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${{{\\rm{PV}}}}_{{DL}}$$\\end{document} when using the reference standard PVref\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${{{\\rm{PV}}}}_{{ref}}$$\\end{document} (mean difference (95% limits of agreement) PVCP\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${{{\\rm{PV}}}}_{{CP}}$$\\end{document}: 1.27 mL (− 13.64; 16.17 mL) PVDL\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${{{\\rm{PV}}}}_{{DL}}$$\\end{document}: 6.07 mL (− 14.29; 26.42 mL)), with an excellent ICC (PVCP\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${{{\\rm{PV}}}}_{{CP}}$$\\end{document}: 0.97 (95% CI: 0.97 to 0.98)).ConclusionUncertainty quantification through CP increases the accuracy and reliability of DL-based PV assessment in patients at risk of PC.Critical relevance statementConformal prediction can flag uncertain pixel predictions of DL-based prostate MRI segmentation at a desired confidence level, increasing the reliability and safety of prostate volume assessment in patients at risk of prostate cancer.Key PointsConformal prediction can flag uncertain pixel predictions of prostate segmentations at a user-defined confidence level.Deep learning with conformal prediction shows high accuracy in prostate volumetric assessment.Agreement between automatic and ellipsoid-derived volume was significantly larger with conformal prediction.Graphical

Masked Image Modeling Meets Self-Distillation: A Transformer-Based Prostate Gland Segmentation Framework for Pathology Slides

Masked Image Modeling Meets Self-Distillation: A Transformer-Based Prostate Gland Segmentation Framework for Pathology Slides

Enhancing the diagnostic capacity of [18F]PSMA-1007 PET/MRI in primary prostate cancer staging with artificial intelligence and semi-quantitative DCE: an exploratory study

BackgroundTo investigate the ability of artificial intelligence (AI)-based and semi-quantitative dynamic contrast enhanced (DCE) multiparametric MRI (mpMRI), performed within [18F]-PSMA-1007 PET/MRI, in differentiating benign from malignant prostate tissues in patients with primary prostate cancer (PC).ResultsA total of seven patients underwent whole-body [18F]-PSMA-1007 PET/MRI examinations including a pelvic mpMRI protocol with T2w, diffusion weighted imaging (DWI) and DCE image series. Conventional analysis included visual reading of PET/MRI images and Prostate Imaging Reporting & Data System (PI-RADS) scoring of the prostate. On the prostate level, we performed manual segmentations for time-intensity curve parameter formation and semi-quantitative analysis based on DCE segmentation data of PC-suspicious lesions. Moreover, we applied a recently introduced deep learning (DL) pipeline previously trained on 1010 independent MRI examinations with systematic biopsy-enhanced histopathological targeted biopsy lesion ground truth in order to perform AI-based lesion detection, prostate segmentation and derivation of a deep learning PI-RADS score. DICE coefficients between manual and automatic DL-acquired segmentations were compared. On patient-based analysis, PET/MRI revealed PC-suspicious lesions in the prostate gland in 6/7 patients (Gleason Score-GS ≥ 7b) that were histologically confirmed. Four of these patients also showed lymph node metastases, while two of them had bone metastases. One patient with GS 6 showed no PC-suspicious lesions. Based on DCE segmentations, a distinction between PC-suspicious and normal appearing tissue was feasible with the parameters fitted maximum contrast ratio (FMCR) and wash-in-slope. DICE coefficients (manual vs. deep learning) were comparable with literature values at a mean of 0.44. Further, the DL pipeline could identify the intraprostatic PC-suspicious lesions in all six patients with clinically significant PC.ConclusionFirstly, semi-quantitative DCE analysis based on manual segmentations of time-intensity curves was able to distinguish benign from malignant tissues. Moreover, DL analysis of the MRI data could detect clinically significant PC in all cases, demonstrating the feasibility of AI-supported approaches in increasing diagnostic certainty of PSMA-radioligand PET/MRI.

Multi-task Bayesian model combining FDG-PET/CT imaging and clinical data for interpretable high-grade prostate cancer prognosis.

We propose a fully automatic multi-task Bayesian model, named Bayesian Sequential Network(BSN), for predicting high-grade(Gleason 8) prostate cancer(PCa) prognosis using pre-prostatectomy FDG-PET/CT images and clinical data. BSN performs one classification task and five survival tasks: predicting lymph node invasion (LNI), biochemical recurrence-free survival (BCR-FS), metastasis-free survival, definitive androgen deprivation therapy-free survival, castration-resistant PCa-free survival, and PCa-specific survival(PCSS). Experiments are conducted using a dataset of 295patients. BSN outperforms widely used nomograms on all tasks except PCSS, leveraging multi-task learning and imaging data. BSN also provides automated prostate segmentation, uncertainty quantification, personalized feature-based explanations, and introduces dynamic predictions, a novel approach that relies on short-term outcomes to refine long-term prognosis. Overall, BSN shows great promise in its ability to exploit imaging and clinicopathological data to predict poor outcome patients that need treatment intensification with loco-regional or systemic adjuvant therapy for high-risk PCa.

Gradient-Guided Network With Fourier Enhancement for Glioma Segmentation in Multimodal 3D MRI.

Glioma segmentation is a crucial task in computer-aided diagnosis, requiring precise discrimination between lesions and normal tissue at the pixel level. Popular methods neglect crucial edge information, leading to inaccurate contour delineation. Moreover, global information has been proven beneficial for segmentation. The feature representations extracted by convolution neural networks often struggle with local-related information owing to the limited receptive fields. To address these issues, we propose a novel edge-aware segmentation network that incorporates a dual-path gradient-guided training strategy with Fourier edge-enhancement for precise glioma segmentation, a.k.a. GFNet. First, we introduce a Dual-path Gradient-guided Training strategy (DGT) based on a Siamese network guiding the optimizing direction of one path by the gradient from the other path. DGT pays attention to the indistinguishable pixels with large weight-updating gradient, such as the pixels near the boundary, to guide the network training, addressing hard samples. Second, to further perceive the edge information, we derive a Fourier Edge-enhancement Module (FEM) to augment feature edges with high-frequency representations from the spectral domain, providing global information and edge details. Extensive experiments on public glioma segmentation datasets, BraTS2020 and Medical Segmentation Decathlon (MSD) glioma and prostate segmentation, demonstrate that GFNet achieves competitive performance compared to other state-of-the-art methods, both qualitatively and quantitatively.

MDDU-Net: A multi-scale dense connectivity hybrid dilated convolutional U-Net for segmentation in prostate ultrasound images

Ultrasound is one of the most commonly used imaging tools in prostate biopsy and brachytherapy. However, due to issues such as blurred image boundaries, similar intensity distributions, and noise, accurate segmentation of the prostate gland has been challenged. We propose a multi-scale dense connectivity hybrid dilated convolutional U-Net (MDDU-Net) network model segmentation of 2D prostate ultrasound images to improve the segmentation accuracy. Our proposed hybrid dilated convolution (HDC) module consists of standard and dilated convolution, which can expand the receptive field of the network, focus on global information, capture more features, and improve the learning ability of the model. Introducing dense connectivity (Dense) maximizes the flow of information between layers, retains more details, and helps mitigate gradient vanishing. The output features of each convolution layer in the bottleneck and decoder are fused using a multi-scale fusion block (MSFB) to obtain a feature map with richer semantic and detailed information. A dense skip connection provides more raw information to the decoder. To verify the superiority of our proposed method, we performed a 5-fold cross-validation, quantitatively analyzed it using five commonly used medical image evaluation metrics, and compared it with several state-of-the-art segmentation methods. The results show that our method performs better in prostate ultrasound image segmentation and can achieve more accurate prostate segmentation.

Semantic Segmentation of the Prostate Based on Onefold and Joint Multimodal Medical Images Using YOLOv4 and U-Net

Magnetic Resonance Imaging is increasing in importance in prostate cancer diagnosis due to the high accuracy and quality of the examination procedure. However, this process requires a time-consuming analysis of the results. Currently, machine vision is widely used in many areas. It enables automation and support in radiological studies. Successful detection of primary prostate tumors depends on the effective segmentation of the prostate itself. At times, a CT scan may be performed; alternatively, MRI may be the selected option. The data always reach a bottleneck stage. This paper presents the effective training of deep learning models to segment the prostate based on onefold and multimodal medical images. This approach supports the computer-aided diagnosis (CAD) system for radiologists as the first step in cancer exams. A comparison of two approaches designed for prostate segmentation is described. The first combines YOLOv4, the object detection neural network, and U-Net for a semantic segmentation based on onefold modality MRI images. The second presents the same method trained on multimodal images—a CT and MRI mixed dataset. The learning process was carried out in a cloud environment using GPU cards. The experiments are based on data from 120 patients who have undergone MRI and CT examinations. Several metrics evaluated the trained models. In the prostate semantic segmentation process, better results were achieved by mixed MRI with CT datasets. The best model achieved the value of 0.9685 for the Sørensen–Dice coefficient for the threshold value of 0.6.

Achieving accurate prostate auto-segmentation on CT in the absence of MR imaging

BackgroundMagnetic resonance imaging (MRI) is considered the gold standard for prostate segmentation. Computed tomography (CT)-based segmentation is prone to observer bias, potentially overestimating the prostate volume by ∼ 30 % compared to MRI. However, MRI accessibility is challenging for patients with contraindications or in rural areas globally with limited clinical resources. PurposeThis study investigates the possibility of achieving MRI-level prostate auto-segmentation accuracy using CT-only input via a deep learning (DL) model trained with CT-MRI registered segmentation. Methods and MaterialsA cohort of 111 definitive prostate radiotherapy patients with both CT and MRI images was retrospectively grouped into training (n = 37) and validation (n = 20) (where reference contours were derived from CT-MRI registration), and testing (n = 54) sets. Two commercial DL models were benchmarked against the reference contours in the training and validation sets. A custom DL model was incrementally retrained using the training dataset, quantitatively evaluated on the validation dataset, and qualitatively assessed by two different physician groups on the validation and testing datasets. A contour quality assurance (QA) model, established from the proposed model on the validation dataset, was applied to the test group to identify potential errors, confirmed by human visual inspection. ResultsTwo commercial models exhibited large deviations in the prostate apex with CT-only input (median: 0.77/0.78 for Dice similarity coefficient (DSC), and 0.80 cm/0.83 cm for 95 % directed Hausdorff Distance (HD95), respectively). The proposed model demonstrated superior geometric similarity compared to commercial models, particularly in the apex region, with improvements of 0.05/0.17 cm and 0.06/0.25 cm in median DSC/HD95, respectively. Physician evaluation on MRI-CT registration data rated 69 %-78 % of the proposed model’s contours as clinically acceptable without modifications. Additionally, 73 % of cases flagged by the contour quality assurance (QA) model were confirmed via visual inspection. ConclusionsThe proposed incremental learning strategy based on CT-MRI registration information enhances prostate segmentation accuracy when MRI availability is limited clinically.

Advancements in prostate zone segmentation: integrating attention mechanisms into the nnU-Net framework

Abstract Prostate cancer is one of the most lethal cancers in the world. Early diagnosis is essential for successful treatment of prostate cancer. Segmentation of prostate zones in magnetic resonance images is an important task in the diagnosis of prostate cancer. Currently, the state-of-the-art method for this task is no-new U-Net. In this paper, a method to incorporate the attention U-Net architecture into no-new U-Net is proposed and compared with a classical U-net architecture as research. The experimental results indicate that there is no significant statistical difference between the proposed modification of no-new U-Net with the generalizability of the attention mechanism or the ability to achieve more accurate results. Moreover, two novel workflows are proposed for prostate segmentation, transitional zone segmentation and peripheral zone calculation workflow, and separate models for peripheral zone and transitional zone segmentation workflow. These workflows are compared with a baseline single peripheral zone and transitional zone segmentation model workflow. The experimental results indicate that separate models for peripheral zone and transitional zone segmentation workflow generalizes better than the baseline between data sets of different sources. In peripheral zone segmentation separate models for peripheral zone and transitional zone segmentation workflow achieves 1.9% higher median Dice score coefficient than the baseline workflow when using the attention U-Net architecture and 5.6% higher median Dice score coefficient when using U-Net architecture. Moreover, in transitional zone segmentation separate models for peripheral zone and transitional zone segmentation workflow achieves 0.4% higher median Dice score coefficient than the baseline workflow when using the attention U-Net architecture and 0.7% higher median Dice score coefficient when using U-Net architecture. Meanwhile, prostate segmentation, transitional zone segmentation and peripheral zone calculation workflow generalizes worse than the baseline. In peripheral zone segmentation prostate segmentation, transitional zone segmentation and peripheral zone calculation workflow achieves 4.6% lower median Dice score coefficient than the baseline workflow when using the attention U-Net architecture and 3.6% lower median Dice score coefficient when using U-Net architecture. In transitional zone segmentation prostate segmentation, transitional zone segmentation and peripheral zone calculation workflow achieves a similar median Dice score coefficient to the baseline workflow.

MixUNETR: A U-shaped network based on W-MSA and depth-wise convolution with channel and spatial interactions for zonal prostate segmentation in MRI

Magnetic resonance imaging (MRI) plays a pivotal role in diagnosing and staging prostate cancer. Precise delineation of the peripheral zone (PZ) and transition zone (TZ) within prostate MRI is essential for accurate diagnosis and subsequent artificial intelligence-driven analysis. However, existing segmentation methods are limited by ambiguous boundaries, shape variations and texture complexities between PZ and TZ. Moreover, they suffer from inadequate modeling capabilities and limited receptive fields. To address these challenges, we propose a Enhanced MixFormer, which integrates window-based multi-head self-attention (W-MSA) and depth-wise convolution with parallel design and cross-branch bidirectional interaction. We further introduce MixUNETR, which use multiple Enhanced MixFormers as encoder to extract features from both PZ and TZ in prostate MRI. This augmentation effectively enlarges the receptive field and enhances the modeling capability of W-MSA, ultimately improving the extraction of both global and local feature information from PZ and TZ, thereby addressing mis-segmentation and challenges in delineating boundaries between them. Extensive experiments were conducted, comparing MixUNETR with several state-of-the-art methods on the Prostate158, ProstateX public datasets and private dataset. The results consistently demonstrate the accuracy and robustness of MixUNETR in MRI prostate segmentation. Our code of methods is available at https://github.com/skyous779/MixUNETR.git.

Multi-label semantic segmentation of magnetic resonance images of the prostate gland

Prostate segmentation is a substantial factor in the diagnostic pathway of suspicious prostate lesions. Medical doctors are assisted by computer-aided detection and diagnosis systems systems and methods derived from artificial intelligence deep learning-based systems have to be trained on existing data. Especially freely available labeled prostate magnetic resonance imaging data is rare. With regard to this problem, we show a method to combine two existing small datasets to form a bigger one. We present a data processing pipeline consisting of a cascaded network architecture that is able to perform multi-label semantic segmentation, hence, capable of classifying each pixel in a T2\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\ extrm{T}_{2}$$\\end{document}-weighted image not only to one class but to a subset of the prostate zones and classes of interest. This delivers richer information such as overlapping zones that are key to medical radiological examination. Additionally, we describe how to integrate expert knowledge in our deep learning system. To increase data variety for training and evaluation we use image augmentation on our two datasets—a freely available dataset and our new open-source dataset. To combine the datasets we denoise the contourings in our dataset by using an effective yet simple algorithm based on standard computer vision methods only. The performance of the presented methodology is compared and evaluated using the dice score metric and 5-fold cross-validation on all datasets. Although we trained on tiny datasets our method achieves excellent segmentation quality and is even able to detect prostate cancer. Our method to combine the two datasets reduces segmentation errors and increases data variety. The proposed architecture significantly improves performance by including expert knowledge via feature-map concatenation. On the initiative for collaborative computer vision benchmarking dataset we achieve on average dice scores of approximately 91% for the whole prostate gland, 67% for the peripheral zone and 75% for the prostate central gland. We find that image augmentation except contrast limited adaptive histogram equalisation did not have much influence on the segmentation quality. Derived and enhanced from existing methods we present an approach that is able to deliver multi-label semantic segmentation results for prostate magnetic resonance imaging. This approach is simple and could be applied to other applications of deep learning as well. It improves the segmentation results by a large margin. Once tweaked to the data, our denoising and combination algorithm delivers robust and accurate results even on data with segmentation errors.

Adaptive wavelet-VNet for single-sample test time adaptation in medical image segmentation.

In medical image segmentation, a domain gap often exists between training and testing datasets due to different scanners or imaging protocols, which leads to performance degradation in deep learning-based segmentation models. Given the high cost of manual labeling and the need for privacy protection, it is often challenging to annotate the testing (target) domain data for model fine-tuning or to collect data from different domains to train domain generalization models. Therefore, using only unlabeled target domain data for test-time adaptation (TTA) presents a more practical but challenging solution. To improve the segmentation accuracy of deep learning-based models on unseen datasets, and especially to enhance the efficiency and stability of TTA for individual samples from heterogeneous domains. In this study, we proposed to dynamically adapt a wavelet-VNet (WaVNet) to unseen target domains with a hybrid objective function, based on each unlabeled test sample during the test time. We embedded multiscale wavelet coefficients into a V-Net encoder and adaptively adjusted the spatial and spectral features according to the input, and the model parameters were optimized by three loss functions. We integrated a shape-aware loss to focus on the foreground segmentations, a Refine loss to correct the incomplete and noisy segmentations caused by domain shifts, and an entropy loss to promote the global consistency of the segmentations. We evaluated the proposed method on multidomain liver and prostate segmentation datasets to assess its advantages over other TTA methods. For the source domain model training of the liver dataset, we used 15 3D MR image samples for training and 5 for validation. Correspondingly, for the prostate dataset, we used 22 3D MR image samples for training and 7 for validation. In the target domain, we used a single 3D MR image sample for adaptation and testing. The total number of testing samples is 60 in the liver dataset (for 3 different domains) and 116 in the prostate dataset (for 6 different domains). The proposed method showed the highest segmentation accuracy among all methods, achieving a mean(±SD) Dice coefficient (DSC) of 78.10±5.23% and a mean 95th Hausdorff distance (HD95) of 15.52±5.84mm on the liver dataset; and a mean DSC of 80.02±3.89% and a mean HD95 of 9.18±3.47mm on the prostate dataset. The DSC is 11.67% (in absolute terms) and 15.27% higher than that of the baseline (no adaptation) method, for the liver and the prostate datasets, respectively. The proposed adaptive WaVNet enhanced the image segmentation accuracy from unseen domains during the test time via unsupervised learning and multi-objective optimization. It can benefit clinical applications where data are scarce or with changing data distributions, including online adaptive radiotherapy. The code will be released at: https://github.com/sanny1226/WaVNet.

Leveraging SAM for automatic prostate segmentation on micro-ultrasound images

Purpose: Medical image segmentation models are essential for efficiently diagnosing prostate cancer. Current models for segmentation of micro ultrasound images do not utilize foundation models, or geometric and spatial data from the ultrasound image. We aim to leverage the Segment Anything Model (SAM) as a pretrained backbone to create a fully automatic prostate segmentation model and investigate prompting with positonal information such as the slice frame number and previous segmentations. Methods: The Segment Anything Model (SAM) was fine-tuned on Micro-Ultrasound images1 and adapted for the context of clinical prostate segmentation. We explored different fine-tuning methods and prompting combinations fit for automatic segmentation. Dice coefficient (DSC) and Hausdorff 95% distance (HD95) were used as evaluation metrics to compare our model against past models. Results: In comparison to the state of the art models, SliceTrack-SAM improved the mean Dice coefficient from the MicroSegNet2 model (93.1) to 94.3, and reduced the Hausdorff distance from the nnU-Net model (1.09 mm) to 0.81 mm. Conclusion: In summary, using a fully-finetuned SAM, improves prostate segmentation accuracy. In addition, prompting with geometric and spatial data derived from ultrasound images shows potential to enhance segmentation accuracy, particularly on difficult datasets.

Deep Learning Features Can Improve Radiomics-Based Prostate Cancer Aggressiveness Prediction

PURPOSE Emerging evidence suggests that the use of artificial intelligence can assist in the timely detection and optimization of therapeutic approach in patients with prostate cancer. The conventional perspective on radiomics encompassing segmentation and the extraction of radiomic features considers it as an independent and sequential process. However, it is not necessary to adhere to this viewpoint. In this study, we show that besides generating masks from which radiomic features can be extracted, prostate segmentation and reconstruction models provide valuable information in their feature space, which can improve the quality of radiomic signatures models for disease aggressiveness classification. MATERIALS AND METHODS We perform 2,244 experiments with deep learning features extracted from 13 different models trained using different anatomic zones and characterize how modeling decisions, such as deep feature aggregation and dimensionality reduction, affect performance. RESULTS While models using deep features from full gland and radiomic features consistently lead to improved disease aggressiveness prediction performance, others are detrimental. Our results suggest that the use of deep features can be beneficial, but an appropriate and comprehensive assessment is necessary to ensure that their inclusion does not harm predictive performance. CONCLUSION The study findings reveal that incorporating deep features derived from autoencoder models trained to reconstruct the full prostate gland (both zonal models show worse performance than radiomics only models), combined with radiomic features, often lead to a statistically significant increase in model performance for disease aggressiveness classification. Additionally, the results also demonstrate that the choice of feature selection is key to achieving good performance, with principal component analysis (PCA) and PCA + relief being the best approaches and that there is no clear difference between the three proposed latent representation extraction techniques.

A mixed Mamba U-net for prostate segmentation in MR images

The diagnosis of early prostate cancer depends on the accurate segmentation of prostate regions in magnetic resonance imaging (MRI). However, this segmentation task is challenging due to the particularities of prostate MR images themselves and the limitations of existing methods. To address these issues, we propose a U-shaped encoder-decoder network MM-UNet based on Mamba and CNN for prostate segmentation in MR images. Specifically, we first proposed an adaptive feature fusion module based on channel attention guidance to achieve effective fusion between adjacent hierarchical features and suppress the interference of background noise. Secondly, we propose a global context-aware module based on Mamba, which has strong long-range modeling capabilities and linear complexity, to capture global context information in images. Finally, we propose a multi-scale anisotropic convolution module based on the principle of parallel multi-scale anisotropic convolution blocks and 3D convolution decomposition. Experimental results on two public prostate MR image segmentation datasets demonstrate that the proposed method outperforms competing models in terms of prostate segmentation performance and achieves state-of-the-art performance. In future work, we intend to enhance the model's robustness and extend its applicability to additional medical image segmentation tasks.

A Comparative Analysis of U-Net and Vision Transformer Architectures in Semi-Supervised Prostate Zonal Segmentation.

The precise segmentation of different regions of the prostate is crucial in the diagnosis and treatment of prostate-related diseases. However, the scarcity of labeled prostate data poses a challenge for the accurate segmentation of its different regions. We perform the segmentation of different regions of the prostate using U-Net- and Vision Transformer (ViT)-based architectures. We use five semi-supervised learning methods, including entropy minimization, cross pseudo-supervision, mean teacher, uncertainty-aware mean teacher (UAMT), and interpolation consistency training (ICT) to compare the results with the state-of-the-art prostate semi-supervised segmentation network uncertainty-aware temporal self-learning (UATS). The UAMT method improves the prostate segmentation accuracy and provides stable prostate region segmentation results. ICT plays a more stable role in the prostate region segmentation results, which provides strong support for the medical image segmentation task, and demonstrates the robustness of U-Net for medical image segmentation. UATS is still more applicable to the U-Net backbone and has a very significant effect on a positive prediction rate. However, the performance of ViT in combination with semi-supervision still requires further optimization. This comparative analysis applies various semi-supervised learning methods to prostate zonal segmentation. It guides future prostate segmentation developments and offers insights into utilizing limited labeled data in medical imaging.

MA-SAM: Modality-agnostic SAM adaptation for 3D medical image segmentation

The Segment Anything Model (SAM), a foundation model for general image segmentation, has demonstrated impressive zero-shot performance across numerous natural image segmentation tasks. However, SAM’s performance significantly declines when applied to medical images, primarily due to the substantial disparity between natural and medical image domains. To effectively adapt SAM to medical images, it is important to incorporate critical third-dimensional information, i.e., volumetric or temporal knowledge, during fine-tuning. Simultaneously, we aim to harness SAM’s pre-trained weights within its original 2D backbone to the fullest extent. In this paper, we introduce a modality-agnostic SAM adaptation framework, named as MA-SAM, that is applicable to various volumetric and video medical data. Our method roots in the parameter-efficient fine-tuning strategy to update only a small portion of weight increments while preserving the majority of SAM’s pre-trained weights. By injecting a series of 3D adapters into the transformer blocks of the image encoder, our method enables the pre-trained 2D backbone to extract third-dimensional information from input data. We comprehensively evaluate our method on five medical image segmentation tasks, by using 11 public datasets across CT, MRI, and surgical video data. Remarkably, without using any prompt, our method consistently outperforms various state-of-the-art 3D approaches, surpassing nnU-Net by 0.9%, 2.6%, and 9.9% in Dice for CT multi-organ segmentation, MRI prostate segmentation, and surgical scene segmentation respectively. Our model also demonstrates strong generalization, and excels in challenging tumor segmentation when prompts are used. Our code is available at: https://github.com/cchen-cc/MA-SAM.

Prostate Segmentation in MRI Images using Transfer Learning based Mask RCNN.

The second highest cause of death among males is Prostate Cancer (PCa) in America. Over the globe, it's the usual case in men, and the annual PCa ratio is very surprising. Identical to other prognosis and diagnostic medical systems, deep learning-based automated recognition and detection systems (i.e., Computer Aided Detection (CAD) systems) have gained enormous attention in PCA. These paradigms have attained promising results with a high segmentation, detection, and classification accuracy ratio. Numerous researchers claimed efficient results from deep learning-based approaches compared to other ordinary systems that utilized pathological samples. This research is intended to perform prostate segmentation using transfer learning-based Mask R-CNN, which is consequently helpful in prostate cancer detection. Lastly, limitations in current work, research findings, and prospects have been discussed.

314 Development of an In-House Deep Learning Model for Prostate Segmentation in Radiotherapy Planning

314 Development of an In-House Deep Learning Model for Prostate Segmentation in Radiotherapy Planning

Deep-learning-based segmentation using individual patient data on prostate cancer radiation therapy.

Organ-at-risk segmentation is essential in adaptive radiotherapy (ART). Learning-based automatic segmentation can reduce committed labor and accelerate the ART process. In this study, an auto-segmentation model was developed by employing individual patient datasets and a deep-learning-based augmentation method for tailoring radiation therapy according to the changes in the target and organ of interest in patients with prostate cancer. Two computed tomography (CT) datasets with well-defined labels, including contoured prostate, bladder, and rectum, were obtained from 18 patients. The labels of the CT images captured during radiation therapy (CT2nd) were predicted using CT images scanned before radiation therapy (CT1st). From the deformable vector fields (DVFs) created by using the VoxelMorph method, 10 DVFs were extracted when each of the modified CT and CT2nd images were deformed and registered to the fixed CT1st image. Augmented images were acquired by utilizing 110 extracted DVFs and spatially transforming the CT1st images and labels. An nnU-net autosegmentation network was trained by using the augmented images, and the CT2nd label was predicted. A patient-specific model was created for 18 patients, and the performances of the individual models were evaluated. The results were evaluated by employing the Dice similarity coefficient (DSC), average Hausdorff distance, and mean surface distance. The accuracy of the proposed model was compared with those of models trained with large datasets. Patient-specific models were developed successfully. For the proposed method, the DSC values of the actual and predicted labels for the bladder, prostate, and rectum were 0.94 ± 0.03, 0.84 ± 0.07, and 0.83 ± 0.04, respectively. We demonstrated the feasibility of automatic segmentation by employing individual patient datasets and image augmentation techniques. The proposed method has potential for clinical application in automatic prostate segmentation for ART.