Domain adaptation for segmentation of critical structures for prostate cancer therapy.
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ABSTRACT:
SUBMITTER: Meyer A
PROVIDER: S-EPMC8169882 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:We present an adversarial domain adaptation based deep learning approach for automatic tumor segmentation from T2-weighted MRI. Our approach is composed of two steps: (i) a tumor-aware unsupervised cross-domain adaptation (CT to MRI), followed by (ii) semi-supervised tumor segmentation using Unet trained with synthesized and limited number of original MRIs. We introduced a novel target specific loss, called tumor-aware loss, for unsupervised cross-domain adaptation that helps to preserve tumors on synthesized MRIs produced from CT images. In comparison, state-of-the art adversarial networks trained without our tumor-aware loss produced MRIs with ill-preserved or missing tumors. All networks were trained using labeled CT images from 377 patients with non-small cell lung cancer obtained from the Cancer Imaging Archive and unlabeled T2w MRIs from a completely unrelated cohort of 6 patients with pre-treatment and 36 on-treatment scans. Next, we combined 6 labeled pre-treatment MRI scans with the synthesized MRIs to boost tumor segmentation accuracy through semi-supervised learning. Semi-supervised training of cycle-GAN produced a segmentation accuracy of 0.66 computed using Dice Score Coefficient (DSC). Our method trained with only synthesized MRIs produced an accuracy of 0.74 while the same method trained in semi-supervised setting produced the best accuracy of 0.80 on test. Our results show that tumor-aware adversarial domain adaptation helps to achieve reasonably accurate cancer segmentation from limited MRI data by leveraging large CT datasets.
| S-EPMC6169798 | biostudies-literature
Project description:Automated cellular instance segmentation is a process utilized for accelerating biological research for the past two decades, and recent advancements have produced higher quality results with less effort from the biologist. Most current endeavors focus on completely cutting the researcher out of the picture by generating highly generalized models. However, these models invariably fail when faced with novel data, distributed differently than the ones used for training. Rather than approaching the problem with methods that presume the availability of large amounts of target data and computing power for retraining, in this work we address the even greater challenge of designing an approach that requires minimal amounts of new annotated data as well as training time. We do so by designing specialized contrastive losses that leverage the few annotated samples very efficiently. A large set of results show that 3 to 5 annotations lead to models with accuracy that: 1) significantly mitigate the covariate shift effects; 2) matches or surpasses other adaptation methods; 3) even approaches methods that have been fully retrained on the target distribution. The adaptation training is only a few minutes, paving a path towards a balance between model performance, computing requirements and expert-level annotation needs.
| S-EPMC10760785 | biostudies-literature
Project description:Background and purposeMagnetic resonance imaging (MRI) is increasingly used in radiation therapy planning of prostate cancer (PC) to reduce target volume delineation uncertainty. This study aimed to assess and validate the performance of a fully automated segmentation tool (AST) in MRI based radiation therapy planning of PC.Material and methodsPelvic structures of 65 PC patients delineated in an MRI-only workflow according to established guidelines were included in the analysis. Automatic vs manual segmentation by an experienced oncologist was compared with geometrical parameters, such as the dice similarity coefficient (DSC). Fifteen patients had a second MRI within 15 days to assess repeatability of the AST for prostate and seminal vesicles. Furthermore, we investigated whether hormonal therapy or body mass index (BMI) affected the AST results.ResultsThe AST showed high agreement with manual segmentation expressed as DSC (mean, SD) for delineating prostate (0.84, 0.04), bladder (0.92, 0.04) and rectum (0.86, 0.04). For seminal vesicles (0.56, 0.17) and penile bulb (0.69, 0.12) the respective agreement was moderate. Performance of AST was not influenced by neoadjuvant hormonal therapy, although those on treatment had significantly smaller prostates than the hormone-naïve patients (p < 0.0001). In repeat assessment, consistency of prostate delineation resulted in mean DSC of 0.89, (SD 0.03) between the paired MRI scans for AST, while mean DSC of manual delineation was 0.82, (SD 0.05).ConclusionFully automated MRI segmentation tool showed good agreement and repeatability compared with manual segmentation and was found clinically robust in patients with PC. However, manual review and adjustment of some structures in individual cases remain important in clinical use.
| S-EPMC7807774 | biostudies-literature
Project description:Segmenting deep brain structures from magnetic resonance images is important for patient diagnosis, surgical planning, and research. Most current state-of-the-art solutions follow a segmentation-by-registration approach, where subject magnetic resonance imaging (MRIs) are mapped to a template with well-defined segmentations. However, registration-based pipelines are time-consuming, thus, limiting their clinical use. This paper uses deep learning to provide a one-step, robust, and efficient deep brain segmentation solution directly in the native space. The method consists of a preprocessing step to conform all MRI images to the same orientation, followed by a convolutional neural network using the nnU-Net framework. We use a total of 14 datasets from both research and clinical collections. Of these, seven were used for training and validation and seven were retained for testing. We trained the network to segment 30 deep brain structures, as well as a brain mask, using labels generated from a registration-based approach. We evaluated the generalizability of the network by performing a leave-one-dataset-out cross-validation, and independent testing on unseen datasets. Furthermore, we assessed cross-domain transportability by evaluating the results separately on different domains. We achieved an average dice score similarity of 0.89 ± 0.04 on the test datasets when compared to the registration-based gold standard. On our test system, the computation time decreased from 43 min for a reference registration-based pipeline to 1.3 min. Our proposed method is fast, robust, and generalizes with high reliability. It can be extended to the segmentation of other brain structures. It is publicly available on GitHub, and as a pip package for convenient usage.
| S-EPMC9842883 | biostudies-literature
Project description:Accurate segmentation of the prostate from magnetic resonance (MR) images provides useful information for prostate cancer diagnosis and treatment. However, automated prostate segmentation from 3D MR images faces several challenges. The lack of clear edge between the prostate and other anatomical structures makes it challenging to accurately extract the boundaries. The complex background texture and large variation in size, shape and intensity distribution of the prostate itself make segmentation even further complicated. Recently, as deep learning, especially convolutional neural networks (CNNs), emerging as the best performed methods for medical image segmentation, the difficulty in obtaining large number of annotated medical images for training CNNs has become much more pronounced than ever. Since large-scale dataset is one of the critical components for the success of deep learning, lack of sufficient training data makes it difficult to fully train complex CNNs. To tackle the above challenges, in this paper, we propose a boundary-weighted domain adaptive neural network (BOWDA-Net). To make the network more sensitive to the boundaries during segmentation, a boundary-weighted segmentation loss is proposed. Furthermore, an advanced boundary-weighted transfer leaning approach is introduced to address the problem of small medical imaging datasets. We evaluate our proposed model on three different MR prostate datasets. The experimental results demonstrate that the proposed model is more sensitive to object boundaries and outperformed other state-of-the-art methods.
| S-EPMC7015773 | biostudies-literature
Project description:BackgroundDose escalation radiotherapy enables increased control of prostate cancer (PCa) but requires segmentation of dominant index lesions (DIL). This motivates the development of automated methods for fast, accurate, and consistent segmentation of PCa DIL.PurposeTo construct and validate a model for deep-learning-based automatic segmentation of PCa DIL defined by Gleason score (GS) ≥3+4 from MR images applied to MR-guided radiation therapy. Validate generalizability of constructed models across scanner and acquisition differences.MethodsFive deep-learning networks were evaluated on apparent diffusion coefficient (ADC) MRI from 500 lesions in 365 patients arising from internal training Dataset 1 (156 lesions in 125 patients, 1.5Tesla GE MR with endorectal coil), testing using Dataset 1 (35 lesions in 26 patients), external ProstateX Dataset 2 (299 lesions in 204 patients, 3Tesla Siemens MR), and internal inter-rater Dataset 3 (10 lesions in 10 patients, 3Tesla Philips MR). The five networks include: multiple resolution residually connected network (MRRN) and MRRN regularized in training with deep supervision implemented into the last convolutional block (MRRN-DS), Unet, Unet++, ResUnet, and fast panoptic segmentation (FPSnet) as well as fast panoptic segmentation with smoothed labels (FPSnet-SL). Models were evaluated by volumetric DIL segmentation accuracy using Dice similarity coefficient (DSC) and the balanced F1 measure of detection accuracy, as a function of lesion aggressiveness and size (Dataset 1 and 2), and accuracy with respect to two-raters (on Dataset 3). Upon acceptance for publication segmentation models will be made available in an open-source GitHub repository.ResultsIn general, MRRN-DS more accurately segmented tumors than other methods on the testing datasets. MRRN-DS significantly outperformed ResUnet in Dataset2 (DSC of 0.54 vs. 0.44, p < 0.001) and the Unet++ in Dataset3 (DSC of 0.45 vs. p = 0.04). FPSnet-SL was similarly accurate as MRRN-DS in Dataset2 (p = 0.30), but MRRN-DS significantly outperformed FPSnet and FPSnet-SL in both Dataset1 (0.60 vs. 0.51 [p = 0.01] and 0.54 [p = 0.049] respectively) and Dataset3 (0.45 vs. 0.06 [p = 0.002] and 0.24 [p = 0.004] respectively). Finally, MRRN-DS produced slightly higher agreement with experienced radiologist than two radiologists in Dataset 3 (DSC of 0.45 vs. 0.41).ConclusionsMRRN-DS was generalizable to different MR testing datasets acquired using different scanners. It produced slightly higher agreement with an experienced radiologist than that between two radiologists. Finally, MRRN-DS more accurately segmented aggressive lesions, which are generally candidates for radiative dose ablation.
| S-EPMC11098147 | biostudies-literature
Project description:BACKGROUND:The study aims to assess the accuracy of multi-parametric prostate MRI (mpMRI) and 18F-choline PET/CT in tumor segmentation for clinically significant prostate cancer. 18F-choline PET/CT and 3 T mpMRI were performed in 10 prospective subjects prior to prostatectomy. All subjects had a single biopsy-confirmed focus of Gleason ??3+4 cancer. Two radiologists (readers 1 and 2) determined tumor boundaries based on in vivo mpMRI sequences, with clinical and pathologic data available. 18F-choline PET data were co-registered to T2-weighted 3D sequences and a semi-automatic segmentation routine was used to define tumor volumes. Registration of whole-mount surgical pathology to in vivo imaging was conducted utilizing two ex vivo prostate specimen MRIs, followed by gross sectioning of the specimens within a custom-made 3D-printed plastic mold. Overlap and similarity coefficients of manual segmentations (seg1, seg2) and 18F-choline-based segmented lesions (seg3) were compared to the pathologic reference standard. RESULTS:All segmentation methods greatly underestimated the true tumor volumes. Human readers (seg1, seg2) and the PET-based segmentation (seg3) underestimated an average of 79, 80, and 58% of the tumor volumes, respectively. Combining segmentation volumes (union of seg1, seg2, seg3?=?seg4) decreased the mean underestimated tumor volume to 42% of the true tumor volume. When using the combined segmentation with 5 mm contour expansion, the mean underestimated tumor volume was significantly reduced to 0.03?±?0.05 mL (2.04?±?2.84%). Substantial safety margins up to 11-15 mm were needed to include all tumors when the initial segmentation boundaries were drawn by human readers or the semi-automated 18F-choline segmentation tool. Combining MR-based human segmentations with the metabolic information based on 18F-choline PET reduced the necessary safety margin to a maximum of 9 mm to cover all tumors entirely. CONCLUSIONS:To improve the outcome of focal therapies for significant prostate cancer, it is imperative to recognize the full extent of the underestimation of tumor volumes by mpMRI. Combining metabolic information from 18F-choline with MRI-based segmentation can improve tumor coverage. However, this approach requires confirmation in further clinical studies.
| S-EPMC5869349 | biostudies-literature
Project description:Background and purposeWe developed an automatic method to segment cardiac substructures given a radiotherapy planning CT images to support epidemiological studies or clinical trials looking at cardiac disease endpoints after radiotherapy.Material and methodsWe used a most-similar atlas selection algorithm and 3D deformation combined with 30 detailed cardiac atlases. We cross-validated our method within the atlas library by evaluating geometric comparison metrics and by comparing cardiac doses for simulated breast radiotherapy between manual and automatic contours. We analyzed the impact of the number of cardiac atlas in the library and the use of manual guide points on the performance of our method.ResultsThe Dice Similarity Coefficients from the cross-validation reached up to 97% (whole heart) and 80% (chambers). The Average Surface Distance for the coronary arteries was less than 10.3 mm on average, with the best agreement (7.3 mm) in the left anterior descending artery (LAD). The dose comparison for simulated breast radiotherapy showed differences less than 0.06 Gy for the whole heart and atria, and 0.3 Gy for the ventricles. For the coronary arteries, the dose differences were 2.3 Gy (LAD) and 0.3 Gy (other arteries). The sensitivity analysis showed no notable improvement beyond ten atlases and the manual guide points does not significantly improve performance.ConclusionWe developed an automated method to contour cardiac substructures for radiotherapy CTs. When combined with accurate dose calculation techniques, our method should be useful for cardiac dose reconstruction of a large number of patients in epidemiological studies or clinical trials.
| S-EPMC7807574 | biostudies-literature
Project description:In recent years, some convolutional neural networks (CNNs) have been proposed to segment sub-cortical brain structures from magnetic resonance images (MRIs). Although these methods provide accurate segmentation, there is a reproducibility issue regarding segmenting MRI volumes from different image domains - e.g., differences in protocol, scanner, and intensity profile. Thus, the network must be retrained from scratch to perform similarly in different imaging domains, limiting the applicability of such methods in clinical settings. In this paper, we employ the transfer learning strategy to solve the domain shift problem. We reduced the number of training images by leveraging the knowledge obtained by a pretrained network, and improved the training speed by reducing the number of trainable parameters of the CNN. We tested our method on two publicly available datasets - MICCAI 2012 and IBSR - and compared them with a commonly used approach: FIRST. Our method showed similar results to those obtained by a fully trained CNN, and our method used a remarkably smaller number of images from the target domain. Moreover, training the network with only one image from MICCAI 2012 and three images from IBSR datasets was sufficient to significantly outperform FIRST with (p?<?0.001) and (p?<?0.05), respectively.
| S-EPMC6494835 | biostudies-literature
Project description:Robust automated segmentation of white matter hyperintensities (WMHs) in different datasets (domains) is highly challenging due to differences in acquisition (scanner, sequence), population (WMH amount and location) and limited availability of manual segmentations to train supervised algorithms. In this work we explore various domain adaptation techniques such as transfer learning and domain adversarial learning methods, including domain adversarial neural networks and domain unlearning, to improve the generalisability of our recently proposed triplanar ensemble network, which is our baseline model. We used datasets with variations in intensity profile, lesion characteristics and acquired using different scanners. For the source domain, we considered a dataset consisting of data acquired from 3 different scanners, while the target domain consisted of 2 datasets. We evaluated the domain adaptation techniques on the target domain datasets, and additionally evaluated the performance on the source domain test dataset for the adversarial techniques. For transfer learning, we also studied various training options such as minimal number of unfrozen layers and subjects required for fine-tuning in the target domain. On comparing the performance of different techniques on the target dataset, domain adversarial training of neural network gave the best performance, making the technique promising for robust WMH segmentation.
| S-EPMC8573594 | biostudies-literature