An intelligent workflow for sub-nanoscale 3D reconstruction of intact synapses from serial section electron tomography.

BACKGROUND: As an extension of electron tomography (ET), serial section electron tomography (serial section ET) aims to align the tomographic images of multiple thick tissue sections together, to break through the volume limitation of the single section and preserve the sub-nanoscale voxel size. It could be applied to reconstruct the intact synapse, which expands about one micrometer and contains nanoscale vesicles. However, there are several drawbacks of the existing serial section ET methods. First, locating and imaging regions of interest (ROIs) in serial sections during the shooting process is time-consuming. Second, the alignment of ET volumes is difficult due to the missing information caused by section cutting and imaging. Here we report a workflow to simplify the acquisition of ROIs in serial sections, automatically align the volume of serial section ET, and semi-automatically reconstruct the target synaptic structure. RESULTS: We propose an intelligent workflow to reconstruct the intact synapse with sub-nanometer voxel size. Our workflow includes rapid localization of ROIs in serial sections, automatic alignment, restoration, assembly of serial ET volumes, and semi-automatic target structure segmentation. For the localization and acquisition of ROIs in serial sections, we use affine transformations to calculate their approximate position based on their relative location in orderly placed sections. For the alignment of consecutive ET volumes with significantly distinct appearances, we use multi-scale image feature matching and the elastic with belief propagation (BP-Elastic) algorithm to align them from coarse to fine. For the restoration of the missing information in ET, we first estimate the number of lost images based on the pixel changes of adjacent volumes after alignment. Then, we present a missing information generation network that is appropriate for small-sample of ET volume using pre-training interpolation network and distillation learning. And we use it to generate the missing information to achieve the whole volume reconstruction. For the reconstruction of synaptic ultrastructures, we use a 3D neural network to obtain them quickly. In summary, our workflow can quickly locate and acquire ROIs in serial sections, automatically align, restore, assemble serial sections, and obtain the complete segmentation result of the target structure with minimal manual manipulation. Multiple intact synapses in wild-type rat were reconstructed at a voxel size of 0.664 nm/voxel to demonstrate the effectiveness of our workflow. CONCLUSIONS: Our workflow contributes to obtaining intact synaptic structures at the sub-nanometer scale through serial section ET, which contains rapid ROI locating, automatic alignment, volume reconstruction, and semi-automatic synapse reconstruction. We have open-sourced the relevant code in our workflow, so it is easy to apply it to other labs and obtain complete 3D ultrastructures which size is similar to intact synapses with sub-nanometer voxel size.

Semi-supervised auto-segmentation method for pelvic organ-at-risk in magnetic resonance images based on deep-learning.

BACKGROUND AND PURPOSE: In radiotherapy, magnetic resonance (MR) imaging has higher contrast for soft tissues compared to computed tomography (CT) scanning and does not emit radiation. However, manual annotation of the deep learning-based automatic organ-at-risk (OAR) delineation algorithms is expensive, making the collection of large-high-quality annotated datasets a challenge. Therefore, we proposed the low-cost semi-supervised OAR segmentation method using small pelvic MR image annotations. METHODS: We trained a deep learning-based segmentation model using 116 sets of MR images from 116 patients. The bladder, femoral heads, rectum, and small intestine were selected as OAR regions. To generate the training set, we utilized a semi-supervised method and ensemble learning techniques. Additionally, we employed a post-processing algorithm to correct the self-annotation data. Both 2D and 3D auto-segmentation networks were evaluated for their performance. Furthermore, we evaluated the performance of semi-supervised method for 50 labeled data and only 10 labeled data. RESULTS: The Dice similarity coefficient (DSC) of the bladder, femoral heads, rectum and small intestine between segmentation results and reference masks is 0.954, 0.984, 0.908, 0.852 only using self-annotation and post-processing methods of 2D segmentation model. The DSC of corresponding OARs is 0.871, 0.975, 0.975, 0.783, 0.724 using 3D segmentation network, 0.896, 0.984, 0.890, 0.828 using 2D segmentation network and common supervised method. CONCLUSION: The outcomes of our study demonstrate that it is possible to train a multi-OAR segmentation model using small annotation samples and additional unlabeled data. To effectively annotate the dataset, ensemble learning and post-processing methods were employed. Additionally, when dealing with anisotropy and limited sample sizes, the 2D model outperformed the 3D model in terms of performance.

Gross failure rates and failure modes for a commercial AI-based auto-segmentation algorithm in head and neck cancer patients.

PURPOSE: Artificial intelligence (AI) based commercial software can be used to automatically delineate organs at risk (OAR), with potential for efficiency savings in the radiotherapy treatment planning pathway, and reduction of inter- and intra-observer variability. There has been little research investigating gross failure rates and failure modes of such systems. METHOD: 50 head and neck (H&N) patient data sets with "gold standard" contours were compared to AI-generated contours to produce expected mean and standard deviation values for the Dice Similarity Coefficient (DSC), for four common H&N OARs (brainstem, mandible, left and right parotid). An AI-based commercial system was applied to 500 H&N patients. AI-generated contours were compared to manual contours, outlined by an expert human, and a gross failure was set at three standard deviations below the expected mean DSC. Failures were inspected to assess reason for failure of the AI-based system with failures relating to suboptimal manual contouring censored. True failures were classified into 4 sub-types (setup position, anatomy, image artefacts and unknown). RESULTS: There were 24 true failures of the AI-based commercial software, a gross failure rate of 1.2%. Fifteen failures were due to patient anatomy, four were due to dental image artefacts, three were due to patient position and two were unknown. True failure rates by OAR were 0.4% (brainstem), 2.2% (mandible), 1.4% (left parotid) and 0.8% (right parotid). CONCLUSION: True failures of the AI-based system were predominantly associated with a non-standard element within the CT scan. It is likely that these non-standard elements were the reason for the gross failure, and suggests that patient datasets used to train the AI model did not contain sufficient heterogeneity of data. Regardless of the reasons for failure, the true failure rate for the AI-based system in the H&N region for the OARs investigated was low (∼1%).

A deep learning-based framework (Co-ReTr) for auto-segmentation of non-small cell-lung cancer in computed tomography images.

PURPOSE: Deep learning-based auto-segmentation algorithms can improve clinical workflow by defining accurate regions of interest while reducing manual labor. Over the past decade, convolutional neural networks (CNNs) have become prominent in medical image segmentation applications. However, CNNs have limitations in learning long-range spatial dependencies due to the locality of the convolutional layers. Transformers were introduced to address this challenge. In transformers with self-attention mechanism, even the first layer of information processing makes connections between distant image locations. Our paper presents a novel framework that bridges these two unique techniques, CNNs and transformers, to segment the gross tumor volume (GTV) accurately and efficiently in computed tomography (CT) images of non-small cell-lung cancer (NSCLC) patients. METHODS: Under this framework, input of multiple resolution images was used with multi-depth backbones to retain the benefits of high-resolution and low-resolution images in the deep learning architecture. Furthermore, a deformable transformer was utilized to learn the long-range dependency on the extracted features. To reduce computational complexity and to efficiently process multi-scale, multi-depth, high-resolution 3D images, this transformer pays attention to small key positions, which were identified by a self-attention mechanism. We evaluated the performance of the proposed framework on a NSCLC dataset which contains 563 training images and 113 test images. Our novel deep learning algorithm was benchmarked against five other similar deep learning models. RESULTS: The experimental results indicate that our proposed framework outperforms other CNN-based, transformer-based, and hybrid methods in terms of Dice score (0.92) and Hausdorff Distance (1.33). Therefore, our proposed model could potentially improve the efficiency of auto-segmentation of early-stage NSCLC during the clinical workflow. This type of framework may potentially facilitate online adaptive radiotherapy, where an efficient auto-segmentation workflow is required. CONCLUSIONS: Our deep learning framework, based on CNN and transformer, performs auto-segmentation efficiently and could potentially assist clinical radiotherapy workflow.

Artificial intelligence in radiotherapy.

Radiotherapy is a discipline closely integrated with computer science. Artificial intelligence (AI) has developed rapidly over the past few years. With the explosive growth of medical big data, AI promises to revolutionize the field of radiotherapy through highly automated workflow, enhanced quality assurance, improved regional balances of expert experiences, and individualized treatment guided by multi-omics. In addition to independent researchers, the increasing number of large databases, biobanks, and open challenges significantly facilitated AI studies on radiation oncology. This article reviews the latest research, clinical applications, and challenges of AI in each part of radiotherapy including image processing, contouring, planning, quality assurance, motion management, and outcome prediction. By summarizing cutting-edge findings and challenges, we aim to inspire researchers to explore more future possibilities and accelerate the arrival of AI radiotherapy.

Development of a national deep learning-based auto-segmentation model for the heart on clinical delineations from the DBCG RT nation cohort.

BACKGROUND: This study aimed at investigating the feasibility of developing a deep learning-based auto-segmentation model for the heart trained on clinical delineations. MATERIAL AND METHODS: This study included two different datasets. The first dataset contained clinical heart delineations from the DBCG RT Nation study (1,561 patients). The second dataset was smaller (114 patients), but with corrected heart delineations. Before training the model on the clinical delineations an outlier-detection was performed, to remove cases with gross deviations from the delineation guideline. No outlier detection was performed for the dataset with corrected heart delineations. Both models were trained with a 3D full resolution nnUNet. The models were evaluated with the dice similarity coefficient (DSC), 95% Hausdorff distance (HD95) and Mean Surface Distance (MSD). The difference between the models were tested with the Mann-Whitney U-test. The balance of dataset quantity versus quality was investigated, by stepwise reducing the cohort size for the model trained on clinical delineations. RESULTS: During the outlier-detection 137 patients were excluded from the clinical cohort due to non-compliance with delineation guidelines. The model trained on the curated clinical cohort performed with a median DSC of 0.96 (IQR 0.94-0.96), median HD95 of 4.00 mm (IQR 3.00 mm-6.00 mm) and a median MSD of 1.49 mm (IQR 1.12 mm-2.02 mm). The model trained on the dedicated and corrected cohort performed with a median DSC of 0.95 (IQR 0.93-0.96), median HD95 of 5.65 mm (IQR 3.37 mm-8.62 mm) and median MSD of 1.63 mm (IQR 1.35 mm-2.11 mm). The difference between the two models were found non-significant for all metrics (p > 0.05). Reduction of cohort size showed no significant difference for all metrics (p > 0.05). However, with the smallest cohort size, a few outlier structures were found. CONCLUSIONS: This study demonstrated a deep learning-based auto-segmentation model trained on curated clinical delineations which performs on par with a model trained on dedicated delineations, making it easier to develop multi-institutional auto-segmentation models.

A radiomics based approach using adrenal gland and periadrenal fat CT images to allocate COVID-19 health care resources fairly.

BACKGROUND: The value of radiomics features from the adrenal gland and periadrenal fat CT images for predicting disease progression in patients with COVID-19 has not been studied extensively. We assess the value of radiomics features from the adrenal gland and periadrenal fat CT images in predicting COVID-19 disease exacerbation. METHODS: A total of 1,245 patients (685 moderate and 560 severe patients) were enrolled in a retrospective study. We proposed a 3D V-net to segment adrenal glands in onset CT images automatically, and periadrenal fat was obtained using inflation operation around the adrenal gland. Next, we built a clinical model (CM), three radiomics models (adrenal gland model [AM], periadrenal fat model [PM], and fusion of adrenal gland and periadrenal fat model [FM]), and radiomics nomogram (RN) after radiomics features extracted. RESULTS: The auto-segmentation framework yielded a dice value 0.79 in the training set. CM, AM, PM, FM, and RN obtained AUCs of 0.717, 0.716, 0.736, 0.760, and 0.833 in the validation set. FM and RN had better predictive efficacy than CM (P < 0.0001) in the training set. RN showed that there was no significant difference in the validation set (mean absolute error [MAE] = 0.04) and test set (MAE = 0.075) between predictive and actual results. Decision curve analysis showed that if the threshold probability was between 0.4 and 0.8 in the validation set or between 0.3 and 0.7 in the test set, it could gain more net benefits using RN than FM and CM. CONCLUSIONS: Radiomics features extracted from the adrenal gland and periadrenal fat CT images are related to disease exacerbation in patients with COVID-19.

Contour similarity and its implication on inverse prostate SBRT treatment planning.

PURPOSE: Success of auto-segmentation is measured by the similarity between auto and manual contours that is often quantified by Dice coefficient (DC). The dosimetric impact of contour variability on inverse planning has been rarely reported. The main aim of this study is to investigate whether automatically generated organs-at-risk (OARs) could be used in inverse prostate stereotactic body radiation therapy (SBRT) planning and whether the dosimetric parameters are still clinically acceptable after radiation oncologists modify the OARs. METHODS AND MATERIALS: Planning computed tomography images from 10 patients treated with SBRT for prostate cancer were selected and automatically segmented by commercially available atlas-based software. The automatically generated OAR contours were compared with the manually drawn contours. Two volumetric modulated arc therapy (VMAT) plans, autoRec-VMAT (where only automatically generated rectums were used in optimization) and autoAll-VMAT (where automatically generated OARs were used in inverse optimization) were generated. Dosimetric parameters based on the manually drawn PTV and OARs were compared with the clinically approved plans. RESULTS: The DCs for the rectum contours varied from 0.55 to 0.74 with a mean value of 0.665. Differences of D95 of the PTV between autoRec-VMAT and manu-VMAT plans varied from 0.03% to -2.85% with a mean value of -0.64%. Differences of D0.03cc of manual rectum between the two plans varied from -0.86% to 9.94% with a mean value of 2.71%. D95 of PTV between autoAll-VMAT and manu-VMAT plans varied from 0.28% to -2.9% with a mean value -0.83%. Differences of D0.03cc of manual rectum between the two plans varied from -0.76% to 6.72% with a mean value of 2.62%. CONCLUSION: Our study implies that it is possible to use unedited automatically generated OARs to perform initial inverse prostate SBRT planning. After radiation oncologists modify/approve the OARs, the plan qualities based on the manually drawn OARs are still clinically acceptable, and a re-optimization may not be needed.

Geometric and dosimetric evaluation of deep learning based auto-segmentation for clinical target volume on breast cancer.

BACKGROUND: Recently, target auto-segmentation techniques based on deep learning (DL) have shown promising results. However, inaccurate target delineation will directly affect the treatment planning dose distribution and the effect of subsequent radiotherapy work. Evaluation based on geometric metrics alone may not be sufficient for target delineation accuracy assessment. The purpose of this paper is to validate the performance of automatic segmentation with dosimetric metrics and try to construct new evaluation geometric metrics to comprehensively understand the dose-response relationship from the perspective of clinical application. MATERIALS AND METHODS: A DL-based target segmentation model was developed by using 186 manual delineation modified radical mastectomy breast cancer cases. The resulting DL model were used to generate alternative target contours in a new set of 48 patients. The Auto-plan was reoptimized to ensure the same optimized parameters as the reference Manual-plan. To assess the dosimetric impact of target auto-segmentation, not only common geometric metrics but also new spatial parameters with distance and relative volume ( R V ${R}_V$ ) to target were used. Correlations were performed using Spearman's correlation between segmentation evaluation metrics and dosimetric changes. RESULTS: Only strong (|R2 | > 0.6, p < 0.01) or moderate (|R2 | > 0.4, p < 0.01) Pearson correlation was established between the traditional geometric metric and three dosimetric evaluation indices to target (conformity index, homogeneity index, and mean dose). For organs at risk (OARs), inferior or no significant relationship was found between geometric parameters and dosimetric differences. Furthermore, we found that OARs dose distribution was affected by boundary error of target segmentation instead of distance and R V ${R}_V$ to target. CONCLUSIONS: Current geometric metrics could reflect a certain degree of dose effect of target variation. To find target contour variations that do lead to OARs dosimetry changes, clinically oriented metrics that more accurately reflect how segmentation quality affects dosimetry should be constructed.

Evaluation of generalization ability for deep learning-based auto-segmentation accuracy in limited field of view CBCT of male pelvic region.

PURPOSE: The aim of this study was to evaluate generalization ability of segmentation accuracy for limited FOV CBCT in the male pelvic region using a full-image CNN. Auto-segmentation accuracy was evaluated using various datasets with different intensity distributions and FOV sizes. METHODS: A total of 171 CBCT datasets from patients with prostate cancer were enrolled. There were 151, 10, and 10 CBCT datasets acquired from Vero4DRT, TrueBeam STx, and Clinac-iX, respectively. The FOV for Vero4DRT, TrueBeam STx, and Clinac-iX was 20, 26, and 25 cm, respectively. The ROIs, including the bladder, prostate, rectum, and seminal vesicles, were manually delineated. The U2 -Net CNN network architecture was used to train the segmentation model. A total of 131 limited FOV CBCT datasets from Vero4DRT were used for training (104 datasets) and validation (27 datasets); thereafter the rest were for testing. The training routine was set to save the best weight values when the DSC in the validation set was maximized. Segmentation accuracy was qualitatively and quantitatively evaluated between the ground truth and predicted ROIs in the different testing datasets. RESULTS: The mean scores ± standard deviation of visual evaluation for bladder, prostate, rectum, and seminal vesicle in all treatment machines were 1.0 ± 0.7, 1.5 ± 0.6, 1.4 ± 0.6, and 2.1 ± 0.8 points, respectively. The median DSC values for all imaging devices were ≥0.94 for the bladder, 0.84-0.87 for the prostate and rectum, and 0.48-0.69 for the seminal vesicles. Although the DSC values for the bladder and seminal vesicles were significantly different among the three imaging devices, the DSC value of the bladder changed by less than 1% point. The median MSD values for all imaging devices were ≤1.2 mm for the bladder and 1.4-2.2 mm for the prostate, rectum, and seminal vesicles. The MSD values for the seminal vesicles were significantly different between the three imaging devices. CONCLUSION: The proposed method is effective for testing datasets with different intensity distributions and FOV from training datasets.

Evaluation of Atlas-based auto-segmentation of liver in MR images for Yttrium-90 selective internal radiation therapy.

PURPOSE: The aim was to explore the feasibility of applying an atlas-based auto-segmentation tool, MIM Atlas Segment, for liver delineation in MR images in Y-90 selective internal radiation therapy (SIRT). MATERIALS AND METHODS: MR images of 41 liver patients treated with resin Y-90 SIRT were included: 20 patients' images were used to create an atlas, and the other 21 patients' images were used for testing. Auto-segmentation of liver in the MR images was performed with MIM Atlas Segment, and various settings for the auto-segmentation (i.e., with and without normalized deformable registration, single atlas-match and multi-atlas match, and multi-atlas match using different finalization methods) were tested. Auto-segmented liver contours were compared with physician manually-delineated contours, using Dice similarity coefficient (DSC) and mean distance to agreement (MDA). Ratio of volume (RV) and ratio of activity (RA) were calculated to further evaluate the auto-segmentation results. RESULTS: Auto-segmentations with normalized deformable registration generated better contours than those without normalized deformable registration. With normalized deformable registration, 3-atlas match using Majority Vote (MV) method generated better results than single-atlas match and 3-atlas match using STAPLE method, and generated similar results as 5-atlas match using MV method or STAPLE method. The average DSC, MDA, and RV of the contours generated with normalized deformable registration are 0.80-0.83, 0.60-0.67, and 0.91-1.00 cm, respectively. The average RA are 1.00-1.01, which indicate that the activities calculated using the auto-segmented liver contours are close to the accurate activities. CONCLUSION: The atlas-based auto-segmentation can be applied to generate initial liver contours in MR images for resin Y-90 SIRT, which can be used for activity calculations after physicians review.

Auto-segmentation of head and neck tumors in positron emission tomography images using non-local means and morphological frameworks.

Purpose: Accurately segmenting head and neck cancer (HNC) tumors in medical images is crucial for effective treatment planning. However, current methods for HNC segmentation are limited in their accuracy and efficiency. The present study aimed to design a model for segmenting HNC tumors in three-dimensional (3D) positron emission tomography (PET) images using Non-Local Means (NLM) and morphological operations. Material and Methods: The proposed model was tested using data from the HECKTOR challenge public dataset, which included 408 patient images with HNC tumors. NLM was utilized for image noise reduction and preservation of critical image information. Following pre-processing, morphological operations were used to assess the similarity of intensity and edge information within the images. The Dice score, Intersection Over Union (IoU), and accuracy were used to evaluate the manual and predicted segmentation results. Results: The proposed model achieved an average Dice score of 81.47 ± 3.15, IoU of 80 ± 4.5, and accuracy of 94.03 ± 4.44, demonstrating its effectiveness in segmenting HNC tumors in PET images. Conclusions: The proposed algorithm provides the capability to produce patient-specific tumor segmentation without manual interaction, addressing the limitations of current methods for HNC segmentation. The model has the potential to improve treatment planning and aid in the development of personalized medicine. Additionally, this model can be extended to effectively segment other organs from limited annotated medical images.

Atlas-based auto-segmentation for delineating the heart and cardiac substructures in breast cancer radiation therapy.

BACKGROUND: This study aimed to develop and validate an automatic multi-atlas segmentation method for delineating the heart and substructures in breast cancer radiation therapy (RT). MATERIAL AND METHODS: The atlas database consisted of non-contrast-enhanced planning CT scans from 42 breast cancer patients, each with one manual delineation of the heart and 22 cardiac substructures. Half of the patients were scanned during free-breathing, the rest were scanned during a deep inspiration breath-hold. The auto-segmentation was developed in the MIM software system and validated geometrically and dosimetrically in two steps: The first validation in a small dataset to ensure consistency of the atlas. This was succeeded by a final test where multiple manual delineations in CT scans of 12 breast cancer patients were compared to the auto-segmentation. For geometric evaluation, the dice similarity coefficient (DSC) and the mean surface distance (MSD) were used. For dosimetric evaluation, the RT doses to each substructure in the manual and the automatic delineations were compared. RESULTS: In the first validation, a high geometric and dosimetric performance between the automatic and manual delineations was observed for all substructures. The final test confirmed a high agreement between the automatic and manual delineations for the heart (DSC = 0.94) and the cardiac chambers (DSC: 0.75-0.86). The difference in MSD between the automatic and manual delineations was low (<4 mm) in all structures. Finally, a high correlation between mean RT doses for the automatic and the manual delineations was observed for the heart and substructures. CONCLUSIONS: An automatic segmentation tool for delineation of the heart and substructures in breast cancer RT was developed and validated with a high correlation between the automatic and manual delineations. The atlas is pivotal for large-scale evaluations of radiation-associated heart disease.

Clinical evaluation of deep learning-based clinical target volume three-channel auto-segmentation algorithm for adaptive radiotherapy in cervical cancer.

OBJECTIVES: Accurate contouring of the clinical target volume (CTV) is a key element of radiotherapy in cervical cancer. We validated a novel deep learning (DL)-based auto-segmentation algorithm for CTVs in cervical cancer called the three-channel adaptive auto-segmentation network (TCAS). METHODS: A total of 107 cases were collected and contoured by senior radiation oncologists (ROs). Each case consisted of the following: (1) contrast-enhanced CT scan for positioning, (2) the related CTV, (3) multiple plain CT scans during treatment and (4) the related CTV. After registration between (1) and (3) for the same patient, the aligned image and CTV were generated. Method 1 is rigid registration, method 2 is deformable registration, and the aligned CTV is seen as the result. Method 3 is rigid registration and TCAS, method 4 is deformable registration and TCAS, and the result is generated by a DL-based method. RESULTS: From the 107 cases, 15 pairs were selected as the test set. The dice similarity coefficient (DSC) of method 1 was 0.8155 ± 0.0368; the DSC of method 2 was 0.8277 ± 0.0315; the DSCs of method 3 and 4 were 0.8914 ± 0.0294 and 0.8921 ± 0.0231, respectively. The mean surface distance and Hausdorff distance of methods 3 and 4 were markedly better than those of method 1 and 2. CONCLUSIONS: The TCAS achieved comparable accuracy to the manual delineation performed by senior ROs and was significantly better than direct registration.

Deep learning-based pancreas volume assessment in individuals with type 1 diabetes.

Pancreas volume is reduced in individuals with diabetes and in autoantibody positive individuals at high risk for developing type 1 diabetes (T1D). Studies investigating pancreas volume are underway to assess pancreas volume in large clinical databases and studies, but manual pancreas annotation is time-consuming and subjective, preventing extension to large studies and databases. This study develops deep learning for automated pancreas volume measurement in individuals with diabetes. A convolutional neural network was trained using manual pancreas annotation on 160 abdominal magnetic resonance imaging (MRI) scans from individuals with T1D, controls, or a combination thereof. Models trained using each cohort were then tested on scans of 25 individuals with T1D. Deep learning and manual segmentations of the pancreas displayed high overlap (Dice coefficient = 0.81) and excellent correlation of pancreas volume measurements (R2 = 0.94). Correlation was highest when training data included individuals both with and without T1D. The pancreas of individuals with T1D can be automatically segmented to measure pancreas volume. This algorithm can be applied to large imaging datasets to quantify the spectrum of human pancreas volume.

Comparison of Eclipse Smart Segmentation and MIM Atlas Segment for liver delineation for yttrium-90 selective internal radiation therapy.

PURPOSE: The aim was to compare Smart Segmentation of Eclipse treatment planning system and Atlas Segment of MIM software for liver delineation for resin yttrium-90 (Y-90) procedures. MATERIALS AND METHODS: CT images of 20 patients treated with resin Y-90 selective internal radiation therapy (SIRT) were tested. Liver contours generated with Smart Segmentation and Atlas Segment were compared with physician manually delineated contours. Dice similarity coefficient (DSC), mean distance to agreement (MDA), and ratio of volume (RV) were calculated. The contours were evaluated with activity calculations and ratio of activity (RA) was calculated. RESULTS: Mean DSCs were 0.77 and 0.83, MDAs were 0.88 and 0.71 cm, mean RVs were 0.95 and 1.02, and mean RAs were 1.00 and 1.00, for Eclipse and MIM results, respectively. CONCLUSION: MIM outperformed Eclipse in both DSC and MDA, whereas the differences in liver volumes and calculated activities were statistically insignificant between the Eclipse and MIM results. Both auto-segmentation tools can be used to generate initial liver contours for resin Y-90 SIRT, which need to be reviewed and edited by physicians.

Deep learning-based auto-segmentation of clinical target volumes for radiotherapy treatment of cervical cancer.

OBJECTIVES: Because radiotherapy is indispensible for treating cervical cancer, it is critical to accurately and efficiently delineate the radiation targets. We evaluated a deep learning (DL)-based auto-segmentation algorithm for automatic contouring of clinical target volumes (CTVs) in cervical cancers. METHODS: Computed tomography (CT) datasets from 535 cervical cancers treated with definitive or postoperative radiotherapy were collected. A DL tool based on VB-Net was developed to delineate CTVs of the pelvic lymph drainage area (dCTV1) and parametrial area (dCTV2) in the definitive radiotherapy group. The training/validation/test number is 157/20/23. CTV of the pelvic lymph drainage area (pCTV1) was delineated in the postoperative radiotherapy group. The training/validation/test number is 272/30/33. Dice similarity coefficient (DSC), mean surface distance (MSD), and Hausdorff distance (HD) were used to evaluate the contouring accuracy. Contouring times were recorded for efficiency comparison. RESULTS: The mean DSC, MSD, and HD values for our DL-based tool were 0.88/1.32 mm/21.60 mm for dCTV1, 0.70/2.42 mm/22.44 mm for dCTV2, and 0.86/1.15 mm/20.78 mm for pCTV1. Only minor modifications were needed for 63.5% of auto-segmentations to meet the clinical requirements. The contouring accuracy of the DL-based tool was comparable to that of senior radiation oncologists and was superior to that of junior/intermediate radiation oncologists. Additionally, DL assistance improved the performance of junior radiation oncologists for dCTV2 and pCTV1 contouring (mean DSC increases: 0.20 for dCTV2, 0.03 for pCTV1; mean contouring time decrease: 9.8 min for dCTV2, 28.9 min for pCTV1). CONCLUSIONS: DL-based auto-segmentation improves CTV contouring accuracy, reduces contouring time, and improves clinical efficiency for treating cervical cancer.

[The Effects of Different Adaptive Statistical Iterative Reconstruction-V and Convolution Kernel Parameters on Auto-Segmentation Stability in CT Images].

Objective The study aims to investigate the effects of different adaptive statistical iterative reconstruction-V（ ASiR-V） and convolution kernel parameters on stability of CT auto-segmentation which is based on deep learning. Method Twenty patients who have received pelvic radiotherapy were selected and different reconstruction parameters were used to establish CT images dataset. Then structures including three soft tissue organs (bladder, bowelbag, small intestine) and five bone organs (left and right femoral head, left and right femur, pelvic) were segmented automatically by deep learning neural network. Performance was evaluated by dice similarity coefficient（ DSC） and Hausdorff distance, using filter back projection(FBP) as the reference. Results Auto-segmentation of deep learning is greatly affected by ASIR-V, but less affected by convolution kernel, especially in soft tissues. Conclusion The stability of auto-segmentation is affected by parameter selection of reconstruction algorithm. In practical application, it is necessary to find a balance between image quality and segmentation quality, or improve segmentation network to enhance the stability of auto-segmentation.

A national study on the inter-observer variability in the delineation of organs at risk in the brain.

BACKGROUND: The Danish Neuro Oncology Group (DNOG) has established national consensus guidelines for the delineation of organs at risk (OAR) structures based on published literature. This study was conducted to finalise these guidelines and evaluate the inter-observer variability of the delineated OAR structures by expert observers. MATERIAL AND METHODS: The DNOG delineation guidelines were formed by participants from all Danish centres that treat brain tumours with radiotherapy. In a two-day workshop, guidelines were discussed and finalised based on a pilot study. Following this, the ten participants contoured the following OARs on T1-weighted gadolinium enhanced MRI from 13 patients with brain tumours: optic tracts, optic nerves, chiasm, spinal cord, brainstem, pituitary gland and hippocampus. The metrics used for comparison were the Dice similarity coefficient (Dice), mean surface distance (MSD) and others. RESULTS: A total of 968 contours were delineated across the 13 patients. On average eight (range six to nine) individual contour sets were made per patient. Good agreement was found across all structures with a median MSD below 1 mm for most structures, with the chiasm performing the best with a median MSD of 0.45 mm. The Dice was as expected highly volume dependent, the brainstem (the largest structure) had the highest Dice value with a median of 0.89 whereas smaller volumes such as the chiasm had a Dice of 0.71. CONCLUSION: Except for the caudal definition of the spinal cord, the variances observed in the contours of OARs in the brain were generally low and consistent. Surface mapping revealed sub-regions of higher variance for some organs. The data set is being prepared as a validation data set for auto-segmentation algorithms for use within the Danish Comprehensive Cancer Centre - Radiotherapy and potential collaborators.

Comparing different CT, PET and MRI multi-modality image combinations for deep learning-based head and neck tumor segmentation.

BACKGROUND: Manual delineation of gross tumor volume (GTV) is essential for radiotherapy treatment planning, but it is time-consuming and suffers inter-observer variability (IOV). In clinics, CT, PET, and MRI are used to inform delineation accuracy due to their different complementary characteristics. This study aimed to investigate deep learning to assist GTV delineation in head and neck squamous cell carcinoma (HNSCC) by comparing various modality combinations. MATERIALS AND METHODS: This retrospective study had 153 patients with multiple sites of HNSCC including their planning CT, PET, and MRI (T1-weighted and T2-weighted). Clinical delineations of gross tumor volume (GTV-T) and involved lymph nodes (GTV-N) were collected as the ground truth. The dataset was randomly divided into 92 patients for training, 31 for validation, and 30 for testing. We applied a residual 3 D UNet as the deep learning architecture. We independently trained the UNet with four different modality combinations (CT-PET-MRI, CT-MRI, CT-PET, and PET-MRI). Additionally, analogical to post-processing, an average fusion of three bi-modality combinations (CT-PET, CT-MRI, and PET-MRI) was produced as an ensemble. Segmentation accuracy was evaluated on the test set, using Dice similarity coefficient (Dice), Hausdorff Distance 95 percentile (HD95), and Mean Surface Distance (MSD). RESULTS: All imaging combinations including PET provided similar average scores in range of Dice: 0.72-0.74, HD95: 8.8-9.5 mm, MSD: 2.6-2.8 mm. Only CT-MRI had a lower score with Dice: 0.58, HD95: 12.9 mm, MSD: 3.7 mm. The average of three bi-modality combinations reached Dice: 0.74, HD95: 7.9 mm, MSD: 2.4 mm. CONCLUSION: Multimodal deep learning-based auto segmentation of HNSCC GTV was demonstrated and inclusion of the PET image was shown to be crucial. Training on combined MRI, PET, and CT data provided limited improvements over CT-PET and PET-MRI. However, when combining three bimodal trained networks into an ensemble, promising improvements were shown.