Comparison of Kidney Segmentation Under Attention U-Net Architectures

One of the most prominent machine learning advantages in the medical industry is the early detection of disease. Automatic kidney detection is of great importance for rapid diagnosis and treatment, where related diseases occupy over 73,750 new cases in the US in 2020 [1]. Today, the performance of diagnosis has been by highly trained radiologists. However, the complex structures contribute to speckle noise and inhomogeneous intensity profiles. Thus, there is a necessity to automate segmentation on kidney ultrasounds using U-Net Deep Learning architectures - an innovative solution for Medical Imaging Analysis. In this research, our focus is on the comparison of Attention U-Net in the context of different backbones such as VGG19, ResNet152V2, and EfficientNetB7. By providing this comparison, we will accomplish a survey for future researchers to more effectively decide on which Attention U-Net architecture to utilize for their segmentation projects.

Healthy Kidney Segmentation in the Dce-Mr Images Using a Convolutional Neural Network and Temporal Signal Characteristics

Quantification of renal perfusion based on dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) requires determination of signal intensity time courses in the region of renal parenchyma. Thus, selection of voxels representing the kidney must be accomplished with special care and constitutes one of the major technical limitations which hampers wider usage of this technique as a standard clinical routine. Manual segmentation of renal compartments—even if performed by experts—is a common source of decreased repeatability and reproducibility. In this paper, we present a processing framework for the automatic kidney segmentation in DCE-MR images. The framework consists of two stages. Firstly, kidney masks are generated using a convolutional neural network. Then, mask voxels are classified to one of three regions—cortex, medulla, and pelvis–based on DCE-MRI signal intensity time courses. The proposed approach was evaluated on a cohort of 10 healthy volunteers who underwent the DCE-MRI examination. MRI scanning was repeated on two time events within a 10-day interval. For semantic segmentation task we employed a classic U-Net architecture, whereas experiments on voxel classification were performed using three alternative algorithms—support vector machines, logistic regression and extreme gradient boosting trees, among which SVM produced the most accurate results. Both segmentation and classification steps were accomplished by a series of models, each trained separately for a given subject using the data from other participants only. The mean achieved accuracy of the whole kidney segmentation was 94% in terms of IoU coefficient. Cortex, medulla and pelvis were segmented with IoU ranging from 90 to 93% depending on the tissue and body side. The results were also validated by comparing image-derived perfusion parameters with ground truth measurements of glomerular filtration rate (GFR). The repeatability of GFR calculation, as assessed by the coefficient of variation was determined at the level of 14.5 and 17.5% for the left and right kidney, respectively and it improved relative to manual segmentation. Reproduciblity, in turn, was evaluated by measuring agreement between image-derived and iohexol-based GFR values. The estimated absolute mean differences were equal to 9.4 and 12.9 mL/min/1.73 m2 for scanning sessions 1 and 2 and the proposed automated segmentation method. The result for session 2 was comparable with manual segmentation, whereas for session 1 reproducibility in the automatic pipeline was weaker.

Three-dimensional kidney’s stones segmentation and chemical composition detection

<p>Kidney stones are a common and extremely painful disease and can affect any part of the urinary tract. Ultrasound and computed tomography (CT) are the most frequent imaging modalities used for patients with acute flank pain. In this paper, we design an automated system for 3D kidney segmentation and stones detection in addition to their number and size evaluation. The proposed system is built based on CT kidney image series of 10 subjects, four healthy subjects (with no stones) and the rest have stones based on medical doctor diagnosis, and its performance is tested based on 32 CT kidney series images. The designed system shows its ability to extract kidney either in abdominal or pelvis non-contrast series CT images, and it distinguishes the stones from the surrounding tissues in the kidney image, besides to its ability to analyze the stones and classify them in vivo for further medical treatment. The result agreed with medical doctor's diagnosis. The system can be improved by analyzing the stones in the laboratory and using a large CT dataset. The present method is not limited to extract stones but, also a new approach is proposed to extract the 3D kidneys as well with accuracy 99%.</p>

Comparison of Kidney Segmentation Under Attention U-Net Architectures

One of the most prominent machine learning advantages in the medical industry is the early detection of disease. Automatic kidney detection is of great importance for rapid diagnosis and treatment, where related diseases occupy over 73,750 new cases in the US in 2020 [1]. Today, the performance of diagnosis has been by highly trained radiologists. However, the complex structures contribute to speckle noise and inhomogeneous intensity profiles. Thus, there is a necessity to automate segmentation on kidney ultrasounds using U-Net Deep Learning architectures - an innovative solution for Medical Imaging Analysis. In this research, our focus is on the comparison of Attention U-Net in the context of different backbones such as VGG19, ResNet152V2, and EfficientNetB7. By providing this comparison, we will accomplish a survey for future researchers to more effectively decide on which Attention U-Net architecture to utilize for their segmentation projects.

Comparison of Kidney Segmentation Under Attention U-Net Architectures

One of the most prominent machine learning advantages in the medical industry is the early detection of disease. Automatic kidney detection is of great importance for rapid diagnosis and treatment, where related diseases occupy over 73,750 new cases in the US in 2020 [1]. Today, the performance of diagnosis has been by highly trained radiologists. However, the complex structures contribute to speckle noise and inhomogeneous intensity profiles. Thus, there is a necessity to automate segmentation on kidney ultrasounds using U-Net Deep Learning architectures - an innovative solution for Medical Imaging Analysis. In this research, our focus is on the comparison of Attention U-Net in the context of different backbones such as VGG19, ResNet152V2, and EfficientNetB7. By providing this comparison, we will accomplish a survey for future researchers to more effectively decide on which Attention U-Net architecture to utilize for their segmentation projects.

Renal Segmentation Using an Improved U-Net3D Model

Hundreds of thousands of people worldwide are diagnosed with kidney cancer each year, and this disease is more common in developed societies. Approximately 30% of patients with kidney cancer are recognized at the metastatic stage. Segmentation is an important process in the computer-aided treatment planning of kidney diseases. For this reason, more importance should be given to studies focused on segmentation as accurate segmentation is of high importance in the medical sense. This paper focuses on an improved version of the existing U-Net3D models. The aim is to assist physicians struggling with kidney segmentation. The improved U-Net3D model showed better performance than U-Net, U-Net+ResNet, and U-Net++ models, with 97.89% accurate segmentation.

Automated and robust organ segmentation for 3D-based internal dose calculation

Purpose In this work, we address image segmentation in the scope of dosimetry using deep learning and make three main contributions: (a) to extend and optimize the architecture of an existing convolutional neural network (CNN) in order to obtain a fast, robust and accurate computed tomography (CT)-based organ segmentation method for kidneys and livers; (b) to train the CNN with an inhomogeneous set of CT scans and validate the CNN for daily dosimetry; and (c) to evaluate dosimetry results obtained using automated organ segmentation in comparison with manual segmentation done by two independent experts. Methods We adapted a performant deep learning approach using CT-images to delineate organ boundaries with sufficiently high accuracy and adequate processing time. The segmented organs were consequently used as binary masks for further convolution with a point spread function to retrieve the activity values from quantitatively reconstructed SPECT images for “volumetric”/3D dosimetry. The resulting activities were used to perform dosimetry calculations with the kidneys as source organs. Results The computational expense of the algorithm was sufficient for clinical daily routine, required minimum pre-processing and performed with acceptable accuracy a Dice coefficient of $$93\%$$ 93 % for liver segmentation and of $$94\%$$ 94 % for kidney segmentation, respectively. In addition, kidney self-absorbed doses calculated using automated segmentation differed by $$7\%$$ 7 % from dosimetry performed by two medical physicists in 8 patients. Conclusion The proposed approach may accelerate volumetric dosimetry of kidneys in molecular radiotherapy with 177Lu-labelled radiopharmaceuticals such as 177Lu-DOTATOC. However, even though a fully automated segmentation methodology based on CT images accelerates organ segmentation and performs with high accuracy, it does not remove the need for supervision and corrections by experts, mostly due to misalignments in the co-registration between SPECT and CT images. Trial registration EudraCT, 2016-001897-13. Registered 26.04.2016, www.clinicaltrialsregister.eu/ctr-search/search?query=2016-001897-13.