Image and Video Processing (eess.IV)

Abstract: The task of medical image segmentation presents unique challenges, necessitating both localized and holistic semantic understanding to accurately delineate areas of interest, such as critical tissues or aberrant features. This complexity is heightened in medical image segmentation due to the high degree of inter-class similarities, intra-class variations, and possible image obfuscation. The segmentation task further diversifies when considering the study of histopathology slides for autoimmune diseases like dermatomyositis. The analysis of cell inflammation and interaction in these cases has been less studied due to constraints in data acquisition pipelines. Despite the progressive strides in medical science, we lack a comprehensive collection of autoimmune diseases. As autoimmune diseases globally escalate in prevalence and exhibit associations with COVID-19, their study becomes increasingly essential. While there is existing research that integrates artificial intelligence in the analysis of various autoimmune diseases, the exploration of dermatomyositis remains relatively underrepresented. In this paper, we present a deep-learning approach tailored for Medical image segmentation. Our proposed method outperforms the current state-of-the-art techniques by an average of 12.26% for U-Net and 12.04% for U-Net++ across the ResNet family of encoders on the dermatomyositis dataset. Furthermore, we probe the importance of optimizing loss function weights and benchmark our methodology on three challenging medical image segmentation tasks

Abstract: We propose to learn non-convex regularizers with a prescribed upper bound on their weak-convexity modulus. Such regularizers give rise to variational denoisers that minimize a convex energy. They rely on few parameters (less than 15,000) and offer a signal-processing interpretation as they mimic handcrafted sparsity-promoting regularizers. Through numerical experiments, we show that such denoisers outperform convex-regularization methods as well as the popular BM3D denoiser. Additionally, the learned regularizer can be deployed to solve inverse problems with iterative schemes that provably converge. For both CT and MRI reconstruction, the regularizer generalizes well and offers an excellent tradeoff between performance, number of parameters, guarantees, and interpretability when compared to other data-driven approaches.

Abstract: Automated organ at risk (OAR) segmentation is crucial for radiation therapy planning in CT scans, but the generated contours by automated models can be inaccurate, potentially leading to treatment planning issues. The reasons for these inaccuracies could be varied, such as unclear organ boundaries or inaccurate ground truth due to annotation errors. To improve the model's performance, it is necessary to identify these failure cases during the training process and to correct them with some potential post-processing techniques. However, this process can be time-consuming, as traditionally it requires manual inspection of the predicted output. This paper proposes a method to automatically identify failure cases by setting a threshold for the combination of Dice and Hausdorff distances. This approach reduces the time-consuming task of visually inspecting predicted outputs, allowing for faster identification of failure case candidates. The method was evaluated on 20 cases of six different organs in CT images from clinical expert curated datasets. By setting the thresholds for the Dice and Hausdorff distances, the study was able to differentiate between various states of failure cases and evaluate over 12 cases visually. This thresholding approach could be extended to other organs, leading to faster identification of failure cases and thereby improving the quality of radiation therapy planning.

Abstract: Early surgical treatment of brain tumors is crucial in reducing patient mortality rates. However, brain tissue deformation (called brain shift) occurs during the surgery, rendering pre-operative images invalid. As a cost-effective and portable tool, intra-operative ultrasound (iUS) can track brain shift, and accurate MRI-iUS registration techniques can update pre-surgical plans and facilitate the interpretation of iUS. This can boost surgical safety and outcomes by maximizing tumor removal while avoiding eloquent regions. However, manual assessment of MRI-iUS registration results in real-time is difficult and prone to errors due to the 3D nature of the data. Automatic algorithms that can quantify the quality of inter-modal medical image registration outcomes can be highly beneficial. Therefore, we propose a novel deep-learning (DL) based framework with the Swin UNETR to automatically assess 3D-patch-wise dense error maps for MRI-iUS registration in iUS-guided brain tumor resection and show its performance with real clinical data for the first time.

Abstract: Purpose: The purpose of this study was to develop and evaluate rule-based algorithms to enhance the extraction of text data, including retinal nerve fiber layer (RNFL) values and other ganglion cell count (GCC) data, from Zeiss Cirrus optical coherence tomography (OCT) scan reports. Methods: DICOM files that contained encapsulated PDF reports with RNFL or Ganglion Cell in their document titles were identified from a clinical imaging repository at a single academic ophthalmic center. PDF reports were then converted into image files and processed using the PaddleOCR Python package for optical character recognition. Rule-based algorithms were designed and iteratively optimized for improved performance in extracting RNFL and GCC data. Evaluation of the algorithms was conducted through manual review of a set of RNFL and GCC reports. Results: The developed algorithms demonstrated high precision in extracting data from both RNFL and GCC scans. Precision was slightly better for the right eye in RNFL extraction (OD: 0.9803 vs. OS: 0.9046), and for the left eye in GCC extraction (OD: 0.9567 vs. OS: 0.9677). Some values presented more challenges in extraction, particularly clock hours 5 and 6 for RNFL thickness, and signal strength for GCC. Conclusions: A customized optical character recognition algorithm can identify numeric results from optical coherence scan reports with high precision. Automated processing of PDF reports can greatly reduce the time to extract OCT results on a large scale.