On robust estimation of the location parameter

A reproducible evaluation of ANTs similarity metric performance in brain image registration.

Medical image registration is an important task in medical image processing. It refers to the process of aligning data sets, possibly from different modalities (e.g., magnetic resonance and computed tomography), different time points (e.g., follow-up scans), and/or different subjects (in case of population studies). A large number of methods for image registration are described in the literature. Unfortunately, there is not one method that works for all applications. We have therefore developed elastix, a publicly available computer program for intensity-based medical image registration. The software consists of a collection of algorithms that are commonly used to solve medical image registration problems. The modular design of elastix allows the user to quickly configure, test, and compare different registration methods for a specific application. The command-line interface enables automated processing of large numbers of data sets, by means of scripting. The usage of elastix for comparing different registration methods is illustrated with three example experiments, in which individual components of the registration method are varied.

elastix : A Toolbox for Intensity-Based Medical Image Registration

MUCKE aims to mine a large volume of images, to structure them conceptually and to use this conceptual structuring in order to improve large-scale image retrieval. The last decade witnessed important progress concerning low-level image representations. However, there are a number problems which need to be solved in order to unleash the full potential of image mining in applications. The central problem with low-level representations is the mismatch between them and the human interpretation of image content. This problem can be instantiated, for instance, by the incapability of existing descriptors to capture spatial relationships between the concepts represented or by their incapability to convey an explanation of why two images are similar in a content-based image retrieval framework. We start by assessing existing local descriptors for image classification and by proposing to use co-occurrence matrices to better capture spatial relationships in images. The main focus in MUCKE is on cleaning large scale Web image corpora and on proposing image representations which are closer to the human interpretation of images. Consequently, we introduce methods which tackle these two problems and compare results to state of the art methods. Note: some aspects of this deliverable are withheld at this time as they are pending review. Please contact the authors for a preview.

http://ieeexplore.ieee.org/iel2/4524/12820/00592460.pdf

Image Processing

Digital audio, video, images, and documents are flying through cyberspace to their respective owners. Unfortunately, along the way, individuals may choose to intervene and take this content for themselves. Digital watermarking and steganography technology greatly reduces the instances of this by limiting or eliminating the ability of third parties to decipher the content that he has taken. The many techiniques of digital watermarking (embedding a code) and steganography (hiding information) continue to evolve as applications that necessitate them do the same. The authors of this second edition provide an update on the framework for applying these techniques that they provided researchers and professionals in the first well-received edition. Steganography and steganalysis (the art of detecting hidden information) have been added to a robust treatment of digital watermarking, as many in each field research and deal with the other. New material includes watermarking with side information, QIM, and dirty-paper codes. The revision and inclusion of new material by these influential authors has created a must-own book for anyone in this profession.

*This new edition now contains essential information on steganalysis and steganography
*New concepts and new applications including QIM introduced
*Digital watermark embedding is given a complete update with new processes and applications

Digital Watermarking and Steganography

Literature on medical imaging segmentation claims that hybrid UNet models containing both Transformer and convolutional blocks perform better than purely convolutional UNet models. This recently touted success of hybrid Transformers warrants an investigation into which of its components contribute to its performance. Also, previous work has a limitation of analysis only at fixed dataset scales as well as unfair comparisons with other models where parameter counts are not equivalent. Here, we investigate the performance of a hybrid Transformer network i.e. the nnFormer for organ segmentation in prostate CT scans. We do this in context of replacing its various components and by constructing learning curves by plotting model performance at different dataset scales. To compare with literature, the first experiment replaces all the shifted-window(swin) Transformer blocks of the nnFormer with convolutions. Results show that the convolution prevails as the data scale increases. In the second experiment, to reduce complexity, the self-attention mechanism within the swin-Transformer block is replaced with an similar albeit simpler spatial mixing operation i.e. max-pooling. We observe improved performance for max-pooling in smaller dataset scales, indicating that the window-based Transformer may not be the best choice in both small and larger dataset scales. Finally, since convolution has an inherent local inductive bias of positional information, we conduct a third experiment to imbibe such a property to the Transformer by exploring two kinds of positional encodings. The results show that there are insignificant improvements after adding positional encoding, indicating the hybrid swin-Transformers deficiency in capturing positional information given our dataset at its various scales. Through this work, we hope to motivate the community to use learning curves under fair experimental settings to evaluate the efficacy of newer architectures like Transformers for their medical imaging tasks. Code is available on https://github.com/prerakmody/ window-transformer-prostate-segmentation.

Analyzing components of a transformer under different dataset scales in 3D prostate CT segmentation

PD-0066 Autocontouring of the mouse thorax using deep learning

Delineation of tumors and organs-at-risk permits detecting and correcting changes in the patients’ anatomy throughout the treatment, making it a core step of adaptive proton therapy (APT). Although AI-based autocontouring technologies have sped up this process, the time needed to perform the quality assessment (QA) of the generated contours remains a bottleneck, taking clinicians between several minutes up to an hour to complete. This paper introduces a fast contouring workflow suitable for time-critical APT, enabling detection of anatomical changes in shorter time frames and with a lower demand of clinical resources. The proposed AI-infused workflow follows two principles uncovered after reviewing the APT literature and conducting several interviews and an observational study in two radiotherapy centers in the Netherlands. First, enable targeted inspection of the generated contours by leveraging AI uncertainty and clinically-relevant features such as the proximity of the organs-at-risk to the tumor. Second, minimize the number of interactions needed to edit faulty delineations with redundancy-aware editing tools that provide the user a sense of predictability and control. We use a proof of concept that we validated with clinicians to demonstrate how current and upcoming AI capabilities support the workflow and how it would fit into clinical practice.

Report on AI-Infused Contouring Workflows for Adaptive Proton Therapy in the Head and Neck

Abstract The shape and distribution of vascular lesions in pulmonary embolism (PE) and chronic thromboembolic pulmonary hypertension (CTEPH) are different. We investigated whether automated quantification of pulmonary vascular morphology and densitometry in arteries and veins imaged by computed tomographic pulmonary angiography (CTPA) could distinguish PE from CTEPH. We analyzed CTPA images from a cohort of 16 PE patients, 6 CTEPH patients, and 15 controls. Pulmonary vessels were extracted with a graph‐cut method, and separated into arteries and veins using deep‐learning classification. Vascular morphology was quantified by the slope (α) and intercept (β) of the vessel radii distribution. To quantify lung perfusion defects, the median pulmonary vascular density was calculated. By combining these measurements with densities measured in parenchymal areas, pulmonary trunk, and descending aorta, a static perfusion curve was constructed. All separate quantifications were compared between the three groups. No vascular morphology differences were detected in contrast to vascular density values. The median vascular density (interquartile range) was −567 (113), −452 (95), and −470 (323) HU, for the control, PE, and CTEPH group. The static perfusion curves showed different patterns between groups, with a statistically significant difference in aorta‐pulmonary trunk gradient between the PE and CTEPH groups (p = 0.008). In this proof of concept study, not vasculature morphology but densities differentiated between patients of three groups. Further technical improvements are needed to allow for accurate differentiation between PE and CTEPH, which in this study was only possible statistically by measuring the density gradient between aorta and pulmonary trunk.

https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pul2.12223

Automated quantification of the pulmonary vasculature in pulmonary embolism and chronic thromboembolic pulmonary hypertension

Non-rigid registration is essential for a wide range of clinical applications, such as intraoperative image-guidance and postoperative follow-up assessment, and longitudinal image analysis for disease diagnosis and monitoring. Vascular structures are a rich descriptor of the organ deformation, since it permeates through all organs within body. As vasculature differs in size, shape and topology, following surgical intervention/treatment or due to disease progression, non-rigid vessel matching remains a challenging task. Recently, hybrid mixture models (HdMM) have been applied to tackle this challenge, and demonstrate significant improvements in terms of accuracy and robustness relative to the state-of-the-art. However, the smoothness constraint enforced on the deformation field with this approach only accounts for the global topology of the vasculature, resulting in a reduced capacity to accurately match localized changes to vascular structures, and preserve local topology. In this work, we proposed a modified version of HdMM by formulating an adaptive kernel, to enforce a local smoothness constraint on the deformation field, henceforth referred to as HdMMad. The proposed HdMMad framework is evaluated with cerebral and pulmonary vasculature, acquired retrospectively. The registration results for both data sets demonstrate that the proposed approach outperforms registration algorithms also designed to preserve local topology. Using HdMMad, around 80% of the initial registration error was reduced, for both data sets.

Marius Staring

Papers

Analyzing components of a transformer under different dataset scales in 3D prostate CT segmentation

PD-0066 Autocontouring of the mouse thorax using deep learning

Report on AI-Infused Contouring Workflows for Adaptive Proton Therapy in the Head and Neck

Automated quantification of the pulmonary vasculature in pulmonary embolism and chronic thromboembolic pulmonary hypertension

Local topology preservation for vascular centerline matching using a hybrid mixture model