Exploration of overlap volumes for radiotherapy plan evaluation with the aim of healthy tissue sparing.

PURPOSE: Development of a novel interactive visualization approach for the exploration of radiotherapy treatment plans with a focus on overlap volumes with the aim of healthy tissue sparing. METHODS: We propose a visualization approach to include overlap volumes in the radiotherapy treatment plan evaluation process. Quantitative properties can be interactively explored to identify critical regions and used to steer the visualization for a detailed inspection of candidates. We evaluated our approach with a user study covering the individual visualizations and their interactions regarding helpfulness, comprehensibility, intuitiveness, decision-making and speed. RESULTS: A user study with three domain experts was conducted using our software and evaluating five data sets each representing a different type of cancer and location by performing a set of tasks and filling out a questionnaire. The results show that the visualizations and interactions help to identify and evaluate overlap volumes according to their physical and dose properties. Furthermore, the task of finding dose hot spots can also benefit from our approach. CONCLUSIONS: The results indicate the potential to enhance the current treatment plan evaluation process in terms of healthy tissue sparing.

Exploring the performance of implicit neural representations for brain image registration.

Pairwise image registration is a necessary prerequisite for brain image comparison and data integration in neuroscience and radiology. In this work, we explore the efficacy of implicit neural representations (INRs) in improving the performance of brain image registration in magnetic resonance imaging. In this setting, INRs serve as a continuous and coordinate based approximation of the deformation field obtained through a multi-layer perceptron. Previous research has demonstrated that sinusoidal representation networks (SIRENs) surpass ReLU models in performance. In this study, we first broaden the range of activation functions to further investigate the registration performance of implicit networks equipped with activation functions that exhibit diverse oscillatory properties. Specifically, in addition to the SIRENs and ReLU, we evaluate activation functions based on snake, sine+, chirp and Morlet wavelet functions. Second, we conduct experiments to relate the hyper-parameters of the models to registration performance. Third, we propose and assess various techniques, including cycle consistency loss, ensembles and cascades of implicit networks, as well as a combined image fusion and registration objective, to enhance the performance of implicit registration networks beyond the standard approach. The investigated implicit methods are compared to the VoxelMorph convolutional neural network and to the symmetric image normalization (SyN) registration algorithm from the Advanced Normalization Tools (ANTs). Our findings not only highlight the remarkable capabilities of implicit networks in addressing pairwise image registration challenges, but also showcase their potential as a powerful and versatile off-the-shelf tool in the fields of neuroscience and radiology.

The Brain/MINDS Marmoset Connectivity Resource: An open-access platform for cellular-level tracing and tractography in the primate brain.

The primate brain has unique anatomical characteristics, which translate into advanced cognitive, sensory, and motor abilities. Thus, it is important that we gain insight on its structure to provide a solid basis for models that will clarify function. Here, we report on the implementation and features of the Brain/MINDS Marmoset Connectivity Resource (BMCR), a new open-access platform that provides access to high-resolution anterograde neuronal tracer data in the marmoset brain, integrated to retrograde tracer and tractography data. Unlike other existing image explorers, the BMCR allows visualization of data from different individuals and modalities in a common reference space. This feature, allied to an unprecedented high resolution, enables analyses of features such as reciprocity, directionality, and spatial segregation of connections. The present release of the BMCR focuses on the prefrontal cortex (PFC), a uniquely developed region of the primate brain that is linked to advanced cognition, including the results of 52 anterograde and 164 retrograde tracer injections in the cortex of the marmoset. Moreover, the inclusion of tractography data from diffusion MRI allows systematic analyses of this noninvasive modality against gold-standard cellular connectivity data, enabling detection of false positives and negatives, which provide a basis for future development of tractography. This paper introduces the BMCR image preprocessing pipeline and resources, which include new tools for exploring and reviewing the data.

Principles of Visualization in Radiation Oncology.

BACKGROUND: Medical visualization employs elements from computer graphics to create meaningful, interactive visual representations of medical data, and it has become an influential field of research for many advanced applications like radiation oncology, among others. Visual representations employ the user's cognitive capabilities to support and accelerate diagnostic, planning, and quality assurance workflows based on involved patient data. SUMMARY: This article discusses the basic underlying principles of visualization in the application domain of radiation oncology. The main visualization strategies, such as slice-based representations and surface and volume rendering are presented. Interaction topics, i.e., the combination of visualization and automated analysis methods, are also discussed. Key Messages: Slice-based representations are a common approach in radiation oncology, while volume visualization also has a long-standing history in the field. Perception within both representations can benefit further from advanced approaches, such as image fusion and multivolume or hybrid rendering. While traditional slice-based and volume representations keep evolving, the dimensionality and complexity of medical data are also increasing. To address this, visual analytics strategies are valuable, particularly for cohort or uncertainty visualization. Interactive visual analytics approaches represent a new opportunity to integrate knowledgeable experts and their cognitive abilities in exploratory processes which cannot be conducted by solely automatized methods.

Visualization of 4D multimodal imaging data and its applications in radiotherapy planning.

PURPOSE: To explore the benefit of using 4D multimodal visualization and interaction techniques for defined radiotherapy planning tasks over a treatment planning system used in clinical routine (C-TPS) without dedicated 4D visualization. METHODS: We developed a 4D visualization system (4D-VS) with dedicated rendering and fusion of 4D multimodal imaging data based on a list of requirements developed in collaboration with radiation oncologists. We conducted a user evaluation in which the benefits of our approach were evaluated in comparison to C-TPS for three specific tasks: assessment of internal target volume (ITV) delineation, classification of tumor location in peripheral or central, and assessment of dose distribution. For all three tasks, we presented test cases for which we measured correctness, certainty, consistency followed by an additional survey regarding specific visualization features. RESULTS: Lower quality of the test ITVs (ground truth quality was available) was more likely to be detected using 4D-VS. ITV ratings were more consistent in 4D-VS and the classification of tumor location had a higher accuracy. Overall evaluation of the survey indicates 4D-VS provides better spatial comprehensibility and simplifies the tasks which were performed during testing. CONCLUSIONS: The use of 4D-VS has improved the assessment of ITV delineations and classification of tumor location. The visualization features of 4D-VS have been identified as helpful for the assessment of dose distribution during user testing.

Visualization of Deformable Image Registration Quality Using Local Image Dissimilarity.

Deformable image registration (DIR) has the potential to improve modern radiotherapy in many aspects, including volume definition, treatment planning and image-guided adaptive radiotherapy. Studies have shown its possible clinical benefits. However, measuring DIR accuracy is difficult without known ground truth, but necessary before integration in the radiotherapy workflow. Visual assessment is an important step towards clinical acceptance. We propose a visualization framework which supports the exploration and the assessment of DIR accuracy. It offers different interaction and visualization features for exploration of candidate regions to simplify the process of visual assessment. The visualization is based on voxel-wise comparison of local image patches for which dissimilarity measures are computed and visualized to indicate locally the registration results. We performed an evaluation with three radiation oncologists to demonstrate the viability of our approach. In the evaluation, lung regions were rated by the participants with regards to their visual accuracy and compared to the registration error measured with expert defined landmarks. Regions rated as "accepted" had an average registration error of 1.8 mm, with the highest single landmark error being 3.3 mm. Additionally, survey results show that the proposed visualizations support a fast and intuitive investigation of DIR accuracy, and are suitable for finding even small errors.

Harmonic filters for 3D multichannel data: rotation invariant detection of mitoses in colorectal cancer.

In this paper, we present a novel approach for a trainable rotation invariant detection of complex structures in 3D microscopic multichannel data using a nonlinear filter approach. The basic idea of our approach is to compute local features in a window around each 3D position and map these features by means of a nonlinear mapping onto new local harmonic descriptors of the local window. These local harmonic descriptors are then combined in a linear way to form the output of the filter. The optimal combination of the computed local harmonic descriptors is determined in previous training step, and allows the filter to be adapted to an arbitrary structure depending on the problem at hand. Our approach is not limited to scalar-valued images and can also be used for vector-valued (multichannel) images such as gradient vector flow fields. We present realizations of a scalar-valued and a vector-valued multichannel filter. Our proposed algorithm was quantitatively evaluated on colorectal cancer cell lines (cells grown under controlled conditions), on which we successfully detected complex 3D mitotic structures. For a qualitative evaluation we tested our algorithms on human 3D tissue samples of colorectal cancer. We compare our results with a steerable filter approach as well as a morphology-based approach.