Brain Tumour Removing and Missing Modality Generation using 3D WDM

This paper presents the second-placed solution for task 8 and the participation solution for task 7 of BraTS 2024. The adoption of automated brain analysis algorithms to support clinical practice is increasing. However, many of these algorithms struggle with the presence of brain lesions or the absence of certain MRI modalities. The alterations in the brain's morphology leads to high variability and thus poor performance of predictive models that were trained only on healthy brains. The lack of information that is usually provided by some of the missing MRI modalities also reduces the reliability of the prediction models trained with all modalities. In order to improve the performance of these models, we propose the use of conditional 3D wavelet diffusion models. The wavelet transform enabled full-resolution image training and prediction on a GPU with 48 GB VRAM, without patching or downsampling, preserving all information for prediction. For the inpainting task of BraTS 2024, the use of a large and variable number of healthy masks and the stability and efficiency of the 3D wavelet diffusion model resulted in 0.007, 22.61 and 0.842 in the validation set and 0.07 , 22.8 and 0.91 in the testing set (MSE, PSNR and SSIM respectively). The code for these tasks is available at https://github.com/ShadowTwin41/BraTS_2023_2024_solutions.

Improved Multi-Task Brain Tumour Segmentation with Synthetic Data Augmentation

This paper presents the winning solution of task 1 and the third-placed solution of task 3 of the BraTS challenge. The use of automated tools in clinical practice has increased due to the development of more and more sophisticated and reliable algorithms. However, achieving clinical standards and developing tools for real-life scenarios is a major challenge. To this end, BraTS has organised tasks to find the most advanced solutions for specific purposes. In this paper, we propose the use of synthetic data to train state-of-the-art frameworks in order to improve the segmentation of adult gliomas in a post-treatment scenario, and the segmentation of meningioma for radiotherapy planning. Our results suggest that the use of synthetic data leads to more robust algorithms, although the synthetic data generation pipeline is not directly suited to the meningioma task. The code for these tasks is available at https://github.com/ShadowTwin41/BraTS_2023_2024_solutions.

Spacewalker: Traversing Representation Spaces for Fast Interactive Exploration and Annotation of Unstructured Data

Unstructured data in industries such as healthcare, finance, and manufacturing presents significant challenges for efficient analysis and decision making. Detecting patterns within this data and understanding their impact is critical but complex without the right tools. Traditionally, these tasks relied on the expertise of data analysts or labor-intensive manual reviews. In response, we introduce Spacewalker, an interactive tool designed to explore and annotate data across multiple modalities. Spacewalker allows users to extract data representations and visualize them in low-dimensional spaces, enabling the detection of semantic similarities. Through extensive user studies, we assess Spacewalker's effectiveness in data annotation and integrity verification. Results show that the tool's ability to traverse latent spaces and perform multi-modal queries significantly enhances the user's capacity to quickly identify relevant data. Moreover, Spacewalker allows for annotation speed-ups far superior to conventional methods, making it a promising tool for efficiently navigating unstructured data and improving decision making processes. The code of this work is open-source and can be found at: https://github.com/code-lukas/Spacewalker

CC-DCNet: Dynamic Convolutional Neural Network with Contrastive Constraints for Identifying Lung Cancer Subtypes on Multi-modality Images

The accurate diagnosis of pathological subtypes of lung cancer is of paramount importance for follow-up treatments and prognosis managements. Assessment methods utilizing deep learning technologies have introduced novel approaches for clinical diagnosis. However, the majority of existing models rely solely on single-modality image input, leading to limited diagnostic accuracy. To this end, we propose a novel deep learning network designed to accurately classify lung cancer subtype with multi-dimensional and multi-modality images, i.e., CT and pathological images. The strength of the proposed model lies in its ability to dynamically process both paired CT-pathological image sets as well as independent CT image sets, and consequently optimize the pathology-related feature extractions from CT images. This adaptive learning approach enhances the flexibility in processing multi-dimensional and multi-modality datasets and results in performance elevating in the model testing phase. We also develop a contrastive constraint module, which quantitatively maps the cross-modality associations through network training, and thereby helps to explore the "gold standard" pathological information from the corresponding CT scans. To evaluate the effectiveness, adaptability, and generalization ability of our model, we conducted extensive experiments on a large-scale multi-center dataset and compared our model with a series of state-of-the-art classification models. The experimental results demonstrated the superiority of our model for lung cancer subtype classification, showcasing significant improvements in accuracy metrics such as ACC, AUC, and F1-score.

Deep Dive into MRI: Exploring Deep Learning Applications in 0.55T and 7T MRI

The development of magnetic resonance imaging (MRI) for medical imaging has provided a leap forward in diagnosis, providing a safe, non-invasive alternative to techniques involving ionising radiation exposure for diagnostic purposes. It was described by Block and Purcel in 1946, and it was not until 1980 that the first clinical application of MRI became available. Since that time the MRI has gone through many advances and has altered the way diagnosing procedures are performed. Due to its ability to improve constantly, MRI has become a commonly used practice among several specialisations in medicine. Particularly starting 0.55T and 7T MRI technologies have pointed out enhanced preservation of image detail and advanced tissue characterisation. This review examines the integration of deep learning (DL) techniques into these MRI modalities, disseminating and exploring the study applications. It highlights how DL contributes to 0.55T and 7T MRI data, showcasing the potential of DL in improving and refining these technologies. The review ends with a brief overview of how MRI technology will evolve in the coming years.

Deep Learning-based Point Cloud Registration for Augmented Reality-guided Surgery

Point cloud registration aligns 3D point clouds using spatial transformations. It is an important task in computer vision, with applications in areas such as augmented reality (AR) and medical imaging. This work explores the intersection of two research trends: the integration of AR into image-guided surgery and the use of deep learning for point cloud registration. The main objective is to evaluate the feasibility of applying deep learning-based point cloud registration methods for image-to-patient registration in augmented reality-guided surgery. We created a dataset of point clouds from medical imaging and corresponding point clouds captured with a popular AR device, the HoloLens 2. We evaluate three well-established deep learning models in registering these data pairs. While we find that some deep learning methods show promise, we show that a conventional registration pipeline still outperforms them on our challenging dataset.

Deep Medial Voxels: Learned Medial Axis Approximations for Anatomical Shape Modeling

Shape reconstruction from imaging volumes is a recurring need in medical image analysis. Common workflows start with a segmentation step, followed by careful post-processing and,finally, ad hoc meshing algorithms. As this sequence can be timeconsuming, neural networks are trained to reconstruct shapes through template deformation. These networks deliver state-ofthe-art results without manual intervention, but, so far, they have primarily been evaluated on anatomical shapes with little topological variety between individuals. In contrast, other works favor learning implicit shape models, which have multiple benefits for meshing and visualization. Our work follows this direction by introducing deep medial voxels, a semi-implicit representation that faithfully approximates the topological skeleton from imaging volumes and eventually leads to shape reconstruction via convolution surfaces. Our reconstruction technique shows potential for both visualization and computer simulations.

How we won BraTS 2023 Adult Glioma challenge? Just faking it! Enhanced Synthetic Data Augmentation and Model Ensemble for brain tumour segmentation

Deep Learning is the state-of-the-art technology for segmenting brain tumours. However, this requires a lot of high-quality data, which is difficult to obtain, especially in the medical field. Therefore, our solutions address this problem by using unconventional mechanisms for data augmentation. Generative adversarial networks and registration are used to massively increase the amount of available samples for training three different deep learning models for brain tumour segmentation, the first task of the BraTS2023 challenge. The first model is the standard nnU-Net, the second is the Swin UNETR and the third is the winning solution of the BraTS 2021 Challenge. The entire pipeline is built on the nnU-Net implementation, except for the generation of the synthetic data. The use of convolutional algorithms and transformers is able to fill each other's knowledge gaps. Using the new metric, our best solution achieves the dice results 0.9005, 0.8673, 0.8509 and HD95 14.940, 14.467, 17.699 (whole tumour, tumour core and enhancing tumour) in the validation set.

Deep PCCT: Photon Counting Computed Tomography Deep Learning Applications Review

Medical imaging faces challenges such as limited spatial resolution, interference from electronic noise and poor contrast-to-noise ratios. Photon Counting Computed Tomography (PCCT) has emerged as a solution, addressing these issues with its innovative technology. This review delves into the recent developments and applications of PCCT in pre-clinical research, emphasizing its potential to overcome traditional imaging limitations. For example PCCT has demonstrated remarkable efficacy in improving the detection of subtle abnormalities in breast, providing a level of detail previously unattainable. Examining the current literature on PCCT, it presents a comprehensive analysis of the technology, highlighting the main features of scanners and their varied applications. In addition, it explores the integration of deep learning into PCCT, along with the study of radiomic features, presenting successful applications in data processing. While acknowledging these advances, it also discusses the existing challenges in this field, paving the way for future research and improvements in medical imaging technologies. Despite the limited number of articles on this subject, due to the recent integration of PCCT at a clinical level, its potential benefits extend to various diagnostic applications.

Cyto R-CNN and CytoNuke Dataset: Towards reliable whole-cell segmentation in bright-field histological images

Background: Cell segmentation in bright-field histological slides is a crucial topic in medical image analysis. Having access to accurate segmentation allows researchers to examine the relationship between cellular morphology and clinical observations. Unfortunately, most segmentation methods known today are limited to nuclei and cannot segmentate the cytoplasm. Material & Methods: We present a new network architecture Cyto R-CNN that is able to accurately segment whole cells (with both the nucleus and the cytoplasm) in bright-field images. We also present a new dataset CytoNuke, consisting of multiple thousand manual annotations of head and neck squamous cell carcinoma cells. Utilizing this dataset, we compared the performance of Cyto R-CNN to other popular cell segmentation algorithms, including QuPath's built-in algorithm, StarDist and Cellpose. To evaluate segmentation performance, we calculated AP50, AP75 and measured 17 morphological and staining-related features for all detected cells. We compared these measurements to the gold standard of manual segmentation using the Kolmogorov-Smirnov test. Results: Cyto R-CNN achieved an AP50 of 58.65% and an AP75 of 11.56% in whole-cell segmentation, outperforming all other methods (QuPath $19.46/0.91\%$; StarDist $45.33/2.32\%$; Cellpose $31.85/5.61\%$). Cell features derived from Cyto R-CNN showed the best agreement to the gold standard ($\bar{D} = 0.15$) outperforming QuPath ($\bar{D} = 0.22$), StarDist ($\bar{D} = 0.25$) and Cellpose ($\bar{D} = 0.23$). Conclusion: Our newly proposed Cyto R-CNN architecture outperforms current algorithms in whole-cell segmentation while providing more reliable cell measurements than any other model. This could improve digital pathology workflows, potentially leading to improved diagnosis. Moreover, our published dataset can be used to develop further models in the future.