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Register a new userMedical imaging data structure extended to multiple modalities and anatomical regions
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Brain Imaging Data Structure (BIDS) allows the user to organise brain imaging data into a clear and easy standard directory structure. BIDS is widely supported by the scientific community and is considered a powerful standard for management. The original BIDS is limited to images or data related to the brain. Medical Imaging Data Structure (MIDS) was therefore conceived with the objective of extending this methodology to other anatomical regions and other types of imaging systems in these areas.
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Since the advent of deep convolutional neural networks (DNNs), computer vision has seen an extremely rapid progress that has led to huge advances in medical imaging. This article does not aim to cover all aspects of the field but focuses on a particular topic, image-to-image translation. Although the topic may not sound familiar, it turns out that many seemingly irrelevant applications can be understood as instances of image-to-image translation. Such applications include (1) noise reduction, (2) super-resolution, (3) image synthesis, and (4) reconstruction. The same underlying principles and algorithms work for various tasks. Our aim is to introduce some of the key ideas on this topic from a uniform point of view. We introduce core ideas and jargon that are specific to image processing by use of DNNs. Having an intuitive grasp of the core ideas of and a knowledge of technical terms would be of great help to the reader for understanding the existing and future applications. Most of the recent applications which build on image-to-image translation are based on one of two fundamental architectures, called pix2pix and CycleGAN, depending on whether the available training data are paired or unpaired. We provide computer codes which implement these two architectures with various enhancements. Our codes are available online with use of the very permissive MIT license. We provide a hands-on tutorial for training a model for denoising based on our codes. We hope that this article, together with the codes, will provide both an overview and the details of the key algorithms, and that it will serve as a basis for the development of new applications.
Artificial intelligence (AI)-based methods are showing promise in multiple medical-imaging applications. Thus, there is substantial interest in clinical translation of these methods, requiring in turn, that they be evaluated rigorously. In this paper, our goal is to lay out a framework for objective task-based evaluation of AI methods. We will also provide a list of tools available in the literature to conduct this evaluation. Further, we outline the important role of physicians in conducting these evaluation studies. The examples in this paper will be proposed in the context of PET with a focus on neural-network-based methods. However, the framework is also applicable to evaluate other medical-imaging modalities and other types of AI methods.
We explore the application of concepts developed in High Energy Physics (HEP) for advanced medical data analysis. Our study case is a problem with high social impact: clinically-feasible Magnetic Resonance Fingerprinting (MRF). MRF is a new, quantitative, imaging technique that replaces multiple qualitative Magnetic Resonance Imaging (MRI) exams with a single, reproducible measurement for increased sensitivity and efficiency. A fast acquisition is followed by a pattern matching (PM) task, where signal responses are matched to entries from a dictionary of simulated, physically-feasible responses, yielding multiple tissue parameters simultaneously. Each pixel signal response in the volume is compared through scalar products with all dictionary entries to choose the best measurement reproduction. MRF is limited by the PM processing time, which scales exponentially with the dictionary dimensionality, i.e. with the number of tissue parameters to be reconstructed. We developed for HEP a powerful, compact, embedded system, optimized for extremely fast PM. This system executes real-time tracking for online event selection in the HEP experiments, exploiting maximum parallelism and pipelining. Track reconstruction is executed in two steps. The Associative Memory (AM) ASIC first implements a PM algorithm by recognizing track candidates at low resolution. The second step, which is implemented into FPGAs (Field Programmable Gate Arrays), refines the AM output finding the track parameters at full resolution. We propose to use this system to perform MRF, to achieve clinically reasonable reconstruction time. This paper proposes an adaptation of the HEP system for medical imaging and shows some preliminary results.
Beam quality optimization in mammography traditionally considers detection of a target obscured by quantum noise on a homogenous background. It can be argued that this scheme does not correspond well to the clinical imaging task because real mammographic images contain a complex superposition of anatomical structures, resulting in anatomical noise that may dominate over quantum noise. Using a newly developed spectral mammography system, we measured the correlation and magnitude of the anatomical noise in a set of mammograms. The results from these measurements were used as input to an observer-model optimization that included quantum noise as well as anatomical noise. We found that, within this framework, the detectability of tumors and microcalcifications behaved very differently with respect to beam quality and dose. The results for small microcalcifications were similar to what traditional optimization methods would yield, which is to be expected since quantum noise dominates over anatomical noise at high spatial frequencies. For larger tumors, however, low-frequency anatomical noise was the limiting factor. Because anatomical structure has similar energy dependence as tumor contrast, optimal x-ray energy was significantly higher and the useful energy region wider than traditional methods suggest. Measurements on a tissue phantom confirmed these theoretical results. Furthermore, since quantum noise constitutes only a small fraction of the noise, the dose could be reduced substantially without sacrificing tumor detectability. Exposure settings used clinically are therefore not necessarily optimal for this imaging task. The impact of these findings on the mammographic imaging task as a whole is, however, at this stage unclear.
We present three imaging modalities that live on the crossroads of seismic and medical imaging. Through the lens of extended source imaging, we can draw deep connections among the fields of wave-equation based seismic and medical imaging, despite first appearances. From the seismic perspective, we underline the importance to work with the correct physics and spatially varying velocity fields. Medical imaging, on the other hand, opens the possibility for new imaging modalities where outside stimuli, such as laser or radar pulses, can not only be used to identify endogenous optical or thermal contrasts but that these sources can also be used to insonify the medium so that images of the whole specimen can in principle be created.
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