Cyclic 2.5D Perceptual Loss for Cross-Modal 3D Image Synthesis: T1 MRI to Tau-PET

Alzheimer's Disease (AD) is the most common form of dementia, characterised by cognitive decline and biomarkers such as tau-proteins. Tau-positron emission tomography (tau-PET), which employs a radiotracer to selectively bind, detect, and visualise tau protein aggregates within the brain, is valuable for early AD diagnosis but is less accessible due to high costs, limited availability, and its invasive nature. Image synthesis with neural networks enables the generation of tau-PET images from more accessible T1-weighted magnetic resonance imaging (MRI) images. To ensure high-quality image synthesis, we propose a cyclic 2.5D perceptual loss combined with mean squared error and structural similarity index measure (SSIM) losses. The cyclic 2.5D perceptual loss sequentially calculates the axial 2D average perceptual loss for a specified number of epochs, followed by the coronal and sagittal planes for the same number of epochs. This sequence is cyclically performed, with intervals reducing as the cycles repeat. We conduct supervised synthesis of tau-PET images from T1w MRI images using 516 paired T1w MRI and tau-PET 3D images from the ADNI database. For the collected data, we perform preprocessing, including intensity standardisation for tau-PET images from each manufacturer. The proposed loss, applied to generative 3D U-Net and its variants, outperformed those with 2.5D and 3D perceptual losses in SSIM and peak signal-to-noise ratio (PSNR). In addition, including the cyclic 2.5D perceptual loss to the original losses of GAN-based image synthesis models such as CycleGAN and Pix2Pix improves SSIM and PSNR by at least 2% and 3%. Furthermore, by-manufacturer PET standardisation helps the models in synthesising high-quality images than min-max PET normalisation.

Why is the winner the best?

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multi-center study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and postprocessing (66%). The "typical" lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work.

Biomedical image analysis competitions: The state of current participation practice

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

Decreasing Annotation Burden of Pairwise Comparisons with Human-in-the-Loop Sorting: Application in Medical Image Artifact Rating

Ranking by pairwise comparisons has shown improved reliability over ordinal classification. However, as the annotations of pairwise comparisons scale quadratically, this becomes less practical when the dataset is large. We propose a method for reducing the number of pairwise comparisons required to rank by a quantitative metric, demonstrating the effectiveness of the approach in ranking medical images by image quality in this proof of concept study. Using the medical image annotation software that we developed, we actively subsample pairwise comparisons using a sorting algorithm with a human rater in the loop. We find that this method substantially reduces the number of comparisons required for a full ordinal ranking without compromising inter-rater reliability when compared to pairwise comparisons without sorting.

Engineering AI Tools for Systematic and Scalable Quality Assessment in Magnetic Resonance Imaging

A desire to achieve large medical imaging datasets keeps increasing as machine learning algorithms, parallel computing, and hardware technology evolve. Accordingly, there is a growing demand in pooling data from multiple clinical and academic institutes to enable large-scale clinical or translational research studies. Magnetic resonance imaging (MRI) is a frequently used, non-invasive imaging modality. However, constructing a big MRI data repository has multiple challenges related to privacy, data size, DICOM format, logistics, and non-standardized images. Not only building the data repository is difficult, but using data pooled from the repository is also challenging, due to heterogeneity in image acquisition, reconstruction, and processing pipelines across MRI vendors and imaging sites. This position paper describes challenges in constructing a large MRI data repository and using data downloaded from such data repositories in various aspects. To help address the challenges, the paper proposes introducing a quality assessment pipeline, with considerations and general design principles.