Datasets play a critical role in medical imaging research, yet issues such as label quality, shortcuts, and metadata are often overlooked. This lack of attention may harm the generalizability of algorithms and, consequently, negatively impact patient outcomes. While existing medical imaging literature reviews mostly focus on machine learning (ML) methods, with only a few focusing on datasets for specific applications, these reviews remain static -- they are published once and not updated thereafter. This fails to account for emerging evidence, such as biases, shortcuts, and additional annotations that other researchers may contribute after the dataset is published. We refer to these newly discovered findings of datasets as research artifacts. To address this gap, we propose a living review that continuously tracks public datasets and their associated research artifacts across multiple medical imaging applications. Our approach includes a framework for the living review to monitor data documentation artifacts, and an SQL database to visualize the citation relationships between research artifact and dataset. Lastly, we discuss key considerations for creating medical imaging datasets, review best practices for data annotation, discuss the significance of shortcuts and demographic diversity, and emphasize the importance of managing datasets throughout their entire lifecycle. Our demo is publicly available at http://130.226.140.142.

Medical image analysis tasks often focus on regions or structures located in a particular location within the patient's body. Often large parts of the image may not be of interest for the image analysis task. When using deep-learning based approaches, this causes an unnecessary increases the computational burden during inference and raises the chance of errors. In this paper, we introduce CTARR, a novel generic method for CT Anatomical Region Recognition. The method serves as a pre-processing step for any deep learning-based CT image analysis pipeline by automatically identifying the pre-defined anatomical region that is relevant for the follow-up task and removing the rest. It can be used in (i) image segmentation to prevent false positives in anatomically implausible regions and speeding up the inference, (ii) image classification to produce image crops that are consistent in their anatomical context, and (iii) image registration by serving as a fast pre-registration step. Our proposed method is based on atlas registration and provides a fast and robust way to crop any anatomical region encoded as one or multiple bounding box(es) from any unlabeled CT scan of the brain, chest, abdomen and/or pelvis. We demonstrate the utility and robustness of the proposed method in the context of medical image segmentation by evaluating it on six datasets of public segmentation challenges. The foreground voxels in the regions of interest are preserved in the vast majority of cases and tasks (97.45-100%) while taking only fractions of a seconds to compute (0.1-0.21s) on a deep learning workstation and greatly reducing the segmentation runtime (2.0-12.7x).

Purpose: To introduce a deep learning model capable of multi-organ segmentation in MRI scans, offering a solution to the current limitations in MRI analysis due to challenges in resolution, standardized intensity values, and variability in sequences. Materials and Methods: he model was trained on 1,200 manually annotated MRI scans from the UK Biobank, 221 in-house MRI scans and 1228 CT scans, leveraging cross-modality transfer learning from CT segmentation models. A human-in-the-loop annotation workflow was employed to efficiently create high-quality segmentations. The model's performance was evaluated on NAKO and the AMOS22 dataset containing 600 and 60 MRI examinations. Dice Similarity Coefficient (DSC) and Hausdorff Distance (HD) was used to assess segmentation accuracy. The model will be open sourced. Results: The model showcased high accuracy in segmenting well-defined organs, achieving Dice Similarity Coefficient (DSC) scores of 0.97 for the right and left lungs, and 0.95 for the heart. It also demonstrated robustness in organs like the liver (DSC: 0.96) and kidneys (DSC: 0.95 left, 0.95 right), which present more variability. However, segmentation of smaller and complex structures such as the portal and splenic veins (DSC: 0.54) and adrenal glands (DSC: 0.65 left, 0.61 right) revealed the need for further model optimization. Conclusion: The proposed model is a robust, tool for accurate segmentation of 40 anatomical structures in MRI and CT images. By leveraging cross-modality learning and interactive annotation, the model achieves strong performance and generalizability across diverse datasets, making it a valuable resource for researchers and clinicians. It is open source and can be downloaded from https://github.com/hhaentze/MRSegmentator.

Segmentation of medical images plays a vital role in many automatic image analysis tools. While segmentation has been well established for computed tomography (CT) scans, with multiple open source models available [1, 2], multi-class segmentation of magnetic resonance imaging (MRI), especially outside the brain, is lacking behind. The main reason for this challenge is that training segmentation models requires a large number of annotated images, and the more classes involved, the greater the annotation effort needed. While this problem can be partially alleviated by using augmented CT scans with existing labels for retraining a model [3], implementing and training an augmented model is resource-intensive, time-consuming, and technically challenging. In this short paper, we demonstrate that image augmentation, specifically inversion, can be sufficient to bridge the gap between MRI and CT segmentation performance and CT segmentation model can be used to generate masks for MR images. One key difference between MRI and CT images is that dense tissue, such as bones, appears bright (hyperdense) in CT scans but dark (hypointense) in MRI images. We attempt to minimize this difference by using negatives of MRI images and analyze whether it has an effect on the semantic segmentation performance of models trained solely on CT data.

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.

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.