Anjany Sekuboyina

Jianning Li, Zongwei Zhou, Jiancheng Yang et al.

Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from numerous shape-related publications in premier vision conferences as well as the growing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models). For the medical domain, we present a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. As of today, MedShapeNet includes 23 dataset with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface (API) and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present use cases in the fields of classification of brain tumors, facial and skull reconstructions, multi-class anatomy completion, education, and 3D printing. In future, we will extend the data and improve the interfaces. The project pages are: https://medshapenet.ikim.nrw/ and https://github.com/Jianningli/medshapenet-feedback

Ibrahim Ethem Hamamci, Sezgin Er, Enis Simsar et al.

Due to the necessity for precise treatment planning, the use of panoramic X-rays to identify different dental diseases has tremendously increased. Although numerous ML models have been developed for the interpretation of panoramic X-rays, there has not been an end-to-end model developed that can identify problematic teeth with dental enumeration and associated diagnoses at the same time. To develop such a model, we structure the three distinct types of annotated data hierarchically following the FDI system, the first labeled with only quadrant, the second labeled with quadrant-enumeration, and the third fully labeled with quadrant-enumeration-diagnosis. To learn from all three hierarchies jointly, we introduce a novel diffusion-based hierarchical multi-label object detection framework by adapting a diffusion-based method that formulates object detection as a denoising diffusion process from noisy boxes to object boxes. Specifically, to take advantage of the hierarchically annotated data, our method utilizes a novel noisy box manipulation technique by adapting the denoising process in the diffusion network with the inference from the previously trained model in hierarchical order. We also utilize a multi-label object detection method to learn efficiently from partial annotations and to give all the needed information about each abnormal tooth for treatment planning. Experimental results show that our method significantly outperforms state-of-the-art object detection methods, including RetinaNet, Faster R-CNN, DETR, and DiffusionDet for the analysis of panoramic X-rays, demonstrating the great potential of our method for hierarchically and partially annotated datasets. The code and the data are available at: https://github.com/ibrahimethemhamamci/HierarchicalDet.

Hendrik Möller, Hanna Schoen, Robert Graf et al.

The human spine commonly consists of seven cervical, twelve thoracic, and five lumbar vertebrae. However, enumeration anomalies may result in individuals having eleven or thirteen thoracic vertebrae and four or six lumbar vertebrae. Although the identification of enumeration anomalies has potential clinical implications for chronic back pain and operation planning, the thoracolumbar junction is often poorly assessed and rarely described in clinical reports. Additionally, even though multiple deep-learning-based vertebra labeling algorithms exist, there is a lack of methods to automatically label enumeration anomalies. Our work closes that gap by introducing "Vertebra Identification with Anomaly Handling" (VERIDAH), a novel vertebra labeling algorithm based on multiple classification heads combined with a weighted vertebra sequence prediction algorithm. We show that our approach surpasses existing models on T2w TSE sagittal (98.30% vs. 94.24% of subjects with all vertebrae correctly labeled, p < 0.001) and CT imaging (99.18% vs. 77.26% of subjects with all vertebrae correctly labeled, p < 0.001) and works in arbitrary field-of-view images. VERIDAH correctly labeled the presence 2 Möller et al. of thoracic enumeration anomalies in 87.80% and 96.30% of T2w and CT images, respectively, and lumbar enumeration anomalies in 94.48% and 97.22% for T2w and CT, respectively. Our code and models are available at: https://github.com/Hendrik-code/spineps.

Robert Graf, Joachim Schmitt, Sarah Schlaeger et al.

Background: Automated segmentation of spinal MR images plays a vital role both scientifically and clinically. However, accurately delineating posterior spine structures presents challenges. Methods: This retrospective study, approved by the ethical committee, involved translating T1w and T2w MR image series into CT images in a total of n=263 pairs of CT/MR series. Landmark-based registration was performed to align image pairs. We compared 2D paired (Pix2Pix, denoising diffusion implicit models (DDIM) image mode, DDIM noise mode) and unpaired (contrastive unpaired translation, SynDiff) image-to-image translation using "peak signal to noise ratio" (PSNR) as quality measure. A publicly available segmentation network segmented the synthesized CT datasets, and Dice scores were evaluated on in-house test sets and the "MRSpineSeg Challenge" volumes. The 2D findings were extended to 3D Pix2Pix and DDIM. Results: 2D paired methods and SynDiff exhibited similar translation performance and Dice scores on paired data. DDIM image mode achieved the highest image quality. SynDiff, Pix2Pix, and DDIM image mode demonstrated similar Dice scores (0.77). For craniocaudal axis rotations, at least two landmarks per vertebra were required for registration. The 3D translation outperformed the 2D approach, resulting in improved Dice scores (0.80) and anatomically accurate segmentations in a higher resolution than the original MR image. Conclusion: Two landmarks per vertebra registration enabled paired image-to-image translation from MR to CT and outperformed all unpaired approaches. The 3D techniques provided anatomically correct segmentations, avoiding underprediction of small structures like the spinous process.

Ibrahim Ethem Hamamci, Sezgin Er, Chenyu Wang et al.

Advancements in medical imaging AI, particularly in 3D imaging, have been limited due to the scarcity of comprehensive datasets. We introduce CT-RATE, a public dataset that pairs 3D medical images with corresponding textual reports. CT-RATE comprises 25,692 non-contrast 3D chest CT scans from 21,304 unique patients. Each scan is accompanied by its corresponding radiology report. Leveraging CT-RATE, we develop CT-CLIP, a CT-focused contrastive language-image pretraining framework designed for broad applications without the need for task-specific training. We demonstrate how CT-CLIP can be used in multi-abnormality detection and case retrieval, and outperforms state-of-the-art fully supervised models across all key metrics. By combining CT-CLIP's vision encoder with a pretrained large language model, we create CT-CHAT, a vision-language foundational chat model for 3D chest CT volumes. Finetuned on over 2.7 million question-answer pairs derived from the CT-RATE dataset, CT-CHAT underscores the necessity for specialized methods in 3D medical imaging. Collectively, the open-source release of CT-RATE, CT-CLIP, and CT-CHAT not only addresses critical challenges in 3D medical imaging but also lays the groundwork for future innovations in medical AI and improved patient care.

Corentin Royer, Bjoern Menze, Anjany Sekuboyina

We introduce MultiMedEval, an open-source toolkit for fair and reproducible evaluation of large, medical vision-language models (VLM). MultiMedEval comprehensively assesses the models' performance on a broad array of six multi-modal tasks, conducted over 23 datasets, and spanning over 11 medical domains. The chosen tasks and performance metrics are based on their widespread adoption in the community and their diversity, ensuring a thorough evaluation of the model's overall generalizability. We open-source a Python toolkit (github.com/corentin-ryr/MultiMedEval) with a simple interface and setup process, enabling the evaluation of any VLM in just a few lines of code. Our goal is to simplify the intricate landscape of VLM evaluation, thus promoting fair and uniform benchmarking of future models.

Hendrik Möller, Robert Graf, Joachim Schmitt et al.

Purpose. To present SPINEPS, an open-source deep learning approach for semantic and instance segmentation of 14 spinal structures (ten vertebra substructures, intervertebral discs, spinal cord, spinal canal, and sacrum) in whole body T2w MRI. Methods. During this HIPPA-compliant, retrospective study, we utilized the public SPIDER dataset (218 subjects, 63% female) and a subset of the German National Cohort (1423 subjects, mean age 53, 49% female) for training and evaluation. We combined CT and T2w segmentations to train models that segment 14 spinal structures in T2w sagittal scans both semantically and instance-wise. Performance evaluation metrics included Dice similarity coefficient, average symmetrical surface distance, panoptic quality, segmentation quality, and recognition quality. Statistical significance was assessed using the Wilcoxon signed-rank test. An in-house dataset was used to qualitatively evaluate out-of-distribution samples. Results. On the public dataset, our approach outperformed the baseline (instance-wise vertebra dice score 0.929 vs. 0.907, p-value<0.001). Training on auto-generated annotations and evaluating on manually corrected test data from the GNC yielded global dice scores of 0.900 for vertebrae, 0.960 for intervertebral discs, and 0.947 for the spinal canal. Incorporating the SPIDER dataset during training increased these scores to 0.920, 0.967, 0.958, respectively. Conclusions. The proposed segmentation approach offers robust segmentation of 14 spinal structures in T2w sagittal images, including the spinal cord, spinal canal, intervertebral discs, endplate, sacrum, and vertebrae. The approach yields both a semantic and instance mask as output, thus being easy to utilize. This marks the first publicly available algorithm for whole spine segmentation in sagittal T2w MR imaging.

Murong Xu, Tamaz Amiranashvili, Fernando Navarro et al.

Accurate delineation of anatomical structures in volumetric CT scans is crucial for diagnosis and treatment planning. While AI has advanced automated segmentation, current approaches typically target individual structures, creating a fragmented landscape of incompatible models with varying performance and disparate evaluation protocols. Foundational segmentation models address these limitations by providing a holistic anatomical view through a single model. Yet, robust clinical deployment demands comprehensive training data, which is lacking in existing whole-body approaches, both in terms of data heterogeneity and, more importantly, anatomical coverage. In this work, rather than pursuing incremental optimizations in model architecture, we present CADS, an open-source framework that prioritizes the systematic integration, standardization, and labeling of heterogeneous data sources for whole-body CT segmentation. At its core is a large-scale dataset of 22,022 CT volumes with complete annotations for 167 anatomical structures, representing a significant advancement in both scale and coverage, with 18 times more scans than existing collections and 60% more distinct anatomical targets. Building on this diverse dataset, we develop the CADS-model using established architectures for accessible and automated full-body CT segmentation. Through comprehensive evaluation across 18 public datasets and an independent real-world hospital cohort, we demonstrate advantages over SoTA approaches. Notably, thorough testing of the model's performance in segmentation tasks from radiation oncology validates its direct utility for clinical interventions. By making our large-scale dataset, our segmentation models, and our clinical software tool publicly available, we aim to advance robust AI solutions in radiology and make comprehensive anatomical analysis accessible to clinicians and researchers alike.

Ibrahim Ethem Hamamci, Sezgin Er, Anjany Sekuboyina et al.

GenerateCT, the first approach to generating 3D medical imaging conditioned on free-form medical text prompts, incorporates a text encoder and three key components: a novel causal vision transformer for encoding 3D CT volumes, a text-image transformer for aligning CT and text tokens, and a text-conditional super-resolution diffusion model. Without directly comparable methods in 3D medical imaging, we benchmarked GenerateCT against cutting-edge methods, demonstrating its superiority across all key metrics. Importantly, we evaluated GenerateCT's clinical applications in a multi-abnormality classification task. First, we established a baseline by training a multi-abnormality classifier on our real dataset. To further assess the model's generalization to external data and performance with unseen prompts in a zero-shot scenario, we employed an external set to train the classifier, setting an additional benchmark. We conducted two experiments in which we doubled the training datasets by synthesizing an equal number of volumes for each set using GenerateCT. The first experiment demonstrated an 11% improvement in the AP score when training the classifier jointly on real and generated volumes. The second experiment showed a 7% improvement when training on both real and generated volumes based on unseen prompts. Moreover, GenerateCT enables the scaling of synthetic training datasets to arbitrary sizes. As an example, we generated 100,000 3D CTs, fivefold the number in our real set, and trained the classifier exclusively on these synthetic CTs. Impressively, this classifier surpassed the performance of the one trained on all available real data by a margin of 8%. Last, domain experts evaluated the generated volumes, confirming a high degree of alignment with the text prompt. Access our code, model weights, training data, and generated data at https://github.com/ibrahimethemhamamci/GenerateCT

Johannes C. Paetzold, Julian McGinnis, Suprosanna Shit et al.

Biological neural networks define the brain function and intelligence of humans and other mammals, and form ultra-large, spatial, structured graphs. Their neuronal organization is closely interconnected with the spatial organization of the brain's microvasculature, which supplies oxygen to the neurons and builds a complementary spatial graph. This vasculature (or the vessel structure) plays an important role in neuroscience; for example, the organization of (and changes to) vessel structure can represent early signs of various pathologies, e.g. Alzheimer's disease or stroke. Recently, advances in tissue clearing have enabled whole brain imaging and segmentation of the entirety of the mouse brain's vasculature. Building on these advances in imaging, we are presenting an extendable dataset of whole-brain vessel graphs based on specific imaging protocols. Specifically, we extract vascular graphs using a refined graph extraction scheme leveraging the volume rendering engine Voreen and provide them in an accessible and adaptable form through the OGB and PyTorch Geometric dataloaders. Moreover, we benchmark numerous state-of-the-art graph learning algorithms on the biologically relevant tasks of vessel prediction and vessel classification using the introduced vessel graph dataset. Our work paves a path towards advancing graph learning research into the field of neuroscience. Complementarily, the presented dataset raises challenging graph learning research questions for the machine learning community, in terms of incorporating biological priors into learning algorithms, or in scaling these algorithms to handle sparse,spatial graphs with millions of nodes and edges. All datasets and code are available for download at https://github.com/jocpae/VesselGraph .

Anjany Sekuboyina, Malek E. Husseini, Amirhossein Bayat et al.

Vertebral labelling and segmentation are two fundamental tasks in an automated spine processing pipeline. Reliable and accurate processing of spine images is expected to benefit clinical decision-support systems for diagnosis, surgery planning, and population-based analysis on spine and bone health. However, designing automated algorithms for spine processing is challenging predominantly due to considerable variations in anatomy and acquisition protocols and due to a severe shortage of publicly available data. Addressing these limitations, the Large Scale Vertebrae Segmentation Challenge (VerSe) was organised in conjunction with the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) in 2019 and 2020, with a call for algorithms towards labelling and segmentation of vertebrae. Two datasets containing a total of 374 multi-detector CT scans from 355 patients were prepared and 4505 vertebrae have individually been annotated at voxel-level by a human-machine hybrid algorithm (https://osf.io/nqjyw/, https://osf.io/t98fz/). A total of 25 algorithms were benchmarked on these datasets. In this work, we present the the results of this evaluation and further investigate the performance-variation at vertebra-level, scan-level, and at different fields-of-view. We also evaluate the generalisability of the approaches to an implicit domain shift in data by evaluating the top performing algorithms of one challenge iteration on data from the other iteration. The principal takeaway from VerSe: the performance of an algorithm in labelling and segmenting a spine scan hinges on its ability to correctly identify vertebrae in cases of rare anatomical variations. The content and code concerning VerSe can be accessed at: https://github.com/anjany/verse.

Kaiyuan Yang, Fabio Musio, Yihui Ma et al.

The Circle of Willis (CoW) is an important network of arteries connecting major circulations of the brain. Its vascular architecture is believed to affect the risk, severity, and clinical outcome of serious neurovascular diseases. However, characterizing the highly variable CoW anatomy is still a manual and time-consuming expert task. The CoW is usually imaged by two non-invasive angiographic imaging modalities, magnetic resonance angiography (MRA) and computed tomography angiography (CTA), but there exist limited datasets with annotations on CoW anatomy, especially for CTA. Therefore, we organized the TopCoW challenge with the release of an annotated CoW dataset. The TopCoW dataset is the first public dataset with voxel-level annotations for 13 CoW vessel components, enabled by virtual reality technology. It is also the first large dataset using 200 pairs of MRA and CTA from the same patients. As part of the benchmark, we invited submissions worldwide and attracted over 250 registered participants from six continents. The submissions were evaluated on both internal and external test datasets of 226 scans from over five centers. The top performing teams achieved over 90% Dice scores at segmenting the CoW components, over 80% F1 scores at detecting key CoW components, and over 70% balanced accuracy at classifying CoW variants for nearly all test sets. The best algorithms also showed clinical potential in classifying fetal-type posterior cerebral artery and locating aneurysms with CoW anatomy. TopCoW demonstrated the utility and versatility of CoW segmentation algorithms for a wide range of downstream clinical applications with explainability. The annotated datasets and best performing algorithms have been released as public Zenodo records to foster further methodological development and clinical tool building.

Haozhe Luo, Ziyu Zhou, Corentin Royer et al.

Vision-language pre-training for chest X-rays has made significant strides, primarily by utilizing paired radiographs and radiology reports. However, existing approaches often face challenges in encoding medical knowledge effectively. While radiology reports provide insights into the current disease manifestation, medical definitions (as used by contemporary methods) tend to be overly abstract, creating a gap in knowledge. To address this, we propose DeViDe, a novel transformer-based method that leverages radiographic descriptions from the open web. These descriptions outline general visual characteristics of diseases in radiographs, and when combined with abstract definitions and radiology reports, provide a holistic snapshot of knowledge. DeViDe incorporates three key features for knowledge-augmented vision language alignment: First, a large-language model-based augmentation is employed to homogenise medical knowledge from diverse sources. Second, this knowledge is aligned with image information at various levels of granularity. Third, a novel projection layer is proposed to handle the complexity of aligning each image with multiple descriptions arising in a multi-label setting. In zero-shot settings, DeViDe performs comparably to fully supervised models on external datasets and achieves state-of-the-art results on three large-scale datasets. Additionally, fine-tuning DeViDe on four downstream tasks and six segmentation tasks showcases its superior performance across data from diverse distributions.

Poulami Sinhamahapatra, Suprosanna Shit, Anjany Sekuboyina et al.

Vertebral fracture grading classifies the severity of vertebral fractures, which is a challenging task in medical imaging and has recently attracted Deep Learning (DL) models. Only a few works attempted to make such models human-interpretable despite the need for transparency and trustworthiness in critical use cases like DL-assisted medical diagnosis. Moreover, such models either rely on post-hoc methods or additional annotations. In this work, we propose a novel interpretable-by-design method, ProtoVerse, to find relevant sub-parts of vertebral fractures (prototypes) that reliably explain the model's decision in a human-understandable way. Specifically, we introduce a novel diversity-promoting loss to mitigate prototype repetitions in small datasets with intricate semantics. We have experimented with the VerSe'19 dataset and outperformed the existing prototype-based method. Further, our model provides superior interpretability against the post-hoc method. Importantly, expert radiologists validated the visual interpretability of our results, showing clinical applicability.

Chengrun Li, Corentin Royer, Haozhe Luo et al.

Most current medical vision language models struggle to jointly generate diagnostic text and pixel-level segmentation masks in response to complex visual questions. This represents a major limitation towards clinical application, as assistive systems that fail to provide both modalities simultaneously offer limited value to medical practitioners. To alleviate this limitation, we first introduce RadDiagSeg-D, a dataset combining abnormality detection, diagnosis, and multi-target segmentation into a unified and hierarchical task. RadDiagSeg-D covers multiple imaging modalities and is precisely designed to support the development of models that produce descriptive text and corresponding segmentation masks in tandem. Subsequently, we leverage the dataset to propose a novel vision-language model, RadDiagSeg-M, capable of joint abnormality detection, diagnosis, and flexible segmentation. RadDiagSeg-M provides highly informative and clinically useful outputs, effectively addressing the need to enrich contextual information for assistive diagnosis. Finally, we benchmark RadDiagSeg-M and showcase its strong performance across all components involved in the task of multi-target text-and-mask generation, establishing a robust and competitive baseline.

Fernando Navarro, Christopher Watanabe, Suprosanna Shit et al.

Self-supervision has demonstrated to be an effective learning strategy when training target tasks on small annotated data-sets. While current research focuses on creating novel pretext tasks to learn meaningful and reusable representations for the target task, these efforts obtain marginal performance gains compared to fully-supervised learning. Meanwhile, little attention has been given to study the robustness of networks trained in a self-supervised manner. In this work, we demonstrate that networks trained via self-supervised learning have superior robustness and generalizability compared to fully-supervised learning in the context of medical imaging. Our experiments on pneumonia detection in X-rays and multi-organ segmentation in CT yield consistent results exposing the hidden benefits of self-supervision for learning robust feature representations.

Christina Bukas, Bailiang Jian, Luis F. Rodriguez Venegas et al.

Symptomatic spinal vertebral compression fractures (VCFs) often require osteoplasty treatment. A cement-like material is injected into the bone to stabilize the fracture, restore the vertebral body height and alleviate pain. Leakage is a common complication and may occur due to too much cement being injected. In this work, we propose an automated patient-specific framework that can allow physicians to calculate an upper bound of cement for the injection and estimate the optimal outcome of osteoplasty. The framework uses the patient CT scan and the fractured vertebra label to build a virtual healthy spine using a high-level approach. Firstly, the fractured spine is segmented with a three-step Convolution Neural Network (CNN) architecture. Next, a per-vertebra rigid registration to a healthy spine atlas restores its curvature. Finally, a GAN-based inpainting approach replaces the fractured vertebra with an estimation of its original shape. Based on this outcome, we then estimate the maximum amount of bone cement for injection. We evaluate our framework by comparing the virtual vertebrae volumes of ten patients to their healthy equivalent and report an average error of 3.88$\pm$7.63\%. The presented pipeline offers a first approach to a personalized automatic high-level framework for planning osteoplasty procedures.

Hans Liebl, David Schinz, Anjany Sekuboyina et al.

With the advent of deep learning algorithms, fully automated radiological image analysis is within reach. In spine imaging, several atlas- and shape-based as well as deep learning segmentation algorithms have been proposed, allowing for subsequent automated analysis of morphology and pathology. The first Large Scale Vertebrae Segmentation Challenge (VerSe 2019) showed that these perform well on normal anatomy, but fail in variants not frequently present in the training dataset. Building on that experience, we report on the largely increased VerSe 2020 dataset and results from the second iteration of the VerSe challenge (MICCAI 2020, Lima, Peru). VerSe 2020 comprises annotated spine computed tomography (CT) images from 300 subjects with 4142 fully visualized and annotated vertebrae, collected across multiple centres from four different scanner manufacturers, enriched with cases that exhibit anatomical variants such as enumeration abnormalities (n=77) and transitional vertebrae (n=161). Metadata includes vertebral labelling information, voxel-level segmentation masks obtained with a human-machine hybrid algorithm and anatomical ratings, to enable the development and benchmarking of robust and accurate segmentation algorithms.

Anjany Sekuboyina, Daniel Oñoro-Rubio, Jens Kleesiek et al.

Multi-label classification of chest X-ray images is frequently performed using discriminative approaches, i.e. learning to map an image directly to its binary labels. Such approaches make it challenging to incorporate auxiliary information such as annotation uncertainty or a dependency among the labels. Building towards this, we propose a novel knowledge graph reformulation of multi-label classification, which not only readily increases predictive performance of an encoder but also serves as a general framework for introducing new domain knowledge. Specifically, we construct a multi-modal knowledge graph out of the chest X-ray images and its labels and pose multi-label classification as a link prediction problem. Incorporating auxiliary information can then simply be achieved by adding additional nodes and relations among them. When tested on a publicly-available radiograph dataset (CheXpert), our relational-reformulation using a naive knowledge graph outperforms the state-of-art by achieving an area-under-ROC curve of 83.5%, an improvement of "sim 1" over a purely discriminative approach.

Fabian Balsiger, Alain Jungo, Naren Akash R J et al.

The MICCAI conference has encountered tremendous growth over the last years in terms of the size of the community, as well as the number of contributions and their technical success. With this growth, however, come new challenges for the community. Methods are more difficult to reproduce and the ever-increasing number of paper submissions to the MICCAI conference poses new questions regarding the selection process and the diversity of topics. To exchange, discuss, and find novel and creative solutions to these challenges, a new format of a hackathon was initiated as a satellite event at the MICCAI 2020 conference: The MICCAI Hackathon. The first edition of the MICCAI Hackathon covered the topics reproducibility, diversity, and selection of MICCAI papers. In the manner of a small think-tank, participants collaborated to find solutions to these challenges. In this report, we summarize the insights from the MICCAI Hackathon into immediate and long-term measures to address these challenges. The proposed measures can be seen as starting points and guidelines for discussions and actions to possibly improve the MICCAI conference with regards to reproducibility, diversity, and selection of papers.

Hongwei Li, Rameshwara G. N. Prasad, Anjany Sekuboyina et al.

Existing medical image super-resolution methods rely on pairs of low- and high- resolution images to learn a mapping in a fully supervised manner. However, such image pairs are often not available in clinical practice. In this paper, we address super-resolution problem in a real-world scenario using unpaired data and synthesize linearly \textbf{eight times} higher resolved Micro-CT images of temporal bone structure, which is embedded in the inner ear. We explore cycle-consistency generative adversarial networks for super-resolution task and equip the translation approach with Bayesian inference. We further introduce \emph{Hu Moment distance} the evaluation metric to quantify the shape of the temporal bone. We evaluate our method on a public inner ear CT dataset and have seen both visual and quantitative improvement over state-of-the-art deep-learning-based methods. In addition, we perform a multi-rater visual evaluation experiment and find that trained experts consistently rate the proposed method the highest quality scores among all methods. Furthermore, we are able to quantify uncertainty in the unpaired translation task and the uncertainty map can provide structural information of the temporal bone.

Malek Husseini, Anjany Sekuboyina, Maximilian Loeffler et al.

Osteoporotic vertebral fractures have a severe impact on patients' overall well-being but are severely under-diagnosed. These fractures present themselves at various levels of severity measured using the Genant's grading scale. Insufficient annotated datasets, severe data-imbalance, and minor difference in appearances between fractured and healthy vertebrae make naive classification approaches result in poor discriminatory performance. Addressing this, we propose a representation learning-inspired approach for automated vertebral fracture detection, aimed at learning latent representations efficient for fracture detection. Building on state-of-art metric losses, we present a novel Grading Loss for learning representations that respect Genant's fracture grading scheme. On a publicly available spine dataset, the proposed loss function achieves a fracture detection F1 score of 81.5%, a 10% increase over a naive classification baseline.

Amirhossein Bayat, Anjany Sekuboyina, Johannes C. Paetzold et al.

The treatment of degenerative spinal disorders requires an understanding of the individual spinal anatomy and curvature in 3D. An upright spinal pose (i.e. standing) under natural weight bearing is crucial for such bio-mechanical analysis. 3D volumetric imaging modalities (e.g. CT and MRI) are performed in patients lying down. On the other hand, radiographs are captured in an upright pose, but result in 2D projections. This work aims to integrate the two realms, i.e. it combines the upright spinal curvature from radiographs with the 3D vertebral shape from CT imaging for synthesizing an upright 3D model of spine, loaded naturally. Specifically, we propose a novel neural network architecture working vertebra-wise, termed \emph{TransVert}, which takes orthogonal 2D radiographs and infers the spine's 3D posture. We validate our architecture on digitally reconstructed radiographs, achieving a 3D reconstruction Dice of $95.52\%$, indicating an almost perfect 2D-to-3D domain translation. Deploying our model on clinical radiographs, we successfully synthesise full-3D, upright, patient-specific spine models for the first time.

Fernando Navarro, Anjany Sekuboyina, Diana Waldmannstetter et al.

Robust localization of organs in computed tomography scans is a constant pre-processing requirement for organ-specific image retrieval, radiotherapy planning, and interventional image analysis. In contrast to current solutions based on exhaustive search or region proposals, which require large amounts of annotated data, we propose a deep reinforcement learning approach for organ localization in CT. In this work, an artificial agent is actively self-taught to localize organs in CT by learning from its asserts and mistakes. Within the context of reinforcement learning, we propose a novel set of actions tailored for organ localization in CT. Our method can use as a plug-and-play module for localizing any organ of interest. We evaluate the proposed solution on the public VISCERAL dataset containing CT scans with varying fields of view and multiple organs. We achieved an overall intersection over union of 0.63, an absolute median wall distance of 2.25 mm, and a median distance between centroids of 3.65 mm.

Ahmad B Qasim, Ivan Ezhov, Suprosanna Shit et al.

Exploiting learning algorithms under scarce data regimes is a limitation and a reality of the medical imaging field. In an attempt to mitigate the problem, we propose a data augmentation protocol based on generative adversarial networks. We condition the networks at a pixel-level (segmentation mask) and at a global-level information (acquisition environment or lesion type). Such conditioning provides immediate access to the image-label pairs while controlling global class specific appearance of the synthesized images. To stimulate synthesis of the features relevant for the segmentation task, an additional passive player in a form of segmentor is introduced into the adversarial game. We validate the approach on two medical datasets: BraTS, ISIC. By controlling the class distribution through injection of synthetic images into the training set we achieve control over the accuracy levels of the datasets' classes.

Suprosanna Shit, Johannes C. Paetzold, Anjany Sekuboyina et al.

Accurate segmentation of tubular, network-like structures, such as vessels, neurons, or roads, is relevant to many fields of research. For such structures, the topology is their most important characteristic; particularly preserving connectedness: in the case of vascular networks, missing a connected vessel entirely alters the blood-flow dynamics. We introduce a novel similarity measure termed centerlineDice (short clDice), which is calculated on the intersection of the segmentation masks and their (morphological) skeleta. We theoretically prove that clDice guarantees topology preservation up to homotopy equivalence for binary 2D and 3D segmentation. Extending this, we propose a computationally efficient, differentiable loss function (soft-clDice) for training arbitrary neural segmentation networks. We benchmark the soft-clDice loss on five public datasets, including vessels, roads and neurons (2D and 3D). Training on soft-clDice leads to segmentation with more accurate connectivity information, higher graph similarity, and better volumetric scores.

Hongwei Li, Timo Loehr, Anjany Sekuboyina et al.

In medical imaging, the heterogeneity of multi-centre data impedes the applicability of deep learning-based methods and results in significant performance degradation when applying models in an unseen data domain, e.g. a new centreor a new scanner. In this paper, we propose an unsupervised domain adaptation framework for boosting image segmentation performance across multiple domains without using any manual annotations from the new target domains, but by re-calibrating the networks on few images from the target domain. To achieve this, we enforce architectures to be adaptive to new data by rejecting improbable segmentation patterns and implicitly learning through semantic and boundary information, thus to capture disease-specific spatial patterns in an adversarial optimization. The adaptation process needs continuous monitoring, however, as we cannot assume the presence of ground-truth masks for the target domain, we propose two new metrics to monitor the adaptation process, and strategies to train the segmentation algorithm in a stable fashion. We build upon well-established 2D and 3D architectures and perform extensive experiments on three cross-centre brain lesion segmentation tasks, involving multicentre public and in-house datasets. We demonstrate that recalibrating the deep networks on a few unlabeled images from the target domain improves the segmentation accuracy significantly.

Anjany Sekuboyina, Markus Rempfler, Alexander Valentinitsch et al.

We propose an auto-encoding network architecture for point clouds (PC) capable of extracting shape signatures without supervision. Building on this, we (i) design a loss function capable of modelling data variance on PCs which are unstructured, and (ii) regularise the latent space as in a variational auto-encoder, both of which increase the auto-encoders' descriptive capacity while making them probabilistic. Evaluating the reconstruction quality of our architectures, we employ them for detecting vertebral fractures without any supervision. By learning to efficiently reconstruct only healthy vertebrae, fractures are detected as anomalous reconstructions. Evaluating on a dataset containing $\sim$1500 vertebrae, we achieve area-under-ROC curve of $>$75%, without using intensity-based features.

Hongwei Li, Johannes C. Paetzold, Anjany Sekuboyina et al.

Synthesizing MR imaging sequences is highly relevant in clinical practice, as single sequences are often missing or are of poor quality (e.g. due to motion). Naturally, the idea arises that a target modality would benefit from multi-modal input, as proprietary information of individual modalities can be synergistic. However, existing methods fail to scale up to multiple non-aligned imaging modalities, facing common drawbacks of complex imaging sequences. We propose a novel, scalable and multi-modal approach called DiamondGAN. Our model is capable of performing exible non-aligned cross-modality synthesis and data infill, when given multiple modalities or any of their arbitrary subsets, learning structured information in an end-to-end fashion. We synthesize two MRI sequences with clinical relevance (i.e., double inversion recovery (DIR) and contrast-enhanced T1 (T1-c)), reconstructed from three common sequences. In addition, we perform a multi-rater visual evaluation experiment and find that trained radiologists are unable to distinguish synthetic DIR images from real ones.

Anjany Sekuboyina, Markus Rempfler, Alexander Valentinitsch et al.

Purpose: To use and test a labelling algorithm that operates on two-dimensional (2D) reformations, rather than three-dimensional (3D) data to locate and identify vertebrae. Methods: We improved the Btrfly Net (described by Sekuboyina et al) that works on sagittal and coronal maximum intensity projections (MIP) and augmented it with two additional components: spine-localization and adversarial a priori-learning. Furthermore, we explored two variants of adversarial training schemes that incorporated the anatomical a priori knowledge into the Btrfly Net. We investigated the superiority of the proposed approach for labelling vertebrae on three datasets: a public benchmarking dataset of 302 CT scans and two in-house datasets with a total of 238 CT scans. We employed Wilcoxon signed-rank test to compute the statistical significance of the improvement in performance observed due to various architectural components in our approach. Results: On the public dataset, our approach using the described Btrfly(pe-eb) network performed on par with current state-of-the-art methods achieving a statistically significant (p < .001) vertebrae identification rate of 88.5+/-0.2 % and localization distances of less than 7-mm. On the in-house datasets that had a higher inter-scan data variability, we obtained an identification rate of 85.1+/-1.2%. Conclusion: An identification performance comparable to existing 3D approaches was achieved when labelling vertebrae on 2D MIPs. The performance was further improved using the proposed adversarial training regime that effectively enforced local spine a priori knowledge during training. Lastly, spine-localization increased the generalizability of our approach by homogenizing the content in the MIPs.

Patrick Bilic, Patrick Christ, Hongwei Bran Li et al.

In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LiTS), which was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2017 and the International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2017 and 2018. The image dataset is diverse and contains primary and secondary tumors with varied sizes and appearances with various lesion-to-background levels (hyper-/hypo-dense), created in collaboration with seven hospitals and research institutions. Seventy-five submitted liver and liver tumor segmentation algorithms were trained on a set of 131 computed tomography (CT) volumes and were tested on 70 unseen test images acquired from different patients. We found that not a single algorithm performed best for both liver and liver tumors in the three events. The best liver segmentation algorithm achieved a Dice score of 0.963, whereas, for tumor segmentation, the best algorithms achieved Dices scores of 0.674 (ISBI 2017), 0.702 (MICCAI 2017), and 0.739 (MICCAI 2018). Retrospectively, we performed additional analysis on liver tumor detection and revealed that not all top-performing segmentation algorithms worked well for tumor detection. The best liver tumor detection method achieved a lesion-wise recall of 0.458 (ISBI 2017), 0.515 (MICCAI 2017), and 0.554 (MICCAI 2018), indicating the need for further research. LiTS remains an active benchmark and resource for research, e.g., contributing the liver-related segmentation tasks in \url{http://medicaldecathlon.com/}. In addition, both data and online evaluation are accessible via \url{www.lits-challenge.com}.

Marie Piraud, Anjany Sekuboyina, Bjoern H. Menze

For many biological image segmentation tasks, including topological knowledge, such as the nesting of classes, can greatly improve results. However, most `out-of-the-box' CNN models are still blind to such prior information. In this paper, we propose a novel approach to encode this information, through a multi-level activation layer and three compatible losses. We benchmark all of them on nuclei segmentation in bright-field microscopy cell images from the 2018 Data Science Bowl challenge, offering an exemplary segmentation task with cells and nested subcellular structures. Our scheme greatly speeds up learning, and outperforms standard multi-class classification with soft-max activation and a previously proposed method stemming from it, improving the Dice score significantly (p-values<0.007). Our approach is conceptually simple, easy to implement and can be integrated in any CNN architecture. It can be generalized to a higher number of classes, with or without further relations of containment.

Anjany Sekuboyina, Markus Rempfler, Jan Kukačka et al.

Robust localisation and identification of vertebrae is essential for automated spine analysis. The contribution of this work to the task is two-fold: (1) Inspired by the human expert, we hypothesise that a sagittal and coronal reformation of the spine contain sufficient information for labelling the vertebrae. Thereby, we propose a butterfly-shaped network architecture (termed Btrfly Net) that efficiently combines the information across reformations. (2) Underpinning the Btrfly net, we present an energy-based adversarial training regime that encodes local spine structure as an anatomical prior into the network, thereby enabling it to achieve state-of-art performance in all standard metrics on a benchmark dataset of 302 scans without any post-processing during inference.

Anjany Sekuboyina, Alexander Valentinitsch, Jan S. Kirschke et al.

Multi-class segmentation of vertebrae is a non-trivial task mainly due to the high correlation in the appearance of adjacent vertebrae. Hence, such a task calls for the consideration of both global and local context. Based on this motivation, we propose a two-staged approach that, given a computed tomography dataset of the spine, segments the five lumbar vertebrae and simultaneously labels them. The first stage employs a multi-layered perceptron performing non-linear regression for locating the lumbar region using the global context. The second stage, comprised of a fully-convolutional deep network, exploits the local context in the localised lumbar region to segment and label the lumbar vertebrae in one go. Aided with practical data augmentation for training, our approach is highly generalisable, capable of successfully segmenting both healthy and abnormal vertebrae (fractured and scoliotic spines). We consistently achieve an average Dice coefficient of over 90 percent on a publicly available dataset of the xVertSeg segmentation challenge of MICCAI 2016. This is particularly noteworthy because the xVertSeg dataset is beset with severe deformities in the form of vertebral fractures and scoliosis.