Behrus Puladi

Jianning Li, André Ferreira, Behrus Puladi et al.

We present a deep learning-based approach for skull reconstruction for MONAI, which has been pre-trained on the MUG500+ skull dataset. The implementation follows the MONAI contribution guidelines, hence, it can be easily tried out and used, and extended by MONAI users. The primary goal of this paper lies in the investigation of open-sourcing codes and pre-trained deep learning models under the MONAI framework. Nowadays, open-sourcing software, especially (pre-trained) deep learning models, has become increasingly important. Over the years, medical image analysis experienced a tremendous transformation. Over a decade ago, algorithms had to be implemented and optimized with low-level programming languages, like C or C++, to run in a reasonable time on a desktop PC, which was not as powerful as today's computers. Nowadays, users have high-level scripting languages like Python, and frameworks like PyTorch and TensorFlow, along with a sea of public code repositories at hand. As a result, implementations that had thousands of lines of C or C++ code in the past, can now be scripted with a few lines and in addition executed in a fraction of the time. To put this even on a higher level, the Medical Open Network for Artificial Intelligence (MONAI) framework tailors medical imaging research to an even more convenient process, which can boost and push the whole field. The MONAI framework is a freely available, community-supported, open-source and PyTorch-based framework, that also enables to provide research contributions with pre-trained models to others. Codes and pre-trained weights for skull reconstruction are publicly available at: https://github.com/Project-MONAI/research-contributions/tree/master/SkullRec

Nikoo Moradi, Gijs Luijten, Behrus Hinrichs-Puladi et al.

Diffusion models produce high-quality synthetic data but suffer from slow inference. We propose 3D Variable-Step Denoising Diffusion Probabilistic Model (VS-DDPM) a framework engineered to maintain generative quality while accelerating inference by several factors. We tested our approach on four tasks (missing MRI, tumor removal, MRI-to-sCT, and CBCT-to-sCT) within the BraTS2025 and SynthRAD2025 challenges. Designed for high efficiency under hardware and time constrains imposed by both challenges. VS-DDPM achieved state-of-the-art (SOTA) performance in missing MRI synthesis, yielding Dice scores of 0.80, 0.83, and 0.88 for the enhancing tumor, tumor core, and whole tumor regions, respectively, alongside a structural similarity index (SSIM) of 0.95. For MRI tumor removal, the model attained a root mean squared error (RMSE) of 0.053, a peak signal-to-noise ratio (PSNR) of 26.77, and an SSIM of 0.918. While the framework demonstrated competitive performance in MRI-to-sCT and CBCT-to-sCT tasks, it did not reach SOTA benchmarks, potentially due to sensitivities in data pre and post-processing pipelines or specific loss function configurations. These results demonstrate that VS-DDPM provides a robust and tunable solution for high-fidelity 3D medical image synthesis. The code is available in https://github.com/andre-fs-ferreira/SynthRAD_by_Faking_it.

Jan Egger, Christina Gsaxner, Xiaojun Chen et al.

At the Worldwide Developers Conference (WWDC) in June 2023, Apple introduced the Vision Pro. The Vision Pro is a Mixed Reality (MR) headset, more specifically it is a Virtual Reality (VR) device with an additional Video See-Through (VST) capability. The VST capability turns the Vision Pro also into an Augmented Reality (AR) device. The AR feature is enabled by streaming the real world via cameras to the (VR) screens in front of the user's eyes. This is of course not unique and similar to other devices, like the Varjo XR-3. Nevertheless, the Vision Pro has some interesting features, like an inside-out screen that can show the headset wearers' eyes to "outsiders" or a button on the top, called "Digital Crown", that allows you to seamlessly blend digital content with your physical space by turning it. In addition, it is untethered, except for the cable to the battery, which makes the headset more agile, compared to the Varjo XR-3. This could actually come closer to the "Ultimate Display", which Ivan Sutherland had already sketched in 1965. Not available to the public yet, like the Ultimate Display, we want to take a look into the crystal ball in this perspective to see if it can overcome some clinical challenges that - especially - AR still faces in the medical domain, but also go beyond and discuss if the Vision Pro could support clinicians in essential tasks to spend more time with their patients.

Hanna Hoffmann, Setareh Bady, Claas de Boer et al.

Achieving high levels of surgical skill through effective training is essential for optimal patient outcomes. Automated, data-driven skill assessment holds significant potential to improve surgical training. While machine learning-based methods are increasingly popular for assessing skills in minimally invasive surgery, their application to open surgery remains limited. We present the results of a dedicated MICCAI challenge designed to benchmark and advance vision-based skill assessment in open surgery. The challenge dataset comprises videos of an open suturing training task recorded with a static GoPro camera in a dry-lab setting, with instrument trajectories available in addition to the primary video modality. The OSS Challenge was hosted over two consecutive years, comprising two and three independent tasks, respectively: (1) classifying skill level into four classes, (2) predicting the full Objective Structured Assessment of Technical Skills across eight categories, and (3) tracking hands and surgical tools. Participants submitted diverse solutions including deep learning-based video models, tracking-driven methods, and hybrid approaches. General-purpose spatiotemporal video models consistently achieved the strongest performance, though conceptually diverse approaches reached competitive levels when well-executed. Predicting fine-grained OSATS scores remains challenging but benefits substantially from increased training data. Keypoint tracking proves difficult given frequent occlusions and out-of-frame instances, limiting current applicability for motion-based skill analysis. This work benchmarks innovative and diverse solutions for surgical skill assessment, highlighting both the promise and current limitations of video-based evaluation in open surgery and identifying critical directions for advancing automated skill assessment toward clinical impact.

Soroosh Tayebi Arasteh, Mina Farajiamiri, Mahshad Lotfinia et al.

Differential privacy (DP) provides formal protection for sensitive data but typically incurs substantial losses in diagnostic performance. Model initialization has emerged as a critical factor in mitigating this degradation, yet the role of modern self-supervised learning under full-model DP remains poorly understood. Here, we present a large-scale evaluation of initialization strategies for differentially private medical image analysis, using chest radiograph classification as a representative benchmark with more than 800,000 images. Using state-of-the-art ConvNeXt models trained with DP-SGD across realistic privacy regimes, we compare non-domain-specific supervised ImageNet initialization, non-domain-specific self-supervised DINOv3 initialization, and domain-specific supervised pretraining on MIMIC-CXR, the largest publicly available chest radiograph dataset. Evaluations are conducted across five external datasets spanning diverse institutions and acquisition settings. We show that DINOv3 initialization consistently improves diagnostic utility relative to ImageNet initialization under DP, but remains inferior to domain-specific supervised pretraining, which achieves performance closest to non-private baselines. We further demonstrate that initialization choice strongly influences demographic fairness, cross-dataset generalization, and robustness to data scale and model capacity under privacy constraints. The results establish initialization strategy as a central determinant of utility, fairness, and generalization in differentially private medical imaging.

Ana Carolina Alves, André Ferreira, Behrus Puladi et al.

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.

Jun Ma, Feifei Li, Sumin Kim et al.

Promptable segmentation foundation models have emerged as a transformative approach to addressing the diverse needs in medical images, but most existing models require expensive computing, posing a big barrier to their adoption in clinical practice. In this work, we organized the first international competition dedicated to promptable medical image segmentation, featuring a large-scale dataset spanning nine common imaging modalities from over 20 different institutions. The top teams developed lightweight segmentation foundation models and implemented an efficient inference pipeline that substantially reduced computational requirements while maintaining state-of-the-art segmentation accuracy. Moreover, the post-challenge phase advanced the algorithms through the design of performance booster and reproducibility tasks, resulting in improved algorithms and validated reproducibility of the winning solution. Furthermore, the best-performing algorithms have been incorporated into the open-source software with a user-friendly interface to facilitate clinical adoption. The data and code are publicly available to foster the further development of medical image segmentation foundation models and pave the way for impactful real-world applications.

André Ferreira, Tiago Jesus, Behrus Puladi et al.

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. In task 1, we achieved a DSC of 0.7900, 0.8076, 0.7760, 0.8926, 0.7874, 0.8938 and a HD95 of 35.63, 30.35, 44.58, 16.87, 38.19, 17.95 for ET, NETC, RC, SNFH, TC and WT, respectively and, in task 3, we achieved a DSC of 0.801 and HD95 of 38.26, in the testing phase. The code for these tasks is available at https://github.com/ShadowTwin41/BraTS_2023_2024_solutions.

André Ferreira, Gijs Luijten, Behrus Puladi et al.

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. The code for these tasks is available at https://github.com/ShadowTwin41/BraTS_2023_2024_solutions.

Patrick Wienholt, Alexander Hermans, Firas Khader et al.

This study investigates the application of ordinal regression methods for categorizing disease severity in chest radiographs. We propose a framework that divides the ordinal regression problem into three parts: a model, a target function, and a classification function. Different encoding methods, including one-hot, Gaussian, progress-bar, and our soft-progress-bar, are applied using ResNet50 and ViT-B-16 deep learning models. We show that the choice of encoding has a strong impact on performance and that the best encoding depends on the chosen weighting of Cohen's kappa and also on the model architecture used. We make our code publicly available on GitHub.

Michael Lackner, Behrus Puladi, Jens Kleesiek et al.

In traumatic medical emergencies, the patients heavily depend on cranioplasty - the craft of neurocranial repair using cranial implants. Despite the improvements made in recent years, the design of a patient-specific implant (PSI) is among the most complex, expensive, and least automated tasks in cranioplasty. Further research in this area is needed. Therefore, we created a prototype application with a graphical user interface (UI) specifically tailored for semi-automatic implant generation, where the users only need to perform high-level actions. A general outline of the proposed implant generation process involves setting an area of interest, aligning the templates, and then creating the implant in voxel space. Furthermore, we show that the alignment can be improved significantly, by only considering clipped geometry in the vicinity of the defect border. The software prototype will be open-sourced at https://github.com/3Descape/Cranial_Implant_Design

Malik Sallam, Jan Egger, Rainer Roehrig et al.

In an era where artificial intelligence (AI) intertwines with medical research, the delineation of truth becomes increasingly complex. This study ostensibly examines a purported novel SARS-CoV-2 variant, dubbed the Omega variant, showcasing 31 unique mutations in the S gene region. However, the real undercurrent of this narrative is a demonstration of the ease with which AI, specifically ChatGPT-4, can fabricate convincing yet entirely fictional scientific data. The so-called Omega variant was identified in a fully vaccinated, previously infected 35-year-old male presenting with severe COVID-19 symptoms. Through a detailed, albeit artificial, genomic analysis and contact tracing, this study mirrors the rigorous methodology of genuine case reports, thereby setting the stage for a compelling but entirely constructed narrative. The entire case study was generated by ChatGPT-4, a large language model by OpenAI. The fabricated Omega variant features an ensemble of mutations, including N501Y and E484K, known for enhancing ACE2 receptor affinity, alongside L452R and P681H, ostensibly indicative of immune evasion. This variant's contrived interaction dynamics - severe symptoms in a vaccinated individual versus mild ones in unvaccinated contacts - were designed to mimic real-world complexities, including suggestions of antibody-dependent enhancement (ADE). While the Omega variant is a product of AI-generated fiction, the implications of this exercise are real and profound. The ease with which AI can generate believable but false scientific information, as illustrated in this case, raises significant concerns about the potential for misinformation in medicine. This study, therefore, serves as a cautionary tale, emphasizing the necessity for critical evaluation of sources, especially in an age where AI tools like ChatGPT are becoming increasingly sophisticated and widespread in their use.

Nikoo Moradi, André Ferreira, Behrus Puladi et al.

Radiation therapy (RT) is essential in treating head and neck cancer (HNC), with magnetic resonance imaging(MRI)-guided RT offering superior soft tissue contrast and functional imaging. However, manual tumor segmentation is time-consuming and complex, and therfore remains a challenge. In this study, we present our solution as team TUMOR to the HNTS-MRG24 MICCAI Challenge which is focused on automated segmentation of primary gross tumor volumes (GTVp) and metastatic lymph node gross tumor volume (GTVn) in pre-RT and mid-RT MRI images. We utilized the HNTS-MRG2024 dataset, which consists of 150 MRI scans from patients diagnosed with HNC, including original and registered pre-RT and mid-RT T2-weighted images with corresponding segmentation masks for GTVp and GTVn. We employed two state-of-the-art models in deep learning, nnUNet and MedNeXt. For Task 1, we pretrained models on pre-RT registered and mid-RT images, followed by fine-tuning on original pre-RT images. For Task 2, we combined registered pre-RT images, registered pre-RT segmentation masks, and mid-RT data as a multi-channel input for training. Our solution for Task 1 achieved 1st place in the final test phase with an aggregated Dice Similarity Coefficient of 0.8254, and our solution for Task 2 ranked 8th with a score of 0.7005. The proposed solution is publicly available at Github Repository.

Ana Carolina Alves, André Ferreira, Gijs Luijten et al.

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.

Johannes Raufeisen, Kunpeng Xie, Fabian Hörst et al.

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.

André Ferreira, Kunpeng Xie, Caroline Wilpert et al.

AI requires extensive datasets, while medical data is subject to high data protection. Anonymization is essential, but poses a challenge for some regions, such as the head, as identifying structures overlap with regions of clinical interest. Synthetic data offers a potential solution, but studies often lack rigorous evaluation of realism and utility. Therefore, we investigate to what extent synthetic data can replace real data in segmentation tasks. We employed head and neck cancer CT scans and brain glioma MRI scans from two large datasets. Synthetic data were generated using generative adversarial networks and diffusion models. We evaluated the quality of the synthetic data using MAE, MS-SSIM, Radiomics and a Visual Turing Test (VTT) performed by 5 radiologists and their usefulness in segmentation tasks using DSC. Radiomics indicates high fidelity of synthetic MRIs, but fall short in producing highly realistic CT tissue, with correlation coefficient of 0.8784 and 0.5461 for MRI and CT tumors, respectively. DSC results indicate limited utility of synthetic data: tumor segmentation achieved DSC=0.064 on CT and 0.834 on MRI, while bone segmentation a mean DSC=0.841. Relation between DSC and correlation is observed, but is limited by the complexity of the task. VTT results show synthetic CTs' utility, but with limited educational applications. Synthetic data can be used independently for the segmentation task, although limited by the complexity of the structures to segment. Advancing generative models to better tolerate heterogeneous inputs and learn subtle details is essential for enhancing their realism and expanding their application potential.