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Motivated by the need for advanced solutions in the segmentation and inpainting of glioma-affected brain regions in multi-modal magnetic resonance imaging (MRI), this study presents an integrated approach leveraging the strengths of ensemble learning with hybrid transformer models and convolutional neural networks (CNNs), alongside the innovative application of 3D Pix2Pix Generative Adversarial Network (GAN). Our methodology combines robust tumor segmentation capabilities, utilizing axial attention and transformer encoders for enhanced spatial relationship modeling, with the ability to synthesize biologically plausible brain tissue through 3D Pix2Pix GAN. This integrated approach addresses the BraTS 2023 cluster challenges by offering precise segmentation and realistic inpainting, tailored for diverse tumor types and sub-regions. The results demonstrate outstanding performance, evidenced by quantitative evaluations such as the Dice Similarity Coefficient (DSC), Hausdorff Distance (HD95) for segmentation, and Structural Similarity Index Measure (SSIM), Peak Signal-to-Noise Ratio (PSNR), and Mean-Square Error (MSE) for inpainting. Qualitative assessments further validate the high-quality, clinically relevant outputs. In conclusion, this study underscores the potential of combining advanced machine learning techniques for comprehensive brain tumor analysis, promising significant advancements in clinical decision-making and patient care within the realm of medical imaging., Comment: Accepted at the MICCAI BraTS Challenge 2023

Accurate segmentation of brain tumors from 3D multimodal MRI is vital for diagnosis and treatment planning across diverse brain tumors. This paper addresses the challenges posed by the BraTS 2023, presenting a unified transfer learning approach that applies to a broader spectrum of brain tumors. We introduce HT-CNNs, an ensemble of Hybrid Transformers and Convolutional Neural Networks optimized through transfer learning for varied brain tumor segmentation. This method captures spatial and contextual details from MRI data, fine-tuned on diverse datasets representing common tumor types. Through transfer learning, HT-CNNs utilize the learned representations from one task to improve generalization in another, harnessing the power of pre-trained models on large datasets and fine-tuning them on specific tumor types. We preprocess diverse datasets from multiple international distributions, ensuring representativeness for the most common brain tumors. Our rigorous evaluation employs standardized quantitative metrics across all tumor types, ensuring robustness and generalizability. The proposed ensemble model achieves superior segmentation results across the BraTS validation datasets over the previous winning methods. Comprehensive quantitative evaluations using the DSC and HD95 demonstrate the effectiveness of our approach. Qualitative segmentation predictions further validate the high-quality outputs produced by our model. Our findings underscore the potential of transfer learning and ensemble approaches in medical image segmentation, indicating a substantial enhancement in clinical decision-making and patient care. Despite facing challenges related to post-processing and domain gaps, our study sets a new precedent for future research for brain tumor segmentation. The docker image for the code and models has been made publicly available, https://hub.docker.com/r/razeineldin/ht-cnns., Comment: Accepted in the Computer Assisted Radiology and Surgery (CARS 2024) Conference

Accurately determining the shape and location of internal structures within deformable objects is crucial for medical tasks that require precise targeting, such as robotic biopsies. We introduce LUDO, a method for accurate low-latency understanding of deformable objects. LUDO reconstructs objects in their deformed state, including their internal structures, from a single-view point cloud observation in under 30 ms using occupancy networks. We demonstrate LUDO's abilities for autonomous targeting of internal regions of interest (ROIs) in highly deformable objects. Additionally, LUDO provides uncertainty estimates and explainability for its predictions, both of which are important in safety-critical applications such as surgical interventions. We evaluate LUDO in real-world robotic experiments, achieving a success rate of 98.9% for puncturing various ROIs inside highly deformable objects. LUDO demonstrates the potential to interact with deformable objects without the need for deformable registration methods.

To track tumors during surgery, information from preoperative CT scans is used to determine their position. However, as the surgeon operates, the tumor may be deformed which presents a major hurdle for accurately resecting the tumor, and can lead to surgical inaccuracy, increased operation time, and excessive margins. This issue is particularly pronounced in robot-assisted partial nephrectomy (RAPN), where the kidney undergoes significant deformations during operation. Toward addressing this, we introduce a occupancy network-based method for the localization of tumors within kidney phantoms undergoing deformations at interactive speeds. We validate our method by introducing a 3D hydrogel kidney phantom embedded with exophytic and endophytic renal tumors. It closely mimics real tissue mechanics to simulate kidney deformation during in vivo surgery, providing excellent contrast and clear delineation of tumor margins to enable automatic threshold-based segmentation. Our findings indicate that the proposed method can localize tumors in moderately deforming kidneys with a margin of 6mm to 10mm, while providing essential volumetric 3D information at over 60Hz. This capability directly enables downstream tasks such as robotic resection., Comment: Accepted at IROS 2024

Endovascular interventions are a life-saving treatment for many diseases, yet suffer from drawbacks such as radiation exposure and potential scarcity of proficient physicians. Robotic assistance during these interventions could be a promising support towards these problems. Research focusing on autonomous endovascular interventions utilizing artificial intelligence-based methodologies is gaining popularity. However, variability in assessment environments hinders the ability to compare and contrast the efficacy of different approaches, primarily due to each study employing a unique evaluation framework. In this study, we present deep reinforcement learning-based autonomous endovascular device navigation on three distinct digital benchmark interventions: BasicWireNav, ArchVariety, and DualDeviceNav. The benchmark interventions were implemented with our modular simulation framework stEVE (simulated EndoVascular Environment). Autonomous controllers were trained solely in simulation and evaluated in simulation and on physical test benches with camera and fluoroscopy feedback. Autonomous control for BasicWireNav and ArchVariety reached high success rates and was successfully transferred from the simulated training environment to the physical test benches, while autonomous control for DualDeviceNav reached a moderate success rate. The experiments demonstrate the feasibility of stEVE and its potential for transferring controllers trained in simulation to real-world scenarios. Nevertheless, they also reveal areas that offer opportunities for future research. This study demonstrates the transferability of autonomous controllers from simulation to the real world in endovascular navigation and lowers the entry barriers and increases the comparability of research on endovascular assistance systems by providing open-source training scripts, benchmarks and the stEVE framework.

Training and prototype development in robot-assisted surgery requires appropriate and safe environments for the execution of surgical procedures. Current dry lab laparoscopy phantoms often lack the ability to mimic complex, interactive surgical tasks. This work presents an interactive surgical phantom for the cholecystectomy. The phantom enables the removal of the gallbladder during cholecystectomy by allowing manipulations and cutting interactions with the synthetic tissue. The force-displacement behavior of the gallbladder is modelled based on retraction demonstrations. The force model is compared to the force model of ex-vivo porcine gallbladders and evaluated on its ability to estimate retraction forces., Comment: As presented at CURAC 2023

We introduce a novel method employing occupancy networks for the precise localization of 67 anatomical structures from single depth images captured from the exterior of the human body. This method considers the anatomical diversity across individuals. Our contributions include the application of occupancy networks for occluded structure localization, a robust method for estimating anatomical positions from depth images, and the creation of detailed, individualized 3D anatomical atlases. This approach promises improvements in medical imaging and automated diagnostic procedures by offering accurate, non-invasive localization of critical anatomical features.

Automation holds the potential to assist surgeons in robotic interventions, shifting their mental work load from visuomotor control to high level decision making. Reinforcement learning has shown promising results in learning complex visuomotor policies, especially in simulation environments where many samples can be collected at low cost. A core challenge is learning policies in simulation that can be deployed in the real world, thereby overcoming the sim-to-real gap. In this work, we bridge the visual sim-to-real gap with an image-based reinforcement learning pipeline based on pixel-level domain adaptation and demonstrate its effectiveness on an image-based task in deformable object manipulation. We choose a tissue retraction task because of its importance in clinical reality of precise cancer surgery. After training in simulation on domain-translated images, our policy requires no retraining to perform tissue retraction with a 50% success rate on the real robotic system using raw RGB images. Furthermore, our sim-to-real transfer method makes no assumptions on the task itself and requires no paired images. This work introduces the first successful application of visual sim-to-real transfer for robotic manipulation of deformable objects in the surgical field, which represents a notable step towards the clinical translation of cognitive surgical robotics.

Policy learning in robot-assisted surgery (RAS) lacks data efficient and versatile methods that exhibit the desired motion quality for delicate surgical interventions. To this end, we introduce Movement Primitive Diffusion (MPD), a novel method for imitation learning (IL) in RAS that focuses on gentle manipulation of deformable objects. The approach combines the versatility of diffusion-based imitation learning (DIL) with the high-quality motion generation capabilities of Probabilistic Dynamic Movement Primitives (ProDMPs). This combination enables MPD to achieve gentle manipulation of deformable objects, while maintaining data efficiency critical for RAS applications where demonstration data is scarce. We evaluate MPD across various simulated and real world robotic tasks on both state and image observations. MPD outperforms state-of-the-art DIL methods in success rate, motion quality, and data efficiency. Project page: https://scheiklp.github.io/movement-primitive-diffusion/

In deformable object manipulation, we often want to interact with specific segments of an object that are only defined in non-deformed models of the object. We thus require a system that can recognize and locate these segments in sensor data of deformed real world objects. This is normally done using deformable object registration, which is problem specific and complex to tune. Recent methods utilize neural occupancy functions to improve deformable object registration by registering to an object reconstruction. Going one step further, we propose a system that in addition to reconstruction learns segmentation of the reconstructed object. As the resulting output already contains the information about the segments, we can skip the registration process. Tested on a variety of deformable objects in simulation and the real world, we demonstrate that our method learns to robustly find these segments. We also introduce a simple sampling algorithm to generate better training data for occupancy learning., Comment: Accepted at WACV 2024

Physical simulations that accurately model reality are crucial for many engineering disciplines such as mechanical engineering and robotic motion planning. In recent years, learned Graph Network Simulators produced accurate mesh-based simulations while requiring only a fraction of the computational cost of traditional simulators. Yet, the resulting predictors are confined to learning from data generated by existing mesh-based simulators and thus cannot include real world sensory information such as point cloud data. As these predictors have to simulate complex physical systems from only an initial state, they exhibit a high error accumulation for long-term predictions. In this work, we integrate sensory information to ground Graph Network Simulators on real world observations. In particular, we predict the mesh state of deformable objects by utilizing point cloud data. The resulting model allows for accurate predictions over longer time horizons, even under uncertainties in the simulation, such as unknown material properties. Since point clouds are usually not available for every time step, especially in online settings, we employ an imputation-based model. The model can make use of such additional information only when provided, and resorts to a standard Graph Network Simulator, otherwise. We experimentally validate our approach on a suite of prediction tasks for mesh-based interactions between soft and rigid bodies. Our method results in utilization of additional point cloud information to accurately predict stable simulations where existing Graph Network Simulators fail., Comment: Accepted as a poster at the 11th International Conference on Learning Representations (ICLR), 2023

Recent advances in reinforcement learning (RL) have increased the promise of introducing cognitive assistance and automation to robot-assisted laparoscopic surgery (RALS). However, progress in algorithms and methods depends on the availability of standardized learning environments that represent skills relevant to RALS. We present LapGym, a framework for building RL environments for RALS that models the challenges posed by surgical tasks, and sofa_env, a diverse suite of 12 environments. Motivated by surgical training, these environments are organized into 4 tracks: Spatial Reasoning, Deformable Object Manipulation & Grasping, Dissection, and Thread Manipulation. Each environment is highly parametrizable for increasing difficulty, resulting in a high performance ceiling for new algorithms. We use Proximal Policy Optimization (PPO) to establish a baseline for model-free RL algorithms, investigating the effect of several environment parameters on task difficulty. Finally, we show that many environments and parameter configurations reflect well-known, open problems in RL research, allowing researchers to continue exploring these fundamental problems in a surgical context. We aim to provide a challenging, standard environment suite for further development of RL for RALS, ultimately helping to realize the full potential of cognitive surgical robotics. LapGym is publicly accessible through GitHub (https://github.com/ScheiklP/lap_gym).

Automatic segmentation is essential for the brain tumor diagnosis, disease prognosis, and follow-up therapy of patients with gliomas. Still, accurate detection of gliomas and their sub-regions in multimodal MRI is very challenging due to the variety of scanners and imaging protocols. Over the last years, the BraTS Challenge has provided a large number of multi-institutional MRI scans as a benchmark for glioma segmentation algorithms. This paper describes our contribution to the BraTS 2022 Continuous Evaluation challenge. We propose a new ensemble of multiple deep learning frameworks namely, DeepSeg, nnU-Net, and DeepSCAN for automatic glioma boundaries detection in pre-operative MRI. It is worth noting that our ensemble models took first place in the final evaluation on the BraTS testing dataset with Dice scores of 0.9294, 0.8788, and 0.8803, and Hausdorf distance of 5.23, 13.54, and 12.05, for the whole tumor, tumor core, and enhancing tumor, respectively. Furthermore, the proposed ensemble method ranked first in the final ranking on another unseen test dataset, namely Sub-Saharan Africa dataset, achieving mean Dice scores of 0.9737, 0.9593, and 0.9022, and HD95 of 2.66, 1.72, 3.32 for the whole tumor, tumor core, and enhancing tumor, respectively. The docker image for the winning submission is publicly available at (https://hub.docker.com/r/razeineldin/camed22)., Comment: Accepted in BraTS 2022 (as part of the BrainLes workshop proceedings distributed by Springer LNCS). arXiv admin note: text overlap with arXiv:2112.06554

Reliable and accurate registration of patient-specific brain magnetic resonance imaging (MRI) scans containing pathologies is challenging due to tissue appearance changes. This paper describes our contribution to the Registration of the longitudinal brain MRI task of the Brain Tumor Sequence Registration Challenge 2022 (BraTS-Reg 2022). We developed an enhanced unsupervised learning-based method that extends the iRegNet. In particular, incorporating an unsupervised learning-based paradigm as well as several minor modifications to the network pipeline, allows the enhanced iRegNet method to achieve respectable results. Experimental findings show that the enhanced self-supervised model is able to improve the initial mean median registration absolute error (MAE) from 8.20 (7.62) mm to the lowest value of 3.51 (3.50) for the training set while achieving an MAE of 2.93 (1.63) mm for the validation set. Additional qualitative validation of this study was conducted through overlaying pre-post MRI pairs before and after the de-formable registration. The proposed method scored 5th place during the testing phase of the MICCAI BraTS-Reg 2022 challenge. The docker image to reproduce our BraTS-Reg submission results will be publicly available., Comment: Accepted in the MICCAI BraTS-Reg 2022 Challenge (as part of the BrainLes workshop proceedings distributed by Springer LNCS)

The semantic segmentation of surgical scenes is a prerequisite for task automation in robot assisted interventions. We propose LapSeg3D, a novel DNN-based approach for the voxel-wise annotation of point clouds representing surgical scenes. As the manual annotation of training data is highly time consuming, we introduce a semi-autonomous clustering-based pipeline for the annotation of the gallbladder, which is used to generate segmented labels for the DNN. When evaluated against manually annotated data, LapSeg3D achieves an F1 score of 0.94 for gallbladder segmentation on various datasets of ex-vivo porcine livers. We show LapSeg3D to generalize accurately across different gallbladders and datasets recorded with different RGB-D camera systems., Comment: 6 pages, 5 figures, accepted at the 2022 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2022), Kyoto, Japan

Registration of longitudinal brain MRI scans containing pathologies is challenging due to dramatic changes in tissue appearance. Although there has been progress in developing general-purpose medical image registration techniques, they have not yet attained the requisite precision and reliability for this task, highlighting its inherent complexity. Here we describe the Brain Tumor Sequence Registration (BraTS-Reg) challenge, as the first public benchmark environment for deformable registration algorithms focusing on estimating correspondences between pre-operative and follow-up scans of the same patient diagnosed with a diffuse brain glioma. The BraTS-Reg data comprise de-identified multi-institutional multi-parametric MRI (mpMRI) scans, curated for size and resolution according to a canonical anatomical template, and divided into training, validation, and testing sets. Clinical experts annotated ground truth (GT) landmark points of anatomical locations distinct across the temporal domain. Quantitative evaluation and ranking were based on the Median Euclidean Error (MEE), Robustness, and the determinant of the Jacobian of the displacement field. The top-ranked methodologies yielded similar performance across all evaluation metrics and shared several methodological commonalities, including pre-alignment, deep neural networks, inverse consistency analysis, and test-time instance optimization per-case basis as a post-processing step. The top-ranked method attained the MEE at or below that of the inter-rater variability for approximately 60% of the evaluated landmarks, underscoring the scope for further accuracy and robustness improvements, especially relative to human experts. The aim of BraTS-Reg is to continue to serve as an active resource for research, with the data and online evaluation tools accessible at https://bratsreg.github.io/.

Glioblastomas are the most aggressive fast-growing primary brain cancer which originate in the glial cells of the brain. Accurate identification of the malignant brain tumor and its sub-regions is still one of the most challenging problems in medical image segmentation. The Brain Tumor Segmentation Challenge (BraTS) has been a popular benchmark for automatic brain glioblastomas segmentation algorithms since its initiation. In this year, BraTS 2021 challenge provides the largest multi-parametric (mpMRI) dataset of 2,000 pre-operative patients. In this paper, we propose a new aggregation of two deep learning frameworks namely, DeepSeg and nnU-Net for automatic glioblastoma recognition in pre-operative mpMRI. Our ensemble method obtains Dice similarity scores of 92.00, 87.33, and 84.10 and Hausdorff Distances of 3.81, 8.91, and 16.02 for the enhancing tumor, tumor core, and whole tumor regions, respectively, on the BraTS 2021 validation set, ranking us among the top ten teams. These experimental findings provide evidence that it can be readily applied clinically and thereby aiding in the brain cancer prognosis, therapy planning, and therapy response monitoring. A docker image for reproducing our segmentation results is available online at (https://hub.docker.com/r/razeineldin/deepseg21)., Comment: Accepted in BraTS 2021 (as part of the BrainLes workshop proceedings distributed by Springer LNCS)

Cognitive cooperative assistance in robot-assisted surgery holds the potential to increase quality of care in minimally invasive interventions. Automation of surgical tasks promises to reduce the mental exertion and fatigue of surgeons. In this work, multi-agent reinforcement learning is demonstrated to be robust to the distribution shift introduced by pairing a learned policy with a human team member. Multi-agent policies are trained directly from images in simulation to control multiple instruments in a sub task of the minimally invasive removal of the gallbladder. These agents are evaluated individually and in cooperation with humans to demonstrate their suitability as autonomous assistants. Compared to human teams, the hybrid teams with artificial agents perform better considering completion time (44.4% to 71.2% shorter) as well as number of collisions (44.7% to 98.0% fewer). Path lengths, however, increase under control of an artificial agent (11.4% to 33.5% longer). A multi-agent formulation of the learning problem was favored over a single-agent formulation on this surgical sub task, due to the sequential learning of the two instruments. This approach may be extended to other tasks that are difficult to formulate within the standard reinforcement learning framework. Multi-agent reinforcement learning may shift the paradigm of cognitive robotic surgery towards seamless cooperation between surgeons and assistive technologies., Comment: Accepted at the 2021 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2021)

PURPOSE: Surgical workflow and skill analysis are key technologies for the next generation of cognitive surgical assistance systems. These systems could increase the safety of the operation through context-sensitive warnings and semi-autonomous robotic assistance or improve training of surgeons via data-driven feedback. In surgical workflow analysis up to 91% average precision has been reported for phase recognition on an open data single-center dataset. In this work we investigated the generalizability of phase recognition algorithms in a multi-center setting including more difficult recognition tasks such as surgical action and surgical skill. METHODS: To achieve this goal, a dataset with 33 laparoscopic cholecystectomy videos from three surgical centers with a total operation time of 22 hours was created. Labels included annotation of seven surgical phases with 250 phase transitions, 5514 occurences of four surgical actions, 6980 occurences of 21 surgical instruments from seven instrument categories and 495 skill classifications in five skill dimensions. The dataset was used in the 2019 Endoscopic Vision challenge, sub-challenge for surgical workflow and skill analysis. Here, 12 teams submitted their machine learning algorithms for recognition of phase, action, instrument and/or skill assessment. RESULTS: F1-scores were achieved for phase recognition between 23.9% and 67.7% (n=9 teams), for instrument presence detection between 38.5% and 63.8% (n=8 teams), but for action recognition only between 21.8% and 23.3% (n=5 teams). The average absolute error for skill assessment was 0.78 (n=1 team). CONCLUSION: Surgical workflow and skill analysis are promising technologies to support the surgical team, but are not solved yet, as shown by our comparison of algorithms. This novel benchmark can be used for comparable evaluation and validation of future work.