Cataract-1K: Cataract Surgery Dataset for Scene Segmentation, Phase Recognition, and Irregularity Detection

In recent years, the landscape of computer-assisted interventions and post-operative surgical video analysis has been dramatically reshaped by deep-learning techniques, resulting in significant advancements in surgeons' skills, operation room management, and overall surgical outcomes. However, the progression of deep-learning-powered surgical technologies is profoundly reliant on large-scale datasets and annotations. Particularly, surgical scene understanding and phase recognition stand as pivotal pillars within the realm of computer-assisted surgery and post-operative assessment of cataract surgery videos. In this context, we present the largest cataract surgery video dataset that addresses diverse requisites for constructing computerized surgical workflow analysis and detecting post-operative irregularities in cataract surgery. We validate the quality of annotations by benchmarking the performance of several state-of-the-art neural network architectures for phase recognition and surgical scene segmentation. Besides, we initiate the research on domain adaptation for instrument segmentation in cataract surgery by evaluating cross-domain instrument segmentation performance in cataract surgery videos. The dataset and annotations will be publicly available upon acceptance of the paper.

Deep-Learning-Assisted Analysis of Cataract Surgery Videos

Following the technological advancements in medicine, the operation rooms are evolving into intelligent environments. The context-aware systems (CAS) can comprehensively interpret the surgical state, enable real-time warning, and support decision-making, especially for novice surgeons. These systems can automatically analyze surgical videos and perform indexing, documentation, and post-operative report generation. The ever-increasing demand for such automatic systems has sparked machine-learning-based approaches for surgical video analysis. This thesis addresses the significant challenges in cataract surgery video analysis to pave the way for building efficient context-aware systems. The main contributions of this thesis are five folds: (1) This thesis demonstrates that spatio-temporal localization of the relevant content can considerably improve phase recognition accuracy. (2) This thesis proposes a novel deep-learning-based framework for relevance-based compression to enable real-time streaming and adaptive storage of cataract surgery videos. (3) Several convolutional modules are proposed to boost the networks' semantic interpretation performance in challenging conditions. These challenges include blur and reflection distortion, transparency, deformability, color and texture variation, blunt edges, and scale variation. (4) This thesis proposes and evaluates the first framework for automatic irregularity detection in cataract surgery videos. (5) To alleviate the requirement for manual pixel-based annotations, this thesis proposes novel strategies for self-supervised representation learning adapted to semantic segmentation.

DeepPyramid+: Medical Image Segmentation using Pyramid View Fusion and Deformable Pyramid Reception

Semantic Segmentation plays a pivotal role in many applications related to medical image and video analysis. However, designing a neural network architecture for medical image and surgical video segmentation is challenging due to the diverse features of relevant classes, including heterogeneity, deformability, transparency, blunt boundaries, and various distortions. We propose a network architecture, DeepPyramid+, which addresses diverse challenges encountered in medical image and surgical video segmentation. The proposed DeepPyramid+ incorporates two major modules, namely "Pyramid View Fusion" (PVF) and "Deformable Pyramid Reception," (DPR), to address the outlined challenges. PVF replicates a deduction process within the neural network, aligning with the human visual system, thereby enhancing the representation of relative information at each pixel position. Complementarily, DPR introduces shape- and scale-adaptive feature extraction techniques using dilated deformable convolutions, enhancing accuracy and robustness in handling heterogeneous classes and deformable shapes. Extensive experiments conducted on diverse datasets, including endometriosis videos, MRI images, OCT scans, and cataract and laparoscopy videos, demonstrate the effectiveness of DeepPyramid+ in handling various challenges such as shape and scale variation, reflection, and blur degradation. DeepPyramid+ demonstrates significant improvements in segmentation performance, achieving up to a 3.65% increase in Dice coefficient for intra-domain segmentation and up to a 17% increase in Dice coefficient for cross-domain segmentation. DeepPyramid+ consistently outperforms state-of-the-art networks across diverse modalities considering different backbone networks, showcasing its versatility.

Predicting Postoperative Intraocular Lens Dislocation in Cataract Surgery via Deep Learning

A critical yet unpredictable complication following cataract surgery is intraocular lens dislocation. Postoperative stability is imperative, as even a tiny decentration of multifocal lenses or inadequate alignment of the torus in toric lenses due to postoperative rotation can lead to a significant drop in visual acuity. Investigating possible intraoperative indicators that can predict post-surgical instabilities of intraocular lenses can help prevent this complication. In this paper, we develop and evaluate the first fully-automatic framework for the computation of lens unfolding delay, rotation, and instability during surgery. Adopting a combination of three types of CNNs, namely recurrent, region-based, and pixel-based, the proposed framework is employed to assess the possibility of predicting post-operative lens dislocation during cataract surgery. This is achieved via performing a large-scale study on the statistical differences between the behavior of different brands of intraocular lenses and aligning the results with expert surgeons' hypotheses and observations about the lenses. We exploit a large-scale dataset of cataract surgery videos featuring four intraocular lens brands. Experimental results confirm the reliability of the proposed framework in evaluating the lens' statistics during the surgery. The Pearson correlation and t-test results reveal significant correlations between lens unfolding delay and lens rotation and significant differences between the intra-operative rotations stability of four groups of lenses. These results suggest that the proposed framework can help surgeons select the lenses based on the patient's eye conditions and predict post-surgical lens dislocation.

Event Recognition in Laparoscopic Gynecology Videos with Hybrid Transformers

Analyzing laparoscopic surgery videos presents a complex and multifaceted challenge, with applications including surgical training, intra-operative surgical complication prediction, and post-operative surgical assessment. Identifying crucial events within these videos is a significant prerequisite in a majority of these applications. In this paper, we introduce a comprehensive dataset tailored for relevant event recognition in laparoscopic gynecology videos. Our dataset includes annotations for critical events associated with major intra-operative challenges and post-operative complications. To validate the precision of our annotations, we assess event recognition performance using several CNN-RNN architectures. Furthermore, we introduce and evaluate a hybrid transformer architecture coupled with a customized training-inference framework to recognize four specific events in laparoscopic surgery videos. Leveraging the Transformer networks, our proposed architecture harnesses inter-frame dependencies to counteract the adverse effects of relevant content occlusion, motion blur, and surgical scene variation, thus significantly enhancing event recognition accuracy. Moreover, we present a frame sampling strategy designed to manage variations in surgical scenes and the surgeons' skill level, resulting in event recognition with high temporal resolution. We empirically demonstrate the superiority of our proposed methodology in event recognition compared to conventional CNN-RNN architectures through a series of extensive experiments.

Action Recognition in Video Recordings from Gynecologic Laparoscopy

Action recognition is a prerequisite for many applications in laparoscopic video analysis including but not limited to surgical training, operation room planning, follow-up surgery preparation, post-operative surgical assessment, and surgical outcome estimation. However, automatic action recognition in laparoscopic surgeries involves numerous challenges such as (I) cross-action and intra-action duration variation, (II) relevant content distortion due to smoke, blood accumulation, fast camera motions, organ movements, object occlusion, and (III) surgical scene variations due to different illuminations and viewpoints. Besides, action annotations in laparoscopy surgeries are limited and expensive due to requiring expert knowledge. In this study, we design and evaluate a CNN-RNN architecture as well as a customized training-inference framework to deal with the mentioned challenges in laparoscopic surgery action recognition. Using stacked recurrent layers, our proposed network takes advantage of inter-frame dependencies to negate the negative effect of content distortion and variation in action recognition. Furthermore, our proposed frame sampling strategy effectively manages the duration variations in surgical actions to enable action recognition with high temporal resolution. Our extensive experiments confirm the superiority of our proposed method in action recognition compared to static CNNs.

Domain Adaptation for Medical Image Segmentation using Transformation-Invariant Self-Training

Models capable of leveraging unlabelled data are crucial in overcoming large distribution gaps between the acquired datasets across different imaging devices and configurations. In this regard, self-training techniques based on pseudo-labeling have been shown to be highly effective for semi-supervised domain adaptation. However, the unreliability of pseudo labels can hinder the capability of self-training techniques to induce abstract representation from the unlabeled target dataset, especially in the case of large distribution gaps. Since the neural network performance should be invariant to image transformations, we look to this fact to identify uncertain pseudo labels. Indeed, we argue that transformation invariant detections can provide more reasonable approximations of ground truth. Accordingly, we propose a semi-supervised learning strategy for domain adaptation termed transformation-invariant self-training (TI-ST). The proposed method assesses pixel-wise pseudo-labels' reliability and filters out unreliable detections during self-training. We perform comprehensive evaluations for domain adaptation using three different modalities of medical images, two different network architectures, and several alternative state-of-the-art domain adaptation methods. Experimental results confirm the superiority of our proposed method in mitigating the lack of target domain annotation and boosting segmentation performance in the target domain.

DeepPyramid: Enabling Pyramid View and Deformable Pyramid Reception for Semantic Segmentation in Cataract Surgery Videos

Semantic segmentation in cataract surgery has a wide range of applications contributing to surgical outcome enhancement and clinical risk reduction. However, the varying issues in segmenting the different relevant structures in these surgeries make the designation of a unique network quite challenging. This paper proposes a semantic segmentation network, termed DeepPyramid, that can deal with these challenges using three novelties: (1) a Pyramid View Fusion module which provides a varying-angle global view of the surrounding region centering at each pixel position in the input convolutional feature map; (2) a Deformable Pyramid Reception module which enables a wide deformable receptive field that can adapt to geometric transformations in the object of interest; and (3) a dedicated Pyramid Loss that adaptively supervises multi-scale semantic feature maps. Combined, we show that these modules can effectively boost semantic segmentation performance, especially in the case of transparency, deformability, scalability, and blunt edges in objects. We demonstrate that our approach performs at a state-of-the-art level and outperforms a number of existing methods with a large margin (3.66% overall improvement in intersection over union compared to the best rival approach).

ReCal-Net: Joint Region-Channel-Wise Calibrated Network for Semantic Segmentation in Cataract Surgery Videos

Semantic segmentation in surgical videos is a prerequisite for a broad range of applications towards improving surgical outcomes and surgical video analysis. However, semantic segmentation in surgical videos involves many challenges. In particular, in cataract surgery, various features of the relevant objects such as blunt edges, color and context variation, reflection, transparency, and motion blur pose a challenge for semantic segmentation. In this paper, we propose a novel convolutional module termed as \textit{ReCal} module, which can calibrate the feature maps by employing region intra-and-inter-dependencies and channel-region cross-dependencies. This calibration strategy can effectively enhance semantic representation by correlating different representations of the same semantic label, considering a multi-angle local view centering around each pixel. Thus the proposed module can deal with distant visual characteristics of unique objects as well as cross-similarities in the visual characteristics of different objects. Moreover, we propose a novel network architecture based on the proposed module termed as ReCal-Net. Experimental results confirm the superiority of ReCal-Net compared to rival state-of-the-art approaches for all relevant objects in cataract surgery. Moreover, ablation studies reveal the effectiveness of the ReCal module in boosting semantic segmentation accuracy.

DeepPyram: Enabling Pyramid View and Deformable Pyramid Reception for Semantic Segmentation in Cataract Surgery Videos

Semantic segmentation in cataract surgery has a wide range of applications contributing to surgical outcome enhancement and clinical risk reduction. However, the varying issues in segmenting the different relevant instances make the designation of a unique network quite challenging. This paper proposes a semantic segmentation network termed as DeepPyram that can achieve superior performance in segmenting relevant objects in cataract surgery videos with varying issues. This superiority mainly originates from three modules: (i) Pyramid View Fusion, which provides a varying-angle global view of the surrounding region centering at each pixel position in the input convolutional feature map; (ii) Deformable Pyramid Reception, which enables a wide deformable receptive field that can adapt to geometric transformations in the object of interest; and (iii) Pyramid Loss that adaptively supervises multi-scale semantic feature maps. These modules can effectively boost semantic segmentation performance, especially in the case of transparency, deformability, scalability, and blunt edges in objects. The proposed approach is evaluated using four datasets of cataract surgery for objects with different contextual features and compared with thirteen state-of-the-art segmentation networks. The experimental results confirm that DeepPyram outperforms the rival approaches without imposing additional trainable parameters. Our comprehensive ablation study further proves the effectiveness of the proposed modules.