Synthesizing Multi-Class Surgical Datasets with Anatomy-Aware Diffusion Models

In computer-assisted surgery, automatically recognizing anatomical organs is crucial for understanding the surgical scene and providing intraoperative assistance. While machine learning models can identify such structures, their deployment is hindered by the need for labeled, diverse surgical datasets with anatomical annotations. Labeling multiple classes (i.e., organs) in a surgical scene is time-intensive, requiring medical experts. Although synthetically generated images can enhance segmentation performance, maintaining both organ structure and texture during generation is challenging. We introduce a multi-stage approach using diffusion models to generate multi-class surgical datasets with annotations. Our framework improves anatomy awareness by training organ specific models with an inpainting objective guided by binary segmentation masks. The organs are generated with an inference pipeline using pre-trained ControlNet to maintain the organ structure. The synthetic multi-class datasets are constructed through an image composition step, ensuring structural and textural consistency. This versatile approach allows the generation of multi-class datasets from real binary datasets and simulated surgical masks. We thoroughly evaluate the generated datasets on image quality and downstream segmentation, achieving a $15\%$ improvement in segmentation scores when combined with real images. Our codebase https://gitlab.com/nct_tso_public/muli-class-image-synthesis

SurgicaL-CD: Generating Surgical Images via Unpaired Image Translation with Latent Consistency Diffusion Models

Computer-assisted surgery (CAS) systems are designed to assist surgeons during procedures, thereby reducing complications and enhancing patient care. Training machine learning models for these systems requires a large corpus of annotated datasets, which is challenging to obtain in the surgical domain due to patient privacy concerns and the significant labeling effort required from doctors. Previous methods have explored unpaired image translation using generative models to create realistic surgical images from simulations. However, these approaches have struggled to produce high-quality, diverse surgical images. In this work, we introduce \emph{SurgicaL-CD}, a consistency-distilled diffusion method to generate realistic surgical images with only a few sampling steps without paired data. We evaluate our approach on three datasets, assessing the generated images in terms of quality and utility as downstream training datasets. Our results demonstrate that our method outperforms GANs and diffusion-based approaches. Our code is available at \url{https://gitlab.com/nct_tso_public/gan2diffusion}.

Using Fiber Optic Bundles to Miniaturize Vision-Based Tactile Sensors

Vision-based tactile sensors have recently become popular due to their combination of low cost, very high spatial resolution, and ease of integration using widely available miniature cameras. The associated field of view and focal length, however, are difficult to package in a human-sized finger. In this paper we employ optical fiber bundles to achieve a form factor that, at 15 mm diameter, is smaller than an average human fingertip. The electronics and camera are also located remotely, further reducing package size. The sensor achieves a spatial resolution of 0.22 mm and a minimum force resolution 5 mN for normal and shear contact forces. With these attributes, the DIGIT Pinki sensor is suitable for applications such as robotic and teleoperated digital palpation. We demonstrate its utility for palpation of the prostate gland and show that it can achieve clinically relevant discrimination of prostate stiffness for phantom and ex vivo tissue.

One model to use them all: Training a segmentation model with complementary datasets

Understanding a surgical scene is crucial for computer-assisted surgery systems to provide any intelligent assistance functionality. One way of achieving this scene understanding is via scene segmentation, where every pixel of a frame is classified and therefore identifies the visible structures and tissues. Progress on fully segmenting surgical scenes has been made using machine learning. However, such models require large amounts of annotated training data, containing examples of all relevant object classes. Such fully annotated datasets are hard to create, as every pixel in a frame needs to be annotated by medical experts and, therefore, are rarely available. In this work, we propose a method to combine multiple partially annotated datasets, which provide complementary annotations, into one model, enabling better scene segmentation and the use of multiple readily available datasets. Our method aims to combine available data with complementary labels by leveraging mutual exclusive properties to maximize information. Specifically, we propose to use positive annotations of other classes as negative samples and to exclude background pixels of binary annotations, as we cannot tell if they contain a class not annotated but predicted by the model. We evaluate our method by training a DeepLabV3 on the publicly available Dresden Surgical Anatomy Dataset, which provides multiple subsets of binary segmented anatomical structures. Our approach successfully combines 6 classes into one model, increasing the overall Dice Score by 4.4% compared to an ensemble of models trained on the classes individually. By including information on multiple classes, we were able to reduce confusion between stomach and colon by 24%. Our results demonstrate the feasibility of training a model on multiple datasets. This paves the way for future work further alleviating the need for one large, fully segmented datasets.

Graph data modelling for outcome prediction in oropharyngeal cancer patients

Graph neural networks (GNNs) are becoming increasingly popular in the medical domain for the tasks of disease classification and outcome prediction. Since patient data is not readily available as a graph, most existing methods either manually define a patient graph, or learn a latent graph based on pairwise similarities between the patients. There are also hypergraph neural network (HGNN)-based methods that were introduced recently to exploit potential higher order associations between the patients by representing them as a hypergraph. In this work, we propose a patient hypergraph network (PHGN), which has been investigated in an inductive learning setup for binary outcome prediction in oropharyngeal cancer (OPC) patients using computed tomography (CT)-based radiomic features for the first time. Additionally, the proposed model was extended to perform time-to-event analyses, and compared with GNN and baseline linear models.

Exploring Semantic Consistency in Unpaired Image Translation to Generate Data for Surgical Applications

In surgical computer vision applications, obtaining labeled training data is challenging due to data-privacy concerns and the need for expert annotation. Unpaired image-to-image translation techniques have been explored to automatically generate large annotated datasets by translating synthetic images to the realistic domain. However, preserving the structure and semantic consistency between the input and translated images presents significant challenges, mainly when there is a distributional mismatch in the semantic characteristics of the domains. This study empirically investigates unpaired image translation methods for generating suitable data in surgical applications, explicitly focusing on semantic consistency. We extensively evaluate various state-of-the-art image translation models on two challenging surgical datasets and downstream semantic segmentation tasks. We find that a simple combination of structural-similarity loss and contrastive learning yields the most promising results. Quantitatively, we show that the data generated with this approach yields higher semantic consistency and can be used more effectively as training data.

TUNeS: A Temporal U-Net with Self-Attention for Video-based Surgical Phase Recognition

To enable context-aware computer assistance in the operating room of the future, cognitive systems need to understand automatically which surgical phase is being performed by the medical team. The primary source of information for surgical phase recognition is typically video, which presents two challenges: extracting meaningful features from the video stream and effectively modeling temporal information in the sequence of visual features. For temporal modeling, attention mechanisms have gained popularity due to their ability to capture long-range dependencies. In this paper, we explore design choices for attention in existing temporal models for surgical phase recognition and propose a novel approach that does not resort to local attention or regularization of attention weights: TUNeS is an efficient and simple temporal model that incorporates self-attention at the coarsest stage of a U-Net-like structure. In addition, we propose to train the feature extractor, a standard CNN, together with an LSTM on preferably long video segments, i.e., with long temporal context. In our experiments, all temporal models performed better on top of feature extractors that were trained with longer temporal context. On top of these contextualized features, TUNeS achieves state-of-the-art results on Cholec80.

Metrics Matter in Surgical Phase Recognition

Surgical phase recognition is a basic component for different context-aware applications in computer- and robot-assisted surgery. In recent years, several methods for automatic surgical phase recognition have been proposed, showing promising results. However, a meaningful comparison of these methods is difficult due to differences in the evaluation process and incomplete reporting of evaluation details. In particular, the details of metric computation can vary widely between different studies. To raise awareness of potential inconsistencies, this paper summarizes common deviations in the evaluation of phase recognition algorithms on the Cholec80 benchmark. In addition, a structured overview of previously reported evaluation results on Cholec80 is provided, taking known differences in evaluation protocols into account. Greater attention to evaluation details could help achieve more consistent and comparable results on the surgical phase recognition task, leading to more reliable conclusions about advancements in the field and, finally, translation into clinical practice.

Surgical tool classification and localization: results and methods from the MICCAI 2022 SurgToolLoc challenge

The ability to automatically detect and track surgical instruments in endoscopic videos can enable transformational interventions. Assessing surgical performance and efficiency, identifying skilled tool use and choreography, and planning operational and logistical aspects of OR resources are just a few of the applications that could benefit. Unfortunately, obtaining the annotations needed to train machine learning models to identify and localize surgical tools is a difficult task. Annotating bounding boxes frame-by-frame is tedious and time-consuming, yet large amounts of data with a wide variety of surgical tools and surgeries must be captured for robust training. Moreover, ongoing annotator training is needed to stay up to date with surgical instrument innovation. In robotic-assisted surgery, however, potentially informative data like timestamps of instrument installation and removal can be programmatically harvested. The ability to rely on tool installation data alone would significantly reduce the workload to train robust tool-tracking models. With this motivation in mind we invited the surgical data science community to participate in the challenge, SurgToolLoc 2022. The goal was to leverage tool presence data as weak labels for machine learning models trained to detect tools and localize them in video frames with bounding boxes. We present the results of this challenge along with many of the team's efforts. We conclude by discussing these results in the broader context of machine learning and surgical data science. The training data used for this challenge consisting of 24,695 video clips with tool presence labels is also being released publicly and can be accessed at https://console.cloud.google.com/storage/browser/isi-surgtoolloc-2022.

Non-rigid Point Cloud Registration for Middle Ear Diagnostics with Endoscopic Optical Coherence Tomography

Purpose: Middle ear infection is the most prevalent inflammatory disease, especially among the pediatric population. Current diagnostic methods are subjective and depend on visual cues from an otoscope, which is limited for otologists to identify pathology. To address this shortcoming, endoscopic optical coherence tomography (OCT) provides both morphological and functional in-vivo measurements of the middle ear. However, due to the shadow of prior structures, interpretation of OCT images is challenging and time-consuming. To facilitate fast diagnosis and measurement, improvement in the readability of OCT data is achieved by merging morphological knowledge from ex-vivo middle ear models with OCT volumetric data, so that OCT applications can be further promoted in daily clinical settings. Methods: We propose C2P-Net: a two-staged non-rigid registration pipeline for complete to partial point clouds, which are sampled from ex-vivo and in-vivo OCT models, respectively. To overcome the lack of labeled training data, a fast and effective generation pipeline in Blender3D is designed to simulate middle ear shapes and extract in-vivo noisy and partial point clouds. Results: We evaluate the performance of C2P-Net through experiments on both synthetic and real OCT datasets. The results demonstrate that C2P-Net is generalized to unseen middle ear point clouds and capable of handling realistic noise and incompleteness in synthetic and real OCT data. Conclusion: In this work, we aim to enable diagnosis of middle ear structures with the assistance of OCT images. We propose C2P-Net: a two-staged non-rigid registration pipeline for point clouds to support the interpretation of in-vivo noisy and partial OCT images for the first time. Code is available at: https://gitlab.com/nct\_tso\_public/c2p-net.