Tracking and Mapping in Medical Computer Vision: A Review

As computer vision algorithms are becoming more capable, their applications in clinical systems will become more pervasive. These applications include diagnostics such as colonoscopy and bronchoscopy, guiding biopsies and minimally invasive interventions and surgery, automating instrument motion and providing image guidance using pre-operative scans. Many of these applications depend on the specific visual nature of medical scenes and require designing and applying algorithms to perform in this environment. In this review, we provide an update to the field of camera-based tracking and scene mapping in surgery and diagnostics in medical computer vision. We begin with describing our review process, which results in a final list of 515 papers that we cover. We then give a high-level summary of the state of the art and provide relevant background for those who need tracking and mapping for their clinical applications. We then review datasets provided in the field and the clinical needs therein. Then, we delve in depth into the algorithmic side, and summarize recent developments, which should be especially useful for algorithm designers and to those looking to understand the capability of off-the-shelf methods. We focus on algorithms for deformable environments while also reviewing the essential building blocks in rigid tracking and mapping since there is a large amount of crossover in methods. Finally, we discuss the current state of the tracking and mapping methods along with needs for future algorithms, needs for quantification, and the viability of clinical applications in the field. We conclude that new methods need to be designed or combined to support clinical applications in deformable environments, and more focus needs to be put into collecting datasets for training and evaluation.

BASED: Bundle-Adjusting Surgical Endoscopic Dynamic Video Reconstruction using Neural Radiance Fields

Reconstruction of deformable scenes from endoscopic videos is important for many applications such as intraoperative navigation, surgical visual perception, and robotic surgery. It is a foundational requirement for realizing autonomous robotic interventions for minimally invasive surgery. However, previous approaches in this domain have been limited by their modular nature and are confined to specific camera and scene settings. Our work adopts the Neural Radiance Fields (NeRF) approach to learning 3D implicit representations of scenes that are both dynamic and deformable over time, and furthermore with unknown camera poses. We demonstrate this approach on endoscopic surgical scenes from robotic surgery. This work removes the constraints of known camera poses and overcomes the drawbacks of the state-of-the-art unstructured dynamic scene reconstruction technique, which relies on the static part of the scene for accurate reconstruction. Through several experimental datasets, we demonstrate the versatility of our proposed model to adapt to diverse camera and scene settings, and show its promise for both current and future robotic surgical systems.

Achieving Autonomous Cloth Manipulation with Optimal Control via Differentiable Physics-Aware Regularization and Safety Constraints

Cloth manipulation is a category of deformable object manipulation of great interest to the robotics community, from applications of automated laundry-folding and home organizing and cleaning to textiles and flexible manufacturing. Despite the desire for automated cloth manipulation, the thin-shell dynamics and under-actuation nature of cloth present significant challenges for robots to effectively interact with them. Many recent works omit explicit modeling in favor of learning-based methods that may yield control policies directly. However, these methods require large training sets that must be collected and curated. In this regard, we create a framework for differentiable modeling of cloth dynamics leveraging an Extended Position-based Dynamics (XPBD) algorithm. Together with the desired control objective, physics-aware regularization terms are designed for better results, including trajectory smoothness and elastic potential energy. In addition, safety constraints, such as avoiding obstacles, can be specified using signed distance functions (SDFs). We formulate the cloth manipulation task with safety constraints as a constrained optimization problem, which can be effectively solved by mainstream gradient-based optimizers thanks to the end-to-end differentiability of our framework. Finally, we assess the proposed framework for manipulation tasks with various safety thresholds and demonstrate the feasibility of result trajectories on a surgical robot. The effects of the regularization terms are analyzed in an additional ablation study.

Real-to-Sim Deformable Object Manipulation: Optimizing Physics Models with Residual Mappings for Robotic Surgery

Accurate deformable object manipulation (DOM) is essential for achieving autonomy in robotic surgery, where soft tissues are being displaced, stretched, and dissected. Many DOM methods can be powered by simulation, which ensures realistic deformation by adhering to the governing physical constraints and allowing for model prediction and control. However, real soft objects in robotic surgery, such as membranes and soft tissues, have complex, anisotropic physical parameters that a simulation with simple initialization from cameras may not fully capture. To use the simulation techniques in real surgical tasks, the "real-to-sim" gap needs to be properly compensated. In this work, we propose an online, adaptive parameter tuning approach for simulation optimization that (1) bridges the real-to-sim gap between a physics simulation and observations obtained 3D perceptions through estimating a residual mapping and (2) optimizes its stiffness parameters online. Our method ensures a small residual gap between the simulation and observation and improves the simulation's predictive capabilities. The effectiveness of the proposed mechanism is evaluated in the manipulation of both a thin-shell and volumetric tissue, representative of most tissue scenarios. This work contributes to the advancement of simulation-based deformable tissue manipulation and holds potential for improving surgical autonomy.

BAA-NGP: Bundle-Adjusting Accelerated Neural Graphics Primitives

Implicit neural representation has emerged as a powerful method for reconstructing 3D scenes from 2D images. Given a set of camera poses and associated images, the models can be trained to synthesize novel, unseen views. In order to expand the use cases for implicit neural representations, we need to incorporate camera pose estimation capabilities as part of the representation learning, as this is necessary for reconstructing scenes from real-world video sequences where cameras are generally not being tracked. Existing approaches like COLMAP and, most recently, bundle-adjusting neural radiance field methods often suffer from lengthy processing times. These delays ranging from hours to days, arise from laborious feature matching, hardware limitations, dense point sampling, and long training times required by a multi-layer perceptron structure with a large number of parameters. To address these challenges, we propose a framework called bundle-adjusting accelerated neural graphics primitives (BAA-NGP). Our approach leverages accelerated sampling and hash encoding to expedite both pose refinement/estimation and 3D scene reconstruction. Experimental results demonstrate that our method achieves a more than 10 to 20 $\times$ speed improvement in novel view synthesis compared to other bundle-adjusting neural radiance field methods without sacrificing the quality of pose estimation.

Learning Sampling Dictionaries for Efficient and Generalizable Robot Motion Planning with Transformers

Motion planning is integral to robotics applications such as autonomous driving, surgical robots, and industrial manipulators. Existing planning methods lack scalability to higher-dimensional spaces, while recent learning based planners have shown promise in accelerating sampling-based motion planners (SMP) but lack generalizability to out-of-distribution environments. To address this, we present a novel approach, Vector Quantized-Motion Planning Transformers (VQ-MPT) that overcomes the key generalization and scaling drawbacks of previous learning-based methods. VQ-MPT consists of two stages. Stage 1 is a Vector Quantized-Variational AutoEncoder model that learns to represent the planning space using a finite number of sampling distributions, and stage 2 is an Auto-Regressive model that constructs a sampling region for SMPs by selecting from the learned sampling distribution sets. By splitting large planning spaces into discrete sets and selectively choosing the sampling regions, our planner pairs well with out-of-the-box SMPs, generating near-optimal paths faster than without VQ-MPT's aid. It is generalizable in that it can be applied to systems of varying complexities, from 2D planar to 14D bi-manual robots with diverse environment representations, including costmaps and point clouds. Trained VQ-MPT models generalize to environments unseen during training and achieve higher success rates than previous methods.

ORRN: An ODE-based Recursive Registration Network for Deformable Respiratory Motion Estimation with Lung 4DCT Images

Deformable Image Registration (DIR) plays a significant role in quantifying deformation in medical data. Recent Deep Learning methods have shown promising accuracy and speedup for registering a pair of medical images. However, in 4D (3D + time) medical data, organ motion, such as respiratory motion and heart beating, can not be effectively modeled by pair-wise methods as they were optimized for image pairs but did not consider the organ motion patterns necessary when considering 4D data. This paper presents ORRN, an Ordinary Differential Equations (ODE)-based recursive image registration network. Our network learns to estimate time-varying voxel velocities for an ODE that models deformation in 4D image data. It adopts a recursive registration strategy to progressively estimate a deformation field through ODE integration of voxel velocities. We evaluate the proposed method on two publicly available lung 4DCT datasets, DIRLab and CREATIS, for two tasks: 1) registering all images to the extreme inhale image for 3D+t deformation tracking and 2) registering extreme exhale to inhale phase images. Our method outperforms other learning-based methods in both tasks, producing the smallest Target Registration Error of 1.24mm and 1.26mm, respectively. Additionally, it produces less than 0.001\% unrealistic image folding, and the computation speed is less than 1 second for each CT volume. ORRN demonstrates promising registration accuracy, deformation plausibility, and computation efficiency on group-wise and pair-wise registration tasks. It has significant implications in enabling fast and accurate respiratory motion estimation for treatment planning in radiation therapy or robot motion planning in thoracic needle insertion.

Biomedical image analysis competitions: The state of current participation practice

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

Suture Thread Spline Reconstruction from Endoscopic Images for Robotic Surgery with Reliability-driven Keypoint Detection

Automating the process of manipulating and delivering sutures during robotic surgery is a prominent problem at the frontier of surgical robotics, as automating this task can significantly reduce surgeons' fatigue during tele-operated surgery and allow them to spend more time addressing higher-level clinical decision making. Accomplishing autonomous suturing and suture manipulation in the real world requires accurate suture thread localization and reconstruction, the process of creating a 3D shape representation of suture thread from 2D stereo camera surgical image pairs. This is a very challenging problem due to how limited pixel information is available for the threads, as well as their sensitivity to lighting and specular reflection. We present a suture thread reconstruction work that uses reliable keypoints and a Minimum Variation Spline (MVS) smoothing optimization to construct a 3D centerline from a segmented surgical image pair. This method is comparable to previous suture thread reconstruction works, with the possible benefit of increased accuracy of grasping point estimation. Our code and datasets will be available at: https://github.com/ucsdarclab/thread-reconstruction.

Configuration Space Decomposition for Scalable Proxy Collision Checking in Robot Planning and Control

Real-time robot motion planning in complex high-dimensional environments remains an open problem. Motion planning algorithms, and their underlying collision checkers, are crucial to any robot control stack. Collision checking takes up a large portion of the computational time in robot motion planning. Existing collision checkers make trade-offs between speed and accuracy and scale poorly to high-dimensional, complex environments. We present a novel space decomposition method using K-Means clustering in the Forward Kinematics space to accelerate proxy collision checking. We train individual configuration space models using Fastron, a kernel perceptron algorithm, on these decomposed subspaces, yielding compact yet highly accurate models that can be queried rapidly and scale better to more complex environments. We demonstrate this new method, called Decomposed Fast Perceptron (D-Fastron), on the 7-DOF Baxter robot producing on average 29x faster collision checks and up to 9.8x faster motion planning compared to state-of-the-art geometric collision checkers.