Hybrid Robotic-assisted Frameworks for Endomicroscopy Scanning in Retinal Surgeries

High-resolution real-time imaging at cellular levelin retinal surgeries is very challenging due to extremely confinedspace within the eyeball and lack of appropriate modalities.Probe-based confocal laser endomicroscopy (pCLE) system,which has a small footprint and provides highly-magnified im-ages, can be a potential imaging modality for improved diagnosis.The ability to visualize in cellular-level the retinal pigmentepithelium and the chorodial blood vessels underneath canprovide useful information for surgical outcomes in conditionssuch as retinal detachment. However, the adoption of pCLE islimited due to narrow field of view and micron-level range offocus. The physiological tremor of surgeons' hand also deterioratethe image quality considerably and leads to poor imaging results. In this paper, a novel image-based hybrid motion controlapproach is proposed to mitigate challenges of using pCLEin retinal surgeries. The proposed framework enables sharedcontrol of the pCLE probe by a surgeon to scan the tissueprecisely without hand tremors and an auto-focus image-basedcontrol algorithm that optimizes quality of pCLE images. Thecontrol strategy is deployed on two semi-autonomous frameworks: cooperative and teleoperated. Both frameworks consist of theSteady-Hand Eye Robot (SHER), whose end-effector holds thepCLE probe...

U-Net Training with Instance-Layer Normalization

Normalization layers are essential in a Deep Convolutional Neural Network (DCNN). Various normalization methods have been proposed. The statistics used to normalize the feature maps can be computed at batch, channel, or instance level. However, in most of existing methods, the normalization for each layer is fixed. Batch-Instance Normalization (BIN) is one of the first proposed methods that combines two different normalization methods and achieve diverse normalization for different layers. However, two potential issues exist in BIN: first, the Clip function is not differentiable at input values of 0 and 1; second, the combined feature map is not with a normalized distribution which is harmful for signal propagation in DCNN. In this paper, an Instance-Layer Normalization (ILN) layer is proposed by using the Sigmoid function for the feature map combination, and cascading group normalization. The performance of ILN is validated on image segmentation of the Right Ventricle (RV) and Left Ventricle (LV) using U-Net as the network architecture. The results show that the proposed ILN outperforms previous traditional and popular normalization methods with noticeable accuracy improvements for most validations, supporting the effectiveness of the proposed ILN.

A Robust Regression Approach for Robot Model Learning

Machine learning and data analysis have been used in many robotics fields, especially for modelling. Data are usually the result of sensor measurements and, as such, they might be subjected to noise and outliers. The presence of outliers has a huge impact on modelling the acquired data, resulting in inappropriate models. In this work a novel approach for outlier detection and rejection for input/output mapping in regression problems is presented. The robustness of the method is shown both through simulated data for linear and nonlinear regression, and real sensory data. Despite being validated by using artificial neural networks, the method can be generalized to any other regression method

One-stage Shape Instantiation from a Single 2D Image to 3D Point Cloud

Shape instantiation which predicts the 3D shape of a dynamic target from one or more 2D images is important for real-time intra-operative navigation. Previously, a general shape instantiation framework was proposed with manual image segmentation to generate a 2D Statistical Shape Model (SSM) and with Kernel Partial Least Square Regression (KPLSR) to learn the relationship between the 2D and 3D SSM for 3D shape prediction. In this paper, the two-stage shape instantiation is improved to be one-stage. PointOutNet with 19 convolutional layers and three fully-connected layers is used as the network structure and Chamfer distance is used as the loss function to predict the 3D target point cloud from a single 2D image. With the proposed one-stage shape instantiation algorithm, a spontaneous image-to-point cloud training and inference can be achieved. A dataset from 27 Right Ventricle (RV) subjects, indicating 609 experiments, were used to validate the proposed one-stage shape instantiation algorithm. An average point cloud-to-point cloud (PC-to-PC) error of 1.72mm has been achieved, which is comparable to the PLSR-based (1.42mm) and KPLSR-based (1.31mm) two-stage shape instantiation algorithm.

AirwayNet: A Voxel-Connectivity Aware Approach for Accurate Airway Segmentation Using Convolutional Neural Networks

Airway segmentation on CT scans is critical for pulmonary disease diagnosis and endobronchial navigation. Manual extraction of airway requires strenuous efforts due to the complicated structure and various appearance of airway. For automatic airway extraction, convolutional neural networks (CNNs) based methods have recently become the state-of-the-art approach. However, there still remains a challenge for CNNs to perceive the tree-like pattern and comprehend the connectivity of airway. To address this, we propose a voxel-connectivity aware approach named AirwayNet for accurate airway segmentation. By connectivity modeling, conventional binary segmentation task is transformed into 26 tasks of connectivity prediction. Thus, our AirwayNet learns both airway structure and relationship between neighboring voxels. To take advantage of context knowledge, lung distance map and voxel coordinates are fed into AirwayNet as additional semantic information. Compared to existing approaches, AirwayNet achieved superior performance, demonstrating the effectiveness of the network's awareness of voxel connectivity.

Real-time 3D Shape Instantiation for Partially-deployed Stent Segment from a Single 2D Fluoroscopic Image in Robot-assisted Fenestrated Endovascular Aortic Repair

In robot-assisted Fenestrated Endovascular Aortic Repair (FEVAR), accurate alignment of stent graft fenestrations or scallops with aortic branches is essential for establishing complete blood flow perfusion. Current navigation is largely based on 2D fluoroscopic images, which lacks 3D anatomical information, thus causing longer operation time as well as high risks of radiation exposure. Previously, 3D shape instantiation frameworks for real-time 3D shape reconstruction of fully-deployed or fully-compressed stent graft from a single 2D fluoroscopic image have been proposed for 3D navigation in robot-assisted FEVAR. However, these methods could not instantiate partially-deployed stent segments, as the 3D marker references are unknown. In this paper, an adapted Graph Convolutional Network (GCN) is proposed to predict 3D marker references from 3D fully-deployed markers. As original GCN is for classification, in this paper, the coarsening layers are removed and the softmax function at the network end is replaced with linear mapping for the regression task. The derived 3D and the 2D marker references are used to instantiate partially-deployed stent segment shape with the existing 3D shape instantiation framework. Validations were performed on three commonly used stent grafts and five patient-specific 3D printed aortic aneurysm phantoms. Comparable performances with average mesh distance errors of 1$\sim$3mm and average angular errors around 7degree were achieved.

Atrous Convolutional Neural Network (ACNN) for Biomedical Semantic Segmentation with Dimensionally Lossless Feature Maps

Deep Convolutional Neural Networks (DCNNs) are showing impressive performances in biomedical semantic segmentation. However, current DCNNs usually use down-sampling layers to achieve significant receptive field increasing and to gain abstract semantic information. These down-sampling layers decrease the spatial dimension of feature maps as well, which is harmful for semantic segmentation. Atrous convolution is an alternative for the down-sampling layer. It could increase the receptive field significantly but also maintain the spatial dimension of feature maps. In this paper, firstly, an atrous rate setting is proposed to achieve the largest and fully-covered receptive field with a minimum number of layers. Secondly, six atrous blocks, three shortcut connections and four normalization methods are explored to select the optimal atrous block, shortcut connection and normalization method. Finally, a new and dimensionally lossless DCNN - Atrous Convolutional Neural Network (ACNN) is proposed with using cascaded atrous II-blocks, residual learning and Fine Group Normalization (FGN). The Right Ventricle (RV), Left Ventricle (LV) and aorta data are used for the validation. The results show that the proposed ACNN achieves comparable segmentation Dice Similarity Coefficients (DSCs) with U-Net, optimized U-Net and the hybrid network, but uses much less parameters. This advantage is considered to benefit from the dimensionally lossless feature maps.

Varifocal-Net: A Chromosome Classification Approach using Deep Convolutional Networks

Chromosome classification is critical for karyotyping in abnormality diagnosis. To expedite diagnosis process, we present a novel method named Varifocal-Net for simultaneous classification of chromosome's type and polarity using deep convolutional networks. The approach consists of one global-scale network (G-Net) and one local-scale network (L-Net). It follows two stages. The first stage is to learn both global and local features. We extract global features and detect finer local regions via the G-Net. With the proposed varifocal mechanism, we zoom into local parts and extract local features via the L-Net. Residual learning and multi-task learning strategies are utilized to promote high-level feature extraction. The detection of discriminative local parts is fulfilled by a localization subnet of the G-Net, whose training process involves both supervised and weekly-supervised learning. The second stage is to build two multi-layer perceptron classifiers that exploit features of both two scales to boost classification performance. Evaluation results from 1909 karyotyping cases demonstrate that our Varifocal-Net achieved the highest accuracy of 0.9805, 0.9909 and average F1-score of 0.9771, 0.9909 for the type and polarity task, respectively. It outperformed state-of-the-art methods, demonstrating the effectiveness of our Varifocal mechanism and multi-scale feature ensemble.

3D Path Planning from a Single 2D Fluoroscopic Image for Robot Assisted Fenestrated Endovascular Aortic Repair

The current standard of intra-operative navigation during Fenestrated Endovascular Aortic Repair (FEVAR) calls for need of 3D alignments between inserted devices and aortic branches. The navigation commonly via 2D fluoroscopic images, lacks anatomical information, resulting in longer operation hours and radiation exposure. In this paper, a framework for real-time 3D robotic path planning from a single 2D fluoroscopic image of Abdominal Aortic Aneurysm (AAA) is introduced. A graph matching method is proposed to establish the correspondence between the 3D preoperative and 2D intra-operative AAA skeletons, and then the two skeletons are registered by skeleton deformation and regularization in respect to skeleton length and smoothness. Furthermore, deep learning was used to segment 3D pre-operative AAA from Computed Tomography (CT) scans to facilitate the framework automation. Simulation, phantom and patient AAA data sets have been used to validate the proposed framework. 3D distance error of 2mm was achieved in the phantom setup. Performance advantages were also achieved in terms of accuracy, robustness and time-efficiency. All the code will be open source.

Normalization in Training Deep Convolutional Neural Networks for 2D Bio-medical Semantic Segmentation

2D bio-medical semantic segmentation is important for surgical robotic vision. Segmentation methods based on Deep Convolutional Neural Network (DCNN) out-perform conventional methods in terms of both the accuracy and automation. One common issue in training DCNN is the internal covariate shift, where the convolutional kernels are trained to fit the distribution change of input feature, hence both the training speed and performance are decreased. Batch Normalization (BN) is the first proposed method for addressing internal covariate shift and is widely used. Later Instance Normalization (IN) and Layer Normalization (LN) were proposed and are used much less than BN. Group Normalization (GN) was proposed very recently and has not been applied into 2D bio-medical semantic segmentation yet. Most DCNN-based bio-medical semantic segmentation adopts BN as the normalization method by default, without reviewing its performance. In this paper, four normalization methods - BN, IN, LN and GN are compared and reviewed in details specifically for 2D bio-medical semantic segmentation. The result proved that GN out-performed the other three normalization methods - BN, IN and LN in 2D bio-medical semantic segmentation regarding both the accuracy and robustness. Unet is adopted as the basic DCNN structure. 37 RVs from both asymptomatic and Hypertrophic Cardiomyopathy (HCM) subjects and 20 aortas from asymptomatic subjects were used for the validation. The code and trained models will be available online.