Force Estimation from OCT Volumes using 3D CNNs

\textit{Purpose} Estimating the interaction forces of instruments and tissue is of interest, particularly to provide haptic feedback during robot assisted minimally invasive interventions. Different approaches based on external and integrated force sensors have been proposed. These are hampered by friction, sensor size, and sterilizability. We investigate a novel approach to estimate the force vector directly from optical coherence tomography image volumes. \textit{Methods} We introduce a novel Siamese 3D CNN architecture. The network takes an undeformed reference volume and a deformed sample volume as an input and outputs the three components of the force vector. We employ a deep residual architecture with bottlenecks for increased efficiency. We compare the Siamese approach to methods using difference volumes and two-dimensional projections. Data was generated using a robotic setup to obtain ground truth force vectors for silicon tissue phantoms as well as porcine tissue. \textit{Results} Our method achieves a mean average error of 7.7 +- 4.3 mN when estimating the force vector. Our novel Siamese 3D CNN architecture outperforms single-path methods that achieve a mean average error of 11.59 +- 6.7 mN. Moreover, the use of volume data leads to significantly higher performance compared to processing only surface information which achieves a mean average error of 24.38 +- 22.0 mN. Based on the tissue dataset, our methods shows good generalization in between different subjects. \textit{Conclusions} We propose a novel image-based force estimation method using optical coherence tomography. We illustrate that capturing the deformation of subsurface structures substantially improves force estimation. Our approach can provide accurate force estimates in surgical setups when using intraoperative optical coherence tomography.Comment: Published in the International Journal of Computer Assisted Radiology and Surger

Two-path 3D CNNs for calibration of system parameters for OCT-based motion compensation

Automatic motion compensation and adjustment of an intraoperative imaging modality's field of view is a common problem during interventions. Optical coherence tomography (OCT) is an imaging modality which is used in interventions due to its high spatial resolution of few micrometers and its temporal resolution of potentially several hundred volumes per second. However, performing motion compensation with OCT is problematic due to its small field of view which might lead to tracked objects being lost quickly. We propose a novel deep learning-based approach that directly learns input parameters of motors that move the scan area for motion compensation from optical coherence tomography volumes. We design a two-path 3D convolutional neural network (CNN) architecture that takes two volumes with an object to be tracked as its input and predicts the necessary motor input parameters to compensate the object's movement. In this way, we learn the calibration between object movement and system parameters for motion compensation with arbitrary objects. Thus, we avoid error-prone hand-eye calibration and handcrafted feature tracking from classical approaches. We achieve an average correlation coefficient of 0.998 between predicted and ground-truth motor parameters which leads to sub-voxel accuracy. Furthermore, we show that our deep learning model is real-time capable for use with the system's high volume acquisition frequency.Comment: Accepted at SPIE: Medical Imaging 201

Learning Preference-Based Similarities from Face Images using Siamese Multi-Task CNNs

Online dating has become a common occurrence over the last few decades. A key challenge for online dating platforms is to determine suitable matches for their users. A lot of dating services rely on self-reported user traits and preferences for matching. At the same time, some services largely rely on user images and thus initial visual preference. Especially for the latter approach, previous research has attempted to capture users' visual preferences for automatic match recommendation. These approaches are mostly based on the assumption that physical attraction is the key factor for relationship formation and personal preferences, interests, and attitude are largely neglected. Deep learning approaches have shown that a variety of properties can be predicted from human faces to some degree, including age, health and even personality traits. Therefore, we investigate the feasibility of bridging image-based matching and matching with personal interests, preferences, and attitude. We approach the problem in a supervised manner by predicting similarity scores between two users based on images of their faces only. The ground-truth for the similarity matching scores is determined by a test that aims to capture users' preferences, interests, and attitude that are relevant for forming romantic relationships. The images are processed by a Siamese Multi-Task deep learning architecture. We find a statistically significant correlation between predicted and target similarity scores. Thus, our results indicate that learning similarities in terms of interests, preferences, and attitude from face images appears to be feasible to some degree

Feasibility of a markerless tracking system based on optical coherence tomography

Clinical tracking systems are popular but typically require specific tracking markers. During the last years, scanning speed of optical coherence tomography (OCT) has increased to A-scan rates above 1 MHz allowing to acquire volume scans of moving objects. Thorefore, we propose a markerless tracking system based on OCT to obtain small volumetric images including information of sub-surface structures at high spatio-temporal resolution. In contrast to conventional vision based approaches, this allows identifying natural landmarks even for smooth and homogeneous surfaces. We describe the optomechanical setup and process flow to evaluate OCT volumes for translations and accordingly adjust the position of the field-of-view to follow moving samples. While our current setup is still preliminary, we demonstrate tracking of motion transversal to the OCT beam of up to 20 mm/s with errors around 0.2 mm and even better for some scenarios. Tracking is evaluated on a clearly structured and on a homogeneous phantom as well as on actual tissue samples. The results show that OCT is promising for fast and precise tracking of smooth, monochromatic objects in medical scenarios.Comment: Accepted at SPIE Medical Imaging 201

Melanoma detection with electrical impedance spectroscopy and dermoscopy using joint deep learning models

The initial assessment of skin lesions is typically based on dermoscopic images. As this is a difficult and time-consuming task, machine learning methods using dermoscopic images have been proposed to assist human experts. Other approaches have studied electrical impedance spectroscopy (EIS) as a basis for clinical decision support systems. Both methods represent different ways of measuring skin lesion properties as dermoscopy relies on visible light and EIS uses electric currents. Thus, the two methods might carry complementary features for lesion classification. Therefore, we propose joint deep learning models considering both EIS and dermoscopy for melanoma detection. For this purpose, we first study machine learning methods for EIS that incorporate domain knowledge and previously used heuristics into the design process. As a result, we propose a recurrent model with state-max-pooling which automatically learns the relevance of different EIS measurements. Second, we combine this new model with different convolutional neural networks that process dermoscopic images. We study ensembling approaches and also propose a cross-attention module guiding information exchange between the EIS and dermoscopy model. In general, combinations of EIS and dermoscopy clearly outperform models that only use either EIS or dermoscopy. We show that our attention-based, combined model outperforms other models with specificities of 34.4% (CI 31.3-38.4), 34.7% (CI 31.0-38.8) and 53.7% (CI 50.1-57.6) for dermoscopy, EIS and the combined model, respectively, at a clinically relevant sensitivity of 98%.Comment: Accepted at SPIE Medical Imaging 202

A Deep Learning Approach for Pose Estimation from Volumetric OCT Data

Tracking the pose of instruments is a central problem in image-guided surgery. For microscopic scenarios, optical coherence tomography (OCT) is increasingly used as an imaging modality. OCT is suitable for accurate pose estimation due to its micrometer range resolution and volumetric field of view. However, OCT image processing is challenging due to speckle noise and reflection artifacts in addition to the images' 3D nature. We address pose estimation from OCT volume data with a new deep learning-based tracking framework. For this purpose, we design a new 3D convolutional neural network (CNN) architecture to directly predict the 6D pose of a small marker geometry from OCT volumes. We use a hexapod robot to automatically acquire labeled data points which we use to train 3D CNN architectures for multi-output regression. We use this setup to provide an in-depth analysis on deep learning-based pose estimation from volumes. Specifically, we demonstrate that exploiting volume information for pose estimation yields higher accuracy than relying on 2D representations with depth information. Supporting this observation, we provide quantitative and qualitative results that 3D CNNs effectively exploit the depth structure of marker objects. Regarding the deep learning aspect, we present efficient design principles for 3D CNNs, making use of insights from the 2D deep learning community. In particular, we present Inception3D as a new architecture which performs best for our application. We show that our deep learning approach reaches errors at our ground-truth label's resolution. We achieve a mean average error of \SI{14.89 \pm 9.3}{\micro\metre} and \SI{0.096 \pm 0.072}{\degree} for position and orientation learning, respectively.Comment: https://doi.org/10.1016/j.media.2018.03.00

Towards Automatic Lesion Classification in the Upper Aerodigestive Tract Using OCT and Deep Transfer Learning Methods

Early detection of cancer is crucial for treatment and overall patient survival. In the upper aerodigestive tract (UADT) the gold standard for identification of malignant tissue is an invasive biopsy. Recently, non-invasive imaging techniques such as confocal laser microscopy and optical coherence tomography (OCT) have been used for tissue assessment. In particular, in a recent study experts classified lesions in the UADT with respect to their invasiveness using OCT images only. As the results were promising, automatic classification of lesions might be feasible which could assist experts in their decision making. Therefore, we address the problem of automatic lesion classification from OCT images. This task is very challenging as the available dataset is extremely small and the data quality is limited. However, as similar issues are typical in many clinical scenarios we study to what extent deep learning approaches can still be trained and used for decision support.Comment: Accepted for publication at CARS 201

A Deep Learning Approach for Motion Forecasting Using 4D OCT Data

Forecasting motion of a specific target object is a common problem for surgical interventions, e.g. for localization of a target region, guidance for surgical interventions, or motion compensation. Optical coherence tomography (OCT) is an imaging modality with a high spatial and temporal resolution. Recently, deep learning methods have shown promising performance for OCT-based motion estimation based on two volumetric images. We extend this approach and investigate whether using a time series of volumes enables motion forecasting. We propose 4D spatio-temporal deep learning for end-to-end motion forecasting and estimation using a stream of OCT volumes. We design and evaluate five different 3D and 4D deep learning methods using a tissue data set. Our best performing 4D method achieves motion forecasting with an overall average correlation coefficient of 97.41%, while also improving motion estimation performance by a factor of 2.5 compared to a previous 3D approach.Comment: Accepted for publication at MIDL 2020: https://openreview.net/forum?id=WVd56kgR

4D Spatio-Temporal Convolutional Networks for Object Position Estimation in OCT Volumes

Tracking and localizing objects is a central problem in computer-assisted surgery. Optical coherence tomography (OCT) can be employed as an optical tracking system, due to its high spatial and temporal resolution. Recently, 3D convolutional neural networks (CNNs) have shown promising performance for pose estimation of a marker object using single volumetric OCT images. While this approach relied on spatial information only, OCT allows for a temporal stream of OCT image volumes capturing the motion of an object at high volumes rates. In this work, we systematically extend 3D CNNs to 4D spatio-temporal CNNs to evaluate the impact of additional temporal information for marker object tracking. Across various architectures, our results demonstrate that using a stream of OCT volumes and employing 4D spatio-temporal convolutions leads to a 30% lower mean absolute error compared to single volume processing with 3D CNNs.Comment: Accepted at CURAC 202

Deep Learning for High Speed Optical Coherence Elastography

Mechanical properties of tissue provide valuable information for identifying lesions. One approach to obtain quantitative estimates of elastic properties is shear wave elastography with optical coherence elastography (OCE). However, given the shear wave velocity, it is still difficult to estimate elastic properties. Hence, we propose deep learning to directly predict elastic tissue properties from OCE data. We acquire 2D images with a frame rate of 30 kHz and use convolutional neural networks to predict gelatin concentration, which we use as a surrogate for tissue elasticity. We compare our deep learning approach to predictions from conventional regression models, using the shear wave velocity as a feature. Mean absolut prediction errors for the conventional approaches range from 1.32$\pm$0.98 p.p. to 1.57$\pm$1.30 p.p. whereas we report an error of 0.90$\pm$0.84 p.p for the convolutional neural network with 3D spatio-temporal input. Our results indicate that deep learning on spatio-temporal data outperforms elastography based on explicit shear wave velocity estimation.Comment: Accepted at IEEE International Symposium on Biomedical Imaging 202