arXiv subjects

Nils Gessert

Publications and source records attributed to Nils Gessert.

32 records · Page 2Linked to original sources

arXiv2019

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.

cs.CV↗

arXiv2019

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.

physics.med-ph↗

arXiv2018

Feasibility of Colon Cancer Detection in Confocal Laser Microscopy Images Using Convolution Neural Networks

Histological evaluation of tissue samples is a typical approach to identify colorectal cancer metastases in the peritoneum. For immediate assessment, reliable and real-time in-vivo imaging would be required. For example, intraoperative confocal laser microscopy has been shown to be suitable for distinguishing organs and also malignant and benign tissue. So far, the analysis is done by human experts. We investigate the feasibility of automatic colon cancer classification from confocal laser microscopy images using deep learning models. We overcome very small dataset sizes through transfer learning with state-of-the-art architectures. We achieve an accuracy of 89.1% for cancer detection in the peritoneum which indicates viability as an intraoperative decision support system.

cs.CV↗

arXiv2018

Bioresorbable Scaffold Visualization in IVOCT Images Using CNNs and Weakly Supervised Localization

Bioresorbable scaffolds have become a popular choice for treatment of coronary heart disease, replacing traditional metal stents. Often, intravascular optical coherence tomography is used to assess potential malapposition after implantation and for follow-up examinations later on. Typically, the scaffold is manually reviewed by an expert, analyzing each of the hundreds of image slices. As this is time consuming, automatic stent detection and visualization approaches have been proposed, mostly for metal stent detection based on classic image processing. As bioresorbable scaffolds are harder to detect, recent approaches have used feature extraction and machine learning methods for automatic detection. However, these methods require detailed, pixel-level labels in each image slice and extensive feature engineering for the particular stent type which might limit the approaches' generalization capabilities. Therefore, we propose a deep learning-based method for bioresorbable scaffold visualization using only image-level labels. A convolutional neural network is trained to predict whether an image slice contains a metal stent, a bioresorbable scaffold, or no device. Then, we derive local stent strut information by employing weakly supervised localization using saliency maps with guided backpropagation. As saliency maps are generally diffuse and noisy, we propose a novel patch-based method with image shifting which allows for high resolution stent visualization. Our convolutional neural network model achieves a classification accuracy of 99.0 % for image-level stent classification which can be used for both high quality in-slice stent visualization and 3D rendering of the stent structure.

cs.CV↗

arXiv2018

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.

cs.CV↗

arXiv2018

Automatic Plaque Detection in IVOCT Pullbacks Using Convolutional Neural Networks

Coronary heart disease is a common cause of death despite being preventable. To treat the underlying plaque deposits in the arterial walls, intravascular optical coherence tomography can be used by experts to detect and characterize the lesions. In clinical routine, hundreds of images are acquired for each patient which requires automatic plaque detection for fast and accurate decision support. So far, automatic approaches rely on classic machine learning methods and deep learning solutions have rarely been studied. Given the success of deep learning methods with other imaging modalities, a thorough understanding of deep learning-based plaque detection for future clinical decision support systems is required. We address this issue with a new dataset consisting of in-vivo patient images labeled by three trained experts. Using this dataset, we employ state-of-the-art deep learning models that directly learn plaque classification from the images. For improved performance, we study different transfer learning approaches. Furthermore, we investigate the use of cartesian and polar image representations and employ data augmentation techniques tailored to each representation. We fuse both representations in a multi-path architecture for more effective feature exploitation. Last, we address the challenge of plaque differentiation in addition to detection. Overall, we find that our combined model performs best with an accuracy of 91.7%, a sensitivity of 90.9% and a specificity of 92.4%. Our results indicate that building a deep learning-based clinical decision support system for plaque detection is feasible.

cs.CV↗

arXiv2018

Skin Lesion Diagnosis using Ensembles, Unscaled Multi-Crop Evaluation and Loss Weighting

In this paper we present the methods of our submission to the ISIC 2018 challenge for skin lesion diagnosis (Task 3). The dataset consists of 10000 images with seven image-level classes to be distinguished by an automated algorithm. We employ an ensemble of convolutional neural networks for this task. In particular, we fine-tune pretrained state-of-the-art deep learning models such as Densenet, SENet and ResNeXt. We identify heavy class imbalance as a key problem for this challenge and consider multiple balancing approaches such as loss weighting and balanced batch sampling. Another important feature of our pipeline is the use of a vast amount of unscaled crops for evaluation. Last, we consider meta learning approaches for the final predictions. Our team placed second at the challenge while being the best approach using only publicly available data.

cs.CV↗

arXiv2018

Towards Head Motion Compensation Using Multi-Scale Convolutional Neural Networks

Head pose estimation and tracking is useful in variety of medical applications. With the advent of RGBD cameras like Kinect, it has become feasible to do markerless tracking by estimating the head pose directly from the point clouds. One specific medical application is robot assisted transcranial magnetic stimulation (TMS) where any patient motion is compensated with the help of a robot. For increased patient comfort, it is important to track the head without markers. In this regard, we address the head pose estimation problem using two different approaches. In the first approach, we build upon the more traditional approach of model based head tracking, where a head model is morphed according to the particular head to be tracked and the morphed model is used to track the head in the point cloud streams. In the second approach, we propose a new multi-scale convolutional neural network architecture for more accurate pose regression. Additionally, we outline a systematic data set acquisition strategy using a head phantom mounted on the robot and ground-truth labels generated using a highly accurate tracking system.

cs.CV↗

arXiv2018

Needle Tip Force Estimation using an OCT Fiber and a Fused convGRU-CNN Architecture

Needle insertion is common during minimally invasive interventions such as biopsy or brachytherapy. During soft tissue needle insertion, forces acting at the needle tip cause tissue deformation and needle deflection. Accurate needle tip force measurement provides information on needle-tissue interaction and helps detecting and compensating potential misplacement. For this purpose we introduce an image-based needle tip force estimation method using an optical fiber imaging the deformation of an epoxy layer below the needle tip over time. For calibration and force estimation, we introduce a novel deep learning-based fused convolutional GRU-CNN model which effectively exploits the spatio-temporal data structure. The needle is easy to manufacture and our model achieves a mean absolute error of 1.76 +- 1.5 mN with a cross-correlation coefficient of 0.9996, clearly outperforming other methods. We test needles with different materials to demonstrate that the approach can be adapted for different sensitivities and force ranges. Furthermore, we validate our approach in an ex-vivo prostate needle insertion scenario.

cs.CV↗

arXiv2018

Adversarial Training for Patient-Independent Feature Learning with IVOCT Data for Plaque Classification

Deep learning methods have shown impressive results for a variety of medical problems over the last few years. However, datasets tend to be small due to time-consuming annotation. As datasets with different patients are often very heterogeneous generalization to new patients can be difficult. This is complicated further if large differences in image acquisition can occur, which is common during intravascular optical coherence tomography for coronary plaque imaging. We address this problem with an adversarial training strategy where we force a part of a deep neural network to learn features that are independent of patient- or acquisitionspecific characteristics. We compare our regularization method to typical data augmentation strategies and show that our approach improves performance for a small medical dataset.

cs.CV↗

arXiv2018

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.

cs.CV↗

arXiv2018

Design and implementation of a wireless instrument adapter

The evaluation of new methods for control and manipulation in minimally invasive robotic surgery requires a realistic setup. To decouple the evaluation of methods from overall clinical systems, we propose an instrument adapter for the S line EndoWrist\c{opyright} instruments of the da Vinci surgical system. The adapter is small and lightweight and can be mounted to any robot to mimic motion. We describe its design and implementation, as well as a setup to calibrate instruments to study precise motion control. Our results indicate that each instrument requires individual calibration. The calibration shows that the system is not fully linear. The repeatability of poses in the same sense of rotation has an RMSE of 0.27°/ and a standard deviation below 0.3° for pitching and 4.7° for yawing averaged over three measurements. When comparing the same poses in clockwise and counter-clockwise direction the RMSE is 12.8° and 5.7° for pitching and yawing, respectively. This is likely due to motor hysteresis.

cs.RO↗

arXiv2018

Plaque Classification in Coronary Arteries from IVOCT Images Using Convolutional Neural Networks and Transfer Learning

Advanced atherosclerosis in the coronary arteries is one of the leading causes of deaths worldwide while being preventable and treatable. In order to image atherosclerotic lesions (plaque), intravascular optical coherence tomography (IVOCT) can be used. The technique provides high-resolution images of arterial walls which allows for early plaque detection by experts. Due to the vast amount of IVOCT images acquired in clinical routines, automatic plaque detection has been addressed. For example, attenuation profiles in single A-Scans of IVOCT images are examined to detect plaque. We address automatic plaque classification from entire IVOCT images, the cross-sectional view of the artery, using deep feature learning. In this way, we take context between A-Scans into account and we directly learn relevant features from the image source without the need for handcrafting features.

cs.CV↗

arXiv2018

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.

cs.CV↗