arXiv subjects

Nassir Navab

Publications and source records attributed to Nassir Navab.

At least 541 records · Page 30Linked to original sources

arXiv2018

StainGAN: Stain Style Transfer for Digital Histological Images

Digitized Histological diagnosis is in increasing demand. However, color variations due to various factors are imposing obstacles to the diagnosis process. The problem of stain color variations is a well-defined problem with many proposed solutions. Most of these solutions are highly dependent on a reference template slide. We propose a deep-learning solution inspired by CycleGANs that is trained end-to-end, eliminating the need for an expert to pick a representative reference slide. Our approach showed superior results quantitatively and qualitatively against the state of the art methods (10% improvement visually using SSIM). We further validated our method on a clinical use-case, namely Breast Cancer tumor classification, showing 12% increase in AUC. The code will be made publicly available.

cs.CV↗

arXiv2018

Guide Me: Interacting with Deep Networks

Interaction and collaboration between humans and intelligent machines has become increasingly important as machine learning methods move into real-world applications that involve end users. While much prior work lies at the intersection of natural language and vision, such as image captioning or image generation from text descriptions, less focus has been placed on the use of language to guide or improve the performance of a learned visual processing algorithm. In this paper, we explore methods to flexibly guide a trained convolutional neural network through user input to improve its performance during inference. We do so by inserting a layer that acts as a spatio-semantic guide into the network. This guide is trained to modify the network's activations, either directly via an energy minimization scheme or indirectly through a recurrent model that translates human language queries to interaction weights. Learning the verbal interaction is fully automatic and does not require manual text annotations. We evaluate the method on two datasets, showing that guiding a pre-trained network can improve performance, and provide extensive insights into the interaction between the guide and the CNN.

cs.CV↗

arXiv2018

Multi-modal Disease Classification in Incomplete Datasets Using Geometric Matrix Completion

In large population-based studies and in clinical routine, tasks like disease diagnosis and progression prediction are inherently based on a rich set of multi-modal data, including imaging and other sensor data, clinical scores, phenotypes, labels and demographics. However, missing features, rater bias and inaccurate measurements are typical ailments of real-life medical datasets. Recently, it has been shown that deep learning with graph convolution neural networks (GCN) can outperform traditional machine learning in disease classification, but missing features remain an open problem. In this work, we follow up on the idea of modeling multi-modal disease classification as a matrix completion problem, with simultaneous classification and non-linear imputation of features. Compared to methods before, we arrange subjects in a graph-structure and solve classification through geometric matrix completion, which simulates a heat diffusion process that is learned and solved with a recurrent neural network. We demonstrate the potential of this method on the ADNI-based TADPOLE dataset and on the task of predicting the transition from MCI to Alzheimer's disease. With an AUC of 0.950 and classification accuracy of 87%, our approach outperforms standard linear and non-linear classifiers, as well as several state-of-the-art results in related literature, including a recently proposed GCN-based approach.

cs.CV↗

arXiv2018

Generalizability vs. Robustness: Adversarial Examples for Medical Imaging

In this paper, for the first time, we propose an evaluation method for deep learning models that assesses the performance of a model not only in an unseen test scenario, but also in extreme cases of noise, outliers and ambiguous input data. To this end, we utilize adversarial examples, images that fool machine learning models, while looking imperceptibly different from original data, as a measure to evaluate the robustness of a variety of medical imaging models. Through extensive experiments on skin lesion classification and whole brain segmentation with state-of-the-art networks such as Inception and UNet, we show that models that achieve comparable performance regarding generalizability may have significant variations in their perception of the underlying data manifold, leading to an extensive performance gap in their robustness.

cs.CV↗

arXiv2018

DeepDRR -- A Catalyst for Machine Learning in Fluoroscopy-guided Procedures

Machine learning-based approaches outperform competing methods in most disciplines relevant to diagnostic radiology. Interventional radiology, however, has not yet benefited substantially from the advent of deep learning, in particular because of two reasons: 1) Most images acquired during the procedure are never archived and are thus not available for learning, and 2) even if they were available, annotations would be a severe challenge due to the vast amounts of data. When considering fluoroscopy-guided procedures, an interesting alternative to true interventional fluoroscopy is in silico simulation of the procedure from 3D diagnostic CT. In this case, labeling is comparably easy and potentially readily available, yet, the appropriateness of resulting synthetic data is dependent on the forward model. In this work, we propose DeepDRR, a framework for fast and realistic simulation of fluoroscopy and digital radiography from CT scans, tightly integrated with the software platforms native to deep learning. We use machine learning for material decomposition and scatter estimation in 3D and 2D, respectively, combined with analytic forward projection and noise injection to achieve the required performance. On the example of anatomical landmark detection in X-ray images of the pelvis, we demonstrate that machine learning models trained on DeepDRRs generalize to unseen clinically acquired data without the need for re-training or domain adaptation. Our results are promising and promote the establishment of machine learning in fluoroscopy-guided procedures.

physics.med-ph↗

arXiv2018

X-ray-transform Invariant Anatomical Landmark Detection for Pelvic Trauma Surgery

X-ray image guidance enables percutaneous alternatives to complex procedures. Unfortunately, the indirect view onto the anatomy in addition to projective simplification substantially increase the task-load for the surgeon. Additional 3D information such as knowledge of anatomical landmarks can benefit surgical decision making in complicated scenarios. Automatic detection of these landmarks in transmission imaging is challenging since image-domain features characteristic to a certain landmark change substantially depending on the viewing direction. Consequently and to the best of our knowledge, the above problem has not yet been addressed. In this work, we present a method to automatically detect anatomical landmarks in X-ray images independent of the viewing direction. To this end, a sequential prediction framework based on convolutional layers is trained on synthetically generated data of the pelvic anatomy to predict 23 landmarks in single X-ray images. View independence is contingent on training conditions and, here, is achieved on a spherical segment covering (120 x 90) degrees in LAO/RAO and CRAN/CAUD, respectively, centered around AP. On synthetic data, the proposed approach achieves a mean prediction error of 5.6 +- 4.5 mm. We demonstrate that the proposed network is immediately applicable to clinically acquired data of the pelvis. In particular, we show that our intra-operative landmark detection together with pre-operative CT enables X-ray pose estimation which, ultimately, benefits initialization of image-based 2D/3D registration.

cs.CV↗

arXiv2018

Closing the Calibration Loop: An Inside-out-tracking Paradigm for Augmented Reality in Orthopedic Surgery

In percutaneous orthopedic interventions the surgeon attempts to reduce and fixate fractures in bony structures. The complexity of these interventions arises when the surgeon performs the challenging task of navigating surgical tools percutaneously only under the guidance of 2D interventional X-ray imaging. Moreover, the intra-operatively acquired data is only visualized indirectly on external displays. In this work, we propose a flexible Augmented Reality (AR) paradigm using optical see-through head mounted displays. The key technical contribution of this work includes the marker-less and dynamic tracking concept which closes the calibration loop between patient, C-arm and the surgeon. This calibration is enabled using Simultaneous Localization and Mapping of the environment of the operating theater. In return, the proposed solution provides in situ visualization of pre- and intra-operative 3D medical data directly at the surgical site. We demonstrate pre-clinical evaluation of a prototype system, and report errors for calibration and target registration. Finally, we demonstrate the usefulness of the proposed inside-out tracking system in achieving "bull's eye" view for C-arm-guided punctures. This AR solution provides an intuitive visualization of the anatomy and can simplify the hand-eye coordination for the orthopedic surgeon.

cs.CV↗

arXiv2018

A Minimalist Approach to Type-Agnostic Detection of Quadrics in Point Clouds

This paper proposes a segmentation-free, automatic and efficient procedure to detect general geometric quadric forms in point clouds, where clutter and occlusions are inevitable. Our everyday world is dominated by man-made objects which are designed using 3D primitives (such as planes, cones, spheres, cylinders, etc.). These objects are also omnipresent in industrial environments. This gives rise to the possibility of abstracting 3D scenes through primitives, thereby positions these geometric forms as an integral part of perception and high level 3D scene understanding. As opposed to state-of-the-art, where a tailored algorithm treats each primitive type separately, we propose to encapsulate all types in a single robust detection procedure. At the center of our approach lies a closed form 3D quadric fit, operating in both primal & dual spaces and requiring as low as 4 oriented-points. Around this fit, we design a novel, local null-space voting strategy to reduce the 4-point case to 3. Voting is coupled with the famous RANSAC and makes our algorithm orders of magnitude faster than its conventional counterparts. This is the first method capable of performing a generic cross-type multi-object primitive detection in difficult scenes. Results on synthetic and real datasets support the validity of our method.

cs.CV↗

arXiv2018

Fast 5DOF Needle Tracking in iOCT

Purpose. Intraoperative Optical Coherence Tomography (iOCT) is an increasingly available imaging technique for ophthalmic microsurgery that provides high-resolution cross-sectional information of the surgical scene. We propose to build on its desirable qualities and present a method for tracking the orientation and location of a surgical needle. Thereby, we enable direct analysis of instrument-tissue interaction directly in OCT space without complex multimodal calibration that would be required with traditional instrument tracking methods. Method. The intersection of the needle with the iOCT scan is detected by a peculiar multi-step ellipse fitting that takes advantage of the directionality of the modality. The geometric modelling allows us to use the ellipse parameters and provide them into a latency aware estimator to infer the 5DOF pose during needle movement. Results. Experiments on phantom data and ex-vivo porcine eyes indicate that the algorithm retains angular precision especially during lateral needle movement and provides a more robust and consistent estimation than baseline methods. Conclusion. Using solely crosssectional iOCT information, we are able to successfully and robustly estimate a 5DOF pose of the instrument in less than 5.5 ms on a CPU.

cs.CV↗

arXiv2018

On-the-fly Augmented Reality for Orthopaedic Surgery Using a Multi-Modal Fiducial

Fluoroscopic X-ray guidance is a cornerstone for percutaneous orthopaedic surgical procedures. However, two-dimensional observations of the three-dimensional anatomy suffer from the effects of projective simplification. Consequently, many X-ray images from various orientations need to be acquired for the surgeon to accurately assess the spatial relations between the patient's anatomy and the surgical tools. In this paper, we present an on-the-fly surgical support system that provides guidance using augmented reality and can be used in quasi-unprepared operating rooms. The proposed system builds upon a multi-modality marker and simultaneous localization and mapping technique to co-calibrate an optical see-through head mounted display to a C-arm fluoroscopy system. Then, annotations on the 2D X-ray images can be rendered as virtual objects in 3D providing surgical guidance. We quantitatively evaluate the components of the proposed system, and finally, design a feasibility study on a semi-anthropomorphic phantom. The accuracy of our system was comparable to the traditional image-guided technique while substantially reducing the number of acquired X-ray images as well as procedure time. Our promising results encourage further research on the interaction between virtual and real objects, that we believe will directly benefit the proposed method. Further, we would like to explore the capabilities of our on-the-fly augmented reality support system in a larger study directed towards common orthopaedic interventions.

cs.CV↗

arXiv2018

Plan in 2D, execute in 3D: An augmented reality solution for cup placement in total hip arthroplasty

Reproducibly achieving proper implant alignment is a critical step in total hip arthroplasty (THA) procedures that has been shown to substantially affect patient outcome. In current practice, correct alignment of the acetabular cup is verified in C-arm X-ray images that are acquired in an anterior-posterior (AP) view. Favorable surgical outcome is, therefore, heavily dependent on the surgeon's experience in understanding the 3D orientation of a hemispheric implant from 2D AP projection images. This work proposes an easy to use intra-operative component planning system based on two C-arm X-ray images that is combined with 3D augmented reality (AR) visualization that simplifies impactor and cup placement according to the planning by providing a real-time RGBD data overlay. We evaluate the feasibility of our system in a user study comprising four orthopedic surgeons at the Johns Hopkins Hospital, and also report errors in translation, anteversion, and abduction as low as 1.98 mm, 1.10 degrees, and 0.53 degrees, respectively. The promising performance of this AR solution shows that deploying this system could eliminate the need for excessive radiation, simplify the intervention, and enable reproducibly accurate placement of acetabular implants.

cs.CV↗

arXiv2017

SSD-6D: Making RGB-based 3D detection and 6D pose estimation great again

We present a novel method for detecting 3D model instances and estimating their 6D poses from RGB data in a single shot. To this end, we extend the popular SSD paradigm to cover the full 6D pose space and train on synthetic model data only. Our approach competes or surpasses current state-of-the-art methods that leverage RGB-D data on multiple challenging datasets. Furthermore, our method produces these results at around 10Hz, which is many times faster than the related methods. For the sake of reproducibility, we make our trained networks and detection code publicly available.

cs.CV↗

arXiv2017

Technical Note: Towards Virtual Monitors for Image Guided Interventions - Real-time Streaming to Optical See-Through Head-Mounted Displays

Purpose: Image guidance is crucial for the success of many interventions. Images are displayed on designated monitors that cannot be positioned optimally due to sterility and spatial constraints. This indirect visualization causes potential occlusion, hinders hand-eye coordination, leads to increased procedure duration and surgeon load. Methods: We propose a virtual monitor system that displays medical images in a mixed reality visualization using optical see-through head-mounted displays. The system streams high-resolution medical images from any modality to the head-mounted display in real-time that are blended with the surgical site. It allows for mixed reality visualization of images in head-, world-, or body-anchored mode and can thus be adapted to specific procedural needs. Results: For typical image sizes, the proposed system exhibits an average end-to-end delay and refresh rate of 214 +- 30 ms and 41:4 +- 32:0 Hz, respectively. Conclusions: The proposed virtual monitor system is capable of real-time mixed reality visualization of medical images. In future, we seek to conduct first pre-clinical studies to quantitatively assess the impact of the system on standard image guided procedures.

cs.OH↗

arXiv2017

Multi-layer Visualization for Medical Mixed Reality

Medical Mixed Reality helps surgeons to contextualize intraoperative data with video of the surgical scene. Nonetheless, the surgical scene and anatomical target are often occluded by surgical instruments and surgeon hands. In this paper and to our knowledge, we propose a multi-layer visualization in Medical Mixed Reality solution which subtly improves a surgeon's visualization by making transparent the occluding objects. As an example scenario, we use an augmented reality C-arm fluoroscope device. A video image is created using a volumetric-based image synthesization technique and stereo-RGBD cameras mounted on the C-arm. From this synthesized view, the background which is occluded by the surgical instruments and surgeon hands is recovered by modifying the volumetric-based image synthesization technique. The occluding objects can, therefore, become transparent over the surgical scene. Experimentation with different augmented reality scenarios yield results demonstrating that the background of the surgical scenes can be recovered with accuracy between 45%-99%. In conclusion, we presented a solution that a Mixed Reality solution for medicine, providing transparency to objects occluding the surgical scene. This work is also the first application of volumetric field for Diminished Reality/ Mixed Reality.

cs.CV↗

arXiv2017

6D Object Pose Estimation with Depth Images: A Seamless Approach for Robotic Interaction and Augmented Reality

To determine the 3D orientation and 3D location of objects in the surroundings of a camera mounted on a robot or mobile device, we developed two powerful algorithms in object detection and temporal tracking that are combined seamlessly for robotic perception and interaction as well as Augmented Reality (AR). A separate evaluation of, respectively, the object detection and the temporal tracker demonstrates the important stride in research as well as the impact on industrial robotic applications and AR. When evaluated on a standard dataset, the detector produced the highest f1-score with a large margin while the tracker generated the best accuracy at a very low latency of approximately 2 ms per frame with one CPU core: both algorithms outperforming the state of the art. When combined, we achieve a powerful framework that is robust to handle multiple instances of the same object under occlusion and clutter while attaining real-time performance. Aiming at stepping beyond the simple scenarios used by current systems, often constrained by having a single object in absence of clutter, averting to touch the object to prevent close-range partial occlusion, selecting brightly colored objects to easily segment them individually or assuming that the object has simple geometric structure, we demonstrate the capacity to handle challenging cases under clutter, partial occlusion and varying lighting conditions with objects of different shapes and sizes.

cs.CV↗

arXiv2017

The TUM LapChole dataset for the M2CAI 2016 workflow challenge

In this technical report we present our collected dataset of laparoscopic cholecystectomies (LapChole). Laparoscopic videos of a total of 20 surgeries were recorded and annotated with surgical phase labels, of which 15 were randomly pre-determined as training data, while the remaining 5 videos are selected as test data. This dataset was later included as part of the M2CAI 2016 workflow detection challenge during MICCAI 2016 in Athens.

cs.CV↗

arXiv2017

Camera Pose Filtering with Local Regression Geodesics on the Riemannian Manifold of Dual Quaternions

Time-varying, smooth trajectory estimation is of great interest to the vision community for accurate and well behaving 3D systems. In this paper, we propose a novel principal component local regression filter acting directly on the Riemannian manifold of unit dual quaternions $\mathbb{D} \mathbb{H}_1$. We use a numerically stable Lie algebra of the dual quaternions together with $\exp$ and $\log$ operators to locally linearize the 6D pose space. Unlike state of the art path smoothing methods which either operate on $SO\left(3\right)$ of rotation matrices or the hypersphere $\mathbb{H}_1$ of quaternions, we treat the orientation and translation jointly on the dual quaternion quadric in the 7-dimensional real projective space $\mathbb{R}\mathbb{P}^7$. We provide an outlier-robust IRLS algorithm for generic pose filtering exploiting this manifold structure. Besides our theoretical analysis, our experiments on synthetic and real data show the practical advantages of the manifold aware filtering on pose tracking and smoothing.

cs.CV↗

arXiv2017

Learning in an Uncertain World: Representing Ambiguity Through Multiple Hypotheses

Many prediction tasks contain uncertainty. In some cases, uncertainty is inherent in the task itself. In future prediction, for example, many distinct outcomes are equally valid. In other cases, uncertainty arises from the way data is labeled. For example, in object detection, many objects of interest often go unlabeled, and in human pose estimation, occluded joints are often labeled with ambiguous values. In this work we focus on a principled approach for handling such scenarios. In particular, we propose a framework for reformulating existing single-prediction models as multiple hypothesis prediction (MHP) models and an associated meta loss and optimization procedure to train them. To demonstrate our approach, we consider four diverse applications: human pose estimation, future prediction, image classification and segmentation. We find that MHP models outperform their single-hypothesis counterparts in all cases, and that MHP models simultaneously expose valuable insights into the variability of predictions.

cs.CV↗