Research in Reconstruction

Table of Content

Abstract
Contact Person and Group Coordination
Research Projects in Reconstruction
Related Publications
Working Group

Contact Person and Group Coordination


Andreas Keil	Nassir Navab

Research Projects in Reconstruction

Estimation of Flow Parameters from X-ray Data

Recognizing stenosis in angiographic images is a quite difficult task. Most methods are only 2D so that overlapping, foreshortening or a bad perspective of the view causes a false diagnoses. The aim of this project is to reconstruct the blood flow from 3D X-ray data to get a realistic and patient specific computer fluid dynamic simulation of the blood flow. With this any type of images concerning blood flow can be simulated. Also the perspective of these images can be chosen by the user without taking X-ray images from the patient.

Stereo Time-of-Flight

This paper describes a novel method to acquire depth images based on combining a pair of ToF^? (Time of Flight) cameras. As opposed to approaches that register point clouds posterior to the image acquisition, we propose to combine the measurements of the two cameras at the acquisition level. To do so, we actively control the infrared lighting of the scene such that the two cameras emit and measure the reflected infrared light first one after the other, and then simultaneously. Assuming the scene is static during these three stages and gathering the obtained depth measurements in each state, we derive a set of constraints that allow us to optimize the two depth images. In terms of hardware requirements, the cameras need to have access to the control of the infrared lights and should work with the same infrared wavelength and with exactly the same modulation frequency. A quantitative evaluation of the performance of the proposed method for different objects and setups is provided based on a simulation of the ToF^? cameras. Results on real images are also provided. In both simulation and real images the stereo-ToF acquisition is able to produce more accurate depth measurements.

Cardiac C-Arm CT

Tomographic reconstruction from rotational cone-beam X-ray data is only solved for static objects of interest (like the abdominal region). In cardiac imaging, a rotational angiography sequence takes about 4 to 6s and therefore spans several heart beats. Since such an acquisition scheme forces a trade-off between consistency of the scene and reasonable baselines between camera positions, standard reconstruction techniques fail at recovering the 3D+t scene. We propose a new reconstruction framework based on variational level sets including a new data term for symbolic reconstruction as well as a novel incorporation of motion into the level set formalism. The resulting simultaneous estimation of shape and motion proves feasible in first experiments.

Reconstruction and Registration of Histology and Phase Contrast Images for Clinical Validation of Imaging Modalities

Before its introduction into the hospital, a new imaging modality has to be validated. In other words, appearing structures need to be correlated to the imaged tissues. Such a cross validation is only meaningful when performed against the gold standard which is histology. Currently, cross validation is performed by qualitative comparison of 3D datasets to 2D histology slices. Since the acquisition of a consistent 3D histology volume is a challenging task, its comparison to the corresponding dataset always remained qualitative.

The classic histology procedure can be divided in four steps: pre processing, cutting, post processing and imaging of the tissues. In the first step, the sample is chemically processed to preserve the tissues and is then embedded in a paraffin block. By using a microtome, it is cut in very thin slices, and put on a glass slide. During post processing the sample is stained to enhance the structures of interest. The imaging is performed with a camera mounted in a microscope, or with a dedicated scanner. Several difficulties inherent to this process can have a dramatic influence on the quality of the reconstructed histology volume. For instance, since the cutting process is done manually, problems like flipping, bending or ripping of the slides may happen. If the knife starts to wear off, some banding will appear over the slices. Moreover, a few slices could be missing. Finally since the staining color is time dependent, variation in the color of the slices can occur.

In this project, we propose to improve the histology procedure and to develop methods towards a consistent reconstruction of 3D histology volumes.

Deformable Guide Wire Tracking

These days, X-ray fluoroscopic imaging is the modality used most widely to guide physicians in angiographic interventions. Current guidance procedures are based on a roadmap, e.g. a digital subtracted angiography (DSA) acquired from a fixed viewpoint and the injection of contrast agent to visualize the current vessel anatomy. Such roadmaps cannot directly be blended with the fluoroscopic sequence due to misalignment caused by respiratory motion. A fundamental step toward a successful integration of any navigation application into clinical routine is the estimation and compensation of respiratory motion. We propose a novel method for deformable tracking of multiple ridge segments based on a MAP-MRF formulation and efficient discrete optimization. Ridges are modeled as B-Spline curves which allows us to apply smooth deformations based on a minimal number of parameters. Our tracking framework is well adapted to the noisy domain of fluoroscopic imaging and the handling of multiple segments.

Assessment of Knee Cartilage

Degeneration of knee joint cartilage is an important and early indicator of osteoarthritis (OA) which is one of the major socio-economic burdens nowadays. Accurate quantification of the articular cartilage degeneration in an early stage using MR images is a promising approach in diagnosis and therapy for this disease. Particularly, volume and thickness measurement of cartilage tissue has been shown to deliver significant parameters in assessment of pathologies. Here, accurate computer-aided diagnosis tools could improve the clinical routine where image segmentation plays a crucial role. In order to overcome the time-consuming and tedious work of manual segmentation, one tries to automate the segmentation as much as possible. We focus on novel atlas-based segmentation methods for knee cartilage as well as improve today’s clinical routine of manual segmentation methods. In addition, we try to evaluate different methods for the assessment of parameters such as volume and thickness which could allow computer-aided diagnosis of knee cartilage pathologies in an early stage.

Endoscopic Video Processing

The diagnosis and surveillance of several gastrointestinal (GI) diseases such as colateral or oesaphageal cancer are performed under endoscopic guidance. However, currently there exists no computer aided navigation tool to support these procedures. The goal of this project is to provide an advanced visualisation and automatic recognition tool in order to support the navigation and targeting in GI endoscopic procedures. The aim of the project is twofold: reconstructing the organ surface from endoscopic videos using monoSLAM and automatically recognising the biopsy locations to support the navigation and targeting in endoscopy.

Related Publications

2012
	A. Hartl, D. I. Shakir, R. Kojchev, N. Navab, S. I. Ziegler, T. Lasser Freehand SPECT reconstructions using look up tables SPIE Medical Imaging Conference, February 4 - February 9 2012, San Diego, USA (bib)
	D. I. Shakir, A. Hartl, F. R. Schneider, J. Pulko, S. I. Ziegler, N. Navab, T. Lasser Two new ad-hoc models of detection physics and their evaluation for navigated beta probe surface imaging (to be presented) Proceedings of SPIE Visualization, Image-Guided Procedures, and Modeling Conference, San Diego, CA, USA, February 2012 (bib)
2011
	J.-H. Choi, A. Maier, A. Keil, R. Fahrig Acquisition of 3D Knee Geometry under Weight-Bearing Conditions using a C-Arm CT Scanner RSNA, Chicago, IL, U.S.A., November 2011 (bib)
	A. Hartl, T. Lasser, N. Navab, S. I. Ziegler Impact of acquisition geometry and physical model on Freehand SPECT reconstructions IEEE Medical Imaging Conference, October 23 - October 29 2011, Valencia, Spain (bib)
	D. I. Shakir, T. Lasser, A. Drzezga, S. I. Ziegler, N. Navab Evaluation of Navigated Beta-Probe Surface Imaging on a Realistic 3D Phantom Proceedings of the IEEE Nuclear Science Symposium and Medical Imaging Conference (NSS-MIC), Valencia, Spain, October 2011 (bib)
	W. Wein, A. Ladikos Detecting Patient Motion in Projection Space for Cone-beam Computed Tomography Medical Image Computing and Computer-Assisted Intervention (MICCAI 2011), Toronto, Canada, September 2011 (bib)
	W. Wein, A. Ladikos, A. Baumgartner Self-calibration of geometric and radiometric parameters for cone-beam computed tomography 11th International Meeting on Fully Three-Dimensional Image Reconstruction in Radiology and Nuclear Medicine, July 11-15 2011, Potsdam, Germany. (bib)
	A. Malecki, T. Biernath, M. Bech, T. Lasser, G. Potdevin, F. Pfeiffer Towards the Reconstruction of 3D Orientation Information from Direction-Sensitive X-Ray Projections Proceedings of Fully3D, Potsdam, Germany, June 2011 (bib)
	D. I. Shakir, A. Hartl, N. Navab, S. I. Ziegler Evaluation of an ad hoc model of detection physics for navigated beta-probe surface imaging Proceedings of SPIE Visualization, Image-Guided Procedures, and Modeling Conference, Lake Buena Vista (Orlando Area), FL, USA, February 2011 (bib)
	T. Lasser, S. I. Ziegler, N. Navab Freehand SPECT in low uptake situations Proceedings of SPIE 7961, 79611Z, 2011 (bib)
	A. Maier, J.-H. Choi, A. Keil, C. Niebler, M. Sarmiento, A. Fieselmann, G. Gold, S. Delp, R. Fahrig Analysis of Vertical and Horizontal Circular C-Arm Trajectories SPIE Medical Imaging, San Diego, CA, U.S.A., Feburary 2011 (bib)
2010
	D. I. Shakir, N. Navab, S. I. Ziegler Acquisition Model for Iterative Reconstruction of Navigated Beta-Probe Surface Images Proceedings of the IEEE Nuclear Science Symposium and Medical Imaging Conference (NSS-MIC), Knoxville, TN, USA, November 2010 (bib)
	D. I. Shakir, J. Bieniarz, S. Pirsig, T. Wendler, N. Navab, S. I. Ziegler A first study on biological feasibility of intraoperative control of tumor resection borders with navigated beta-probe surface imaging Proceedings of the Annual Meeting of the Society of Nuclear Medicine (SNM), Salt Lake City, UT, USA, June 2010 (bib)
	A. Plate, A. Ahmadi, T. Klein, N. Navab, J. Weiße, J. Mehrkens, K. Bötzel Towards a More Objective Visualization of the Midbrain and its Surroundings Using 3D Transcranial Ultrasound 54. Jahrestagung der Deutschen Gesellschaft für Klinische Neurophysiologie und Funktionelle Bildgebung (DGKN), Halle, GER, March 2010 (bib)
	C. Rohkohl, G. Lauritsch, A. Keil, Joachim Hornegger CAVAREV--an open platform for evaluating 3D and 4D cardiac vasculature reconstruction Physics in Medicine and Biology, vol. 55, no. 10, pp. 2905-2915, 2010 (bib)
	M. Blume, A. Martinez-Möller, A. Keil, N. Navab, M. Rafecas Joint Reconstruction of Image and Motion in Gated Positron Emission Tomography IEEE Trans. Med. Imag., vol. 29, no. 11, pp. 1892-1906, November 2010 (bib)
	M. Blume, A. Keil, N. Navab, M. Rafecas Joint Reconstruction of Image and Motion for PET: Displacement Fields Versus a B-Spline Motion Model Proc. IEEE Nuclear Science Symposium and Medical Imaging Conference, Knoxville, TN, U.S.A., October 2010 (bib)
	M. Blume, M. Rafecas Joint Reconstruction of Image and Motion for PET Using Linear Diffusion Regularization Congreso Anual de la Sociedad Espa\~nola de Ingenier\'ia Biom\'edica, Madrid, Spain, November 2010 (bib)
2009
	T. Wendler, K. Herrmann, A. Schnelzer, T. Lasser, J. Traub, O. Kutter, T. Schuster, M. Kiechle, M. Schwaiger, N. Navab, S. I. Ziegler, A. K. Buck Clinical introduction of freehand SPECT for image-guided sentinel lymph node biopsy Proceedings of Annual Congress of the European Association of of Nuclear Medicine (EANM 2009), Barcelona, Spain, October 2009 (bib)
	T. Wendler, X. Feng, K. Herrmann, T. Lasser, J. Traub, S. I. Ziegler, N. Navab, A. K. Buck 2D/3D registration of freehand SPECT and planar scintigraphy for clinical evaluation of 3D thyroid scintigraphy Proceedings of Annual Congress of the European Association of of Nuclear Medicine (EANM 2009), Barcelona, Spain, October 2009 (bib)
	T. Wendler, K. Herrmann, T. Lasser, J. Traub, M. Schwaiger, N. Navab, S. I. Ziegler, A. K. Buck First experience with freehand SPECT for lymphatic mapping in melanoma in upper body Proceedings of Annual Congress of the European Association of of Nuclear Medicine (EANM 2009), Barcelona, Spain, October 2009 (bib)
	T. Wendler, T. Lasser, J. Traub, S. I. Ziegler, N. Navab Freehand SPECT / ultrasound fusion for hybrid image-guided resection Proceedings of Annual Congress of the European Association of of Nuclear Medicine (EANM 2009), Barcelona, Spain, October 2009 (bib)
	T. Lasser, A. Duliu, T. Wendler, S. I. Ziegler, N. Navab Interactive Reconstruction for Freehand SPECT: An Approach to Acquisition Guidance? Proceedings of Annual Congress of the European Association of of Nuclear Medicine (EANM 2009), Barcelona, Spain, October 2009 (bib)
	A. Keil, J. Vogel, G. Lauritsch, N. Navab Dynamic Cone Beam Reconstruction Using a New Level Set Formulation Medical Image Computing and Computer Assisted Intervention (MICCAI), London, UK, September 20-24, 2009. (bib)
	C. Özgür, J. Bieniarz, T. Lasser, S. I. Ziegler, N. Navab, T. Wendler Phenomenological Models for intraoperative Positron Emission Surface Imaging using Handheld Probes Proceedings of World Congress in Medical Physics and Biomedical Engineering (WC 2009), Munich, Germany, September 2009 (bib)
	A. Keil, J. Vogel, G. Lauritsch, N. Navab Dynamic Cone-Beam Reconstruction Using a Variational Level Set Formulation Proc. Int'l Meeting on Fully Three-Dimensional Image Reconstruction in Radiology and Nuclear Medicine (Fully3D), Beijing, P.R. China, September 5-10, 2009. (bib)
	V. Castaneda, S. Atasoy, D. Mateus, N. Navab, A. Meining Reconstructing the Esophagus Surface from Endoscopic Image Sequences 5th Russian-Bavarian Conference on Bio-Medical Engineering, Munich, Germany, July 1-4 2009. (bib)
	A. Ahmadi, T. Klein, N. Navab Advanced Planning and Ultrasound Guidance for Keyhole Neurosurgery in ROBOCAST Russian Bavarian Conference (RBC), Munich, GER, July 2009 (bib)
	A. Ahmadi, T. Klein, N. Navab, R. Roth, R.R. Shamir, L. Joskowicz, E. DeMomi ^?, G. Ferrigno, L. Antiga, R.I. Foroni Advanced Planning and Intra-operative Validation for Robot-Assisted Keyhole Neurosurgery In ROBOCAST International Conference on Advanced Robotics (ICAR), Munich, GER, June 2009 (bib)
	T. Wendler, K. Herrmann, T. Lasser, J. Traub, M. Schwaiger, S. I. Ziegler, N. Navab, A. K. Buck Freehand SPECT: first in-vivo evaluation and comparison to conventional lymphatic mapping Proceedings of Annual Meeting of Society of Nuclear Medicine (SNM 2009), Toronto, Canada, June 2009 (bib)
	M. Blume, A. Keil, N. Navab, M. Rafecas Blind Motion Compensation for Positron-Emission-Tomography SPIE Medical Imaging, Orlando, FL, U.S.A., Feburary 2009 (bib)
	M. Blume, A. Martinez-Möller, A. Keil, N. Navab, M. Rafecas Simultaneous Reconstruction of Image and Motion in Gated Positron-Emission-Tomography Proc. IEEE Nuclear Science Symposium and Medical Imaging Conference, Orlando, FL, U.S.A., October 2009 (bib)
	M. Blume, A. Martinez-Möller, A. Keil, N. Navab, M. Rafecas Joint Reconstruction of Image and Motion in Gated Positron-Emission-Tomography 10th International Meeting on Fully Three-Dimensional Image Reconstruction in Radiology and Nuclear Medicine, Beijing, China, September 2009 (bib)
	T. Felder, M. Blume, J. Oliver, M. Rafecas ML-EM Implementation on a GPU: Avoiding Simultaneous Read-Modify-Write Processes 10th International Meeting on Fully Three-Dimensional Image Reconstruction in Radiology and Nuclear Medicine, Beijing, China, September 2009 (bib)
2008
	T. Lasser, T. Wendler, J. Traub, S. I. Ziegler, N. Navab Definition of optimal collimator geometries for 3D tomographic thyroid scintigraphy using navigated gamma probes Proceedings of Annual Congress of the European Association of Nuclear Medicine (EANM 2008), Munich, Germany, October 2008 (bib)
	T. Wendler, T. Lasser, A. K. Buck, J. Traub, M. Schwaiger, S. I. Ziegler, N. Navab First case report of 3D tomographic thyroid scintigraphy with tracked gamma probes Proceedings of Annual Congress of the European Association of Nuclear Medicine (EANM 2008), Munich, Germany, October 2008, Eur J Nuc Med Mol Imaging, vol. 35 (Suppl. 2), S129 (bib)
	A. Bigdelou, A. Ladikos, N. Navab Shape from Silhouette in Dynamic Scenes Technical Report at Technical University of Munich (TUM), Munich (DE), August 15, 2008 (bib)
	T. Wendler, A. Hartl, T. Lasser, J. Traub, S. I. Ziegler, N. Navab 3D Intra-operative nuclear imaging for SLNB in neck Proceedings of Annual Meeting of Society of Nuclear Medicine (SNM 2008), New Orleans, USA, June 2008 (bib)
	M. Blume, M. Rafecas, S. I. Ziegler, N. Navab Combined Motion Compensation and Reconstruction for PET Proc. IEEE Nuclear Science Symposium and Medical Imaging Conference, Dresden, Germany, October 2008 (bib)