Reconstruction and Registration of Histology and Phase Contrast Images for Clinical Validation of Imaging Modalities In medical collaboration with: Dr. Christian Glaser, Silvia Adam-Neumair In academic collaboration with: Prof. Dr. Franz Pfeiffer, Dr. Paola Coan, Prof. Dietrich Habs This project is funded by the Munich Center of Advanced Photonics (MAP). http://www.munich-photonics.de/ Scientific Director: Prof. Dr. Nassir Navab Contact Person(s): Martin Groher

Keywords: Registration / Visualization, Reconstruction, Medical Imaging, Past Projects

Abstract

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.

Detailed Project Description

Pictures

Figure 1: Phase Contract image of cartilage

Figure 2: Histology processing of cartilage

Figure 3: Image of the paraffin block

Figure 4: Stained histology slice of cartilage

Publications

2012
	Y. Yagi, M. Groher, M. Feuerstein, M. Onozato, H. Heibel, N. Navab Overcoming Challenges in Histology 3D Imaging 11th European Congress on Telepathology and 5th International Congress on Virtual Microscopy, Venice, Italy, June 2011. (bib)
2011
	M. Feuerstein, H. Heibel, J. Gardiazabal, N. Navab, M. Groher Reconstruction of 3-D Histology Images by Simultaneous Deformable Registration Proceedings of Medical Image Computing and Computer-Assisted Intervention (MICCAI 2011), Toronto, Canada, September 2011. The original publication is available online at www.springerlink.com (bib)

Team

Contact Person(s)

Dr. Martin Groher

Working Group

Dr. Hauke Heibel

Dipl.-Ing. Univ. Jose Gardiazabal

Dr. Marco Feuerstein

Dr. Martin Groher

Prof. Dr. Nassir Navab

Dr. Olivier Pauly

Location

Technische Universität München Institut für Informatik / I16 Boltzmannstr. 3 85748 Garching bei München Tel.: +49 89 289-17058 Fax: +49 89 289-17059

Visit our lab at Garching.

Ludwig-Maximilians-Universität München Chirurgische Klinik und Poliklinik - Innenstadt, AG CAS Nussbaumstr. 20 80336 München Room: C2.06 Tel.: +49 89 5160-3615 Tel.: +49 89 5160-3635 Fax: +49 89 5160-3630

Visit our lab at Klinikum Innenstadt.



internal project page

Please contact Martin Groher for available student projects within this research project.