Chair for Computer Aided Medical Procedures & Augmented Reality
Lehrstuhl für Informatikanwendungen in der Medizin & Augmented Reality

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

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).

Scientific Director: Prof. Dr. Nassir Navab

Contact Person(s): Martin Groher

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


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


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


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)
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


Contact Person(s)

Martin Groher
Dr. Martin Groher

Working Group

Hauke Heibel
Dr. Hauke Heibel
Jose Gardiazabal
Dipl.-Ing. Univ. Jose Gardiazabal
Marco Feuerstein
Dr. Marco Feuerstein
Martin Groher
Dr. Martin Groher
Nassir Navab
Prof. Dr. Nassir Navab
Olivier Pauly
Dr. Olivier Pauly


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.

Edit | Attach | Refresh | Diffs | More | Revision r1.1 - 28 Sep 2009 - 09:45 - OlivierPauly

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