Development and validation of a 2D-3D registration tool

It is well-established that most of the metabolic processes taking place in bone span multiple spatial scales, from the cellular to the organ level. Therefore, unravelling the underlying mechanisms governing bone remodelling and regeneration requires a multiscale approach capable of connecting organ and tissue-level analysis with the cellular scale. While the former two are well-established in the field through Finite Element (FE) simulations or morphometry analysis of the structure, the latter has seen modest improvements. In our group, we have developed a Local in vivo Environment (LivE) pipeline which combines in vivo micro-computed tomography (micro-CT) imaging, FE analysis and histological analysis to relate cell-scale to tissue-level activity. An important part of this tool allows registering 2D histological slices to 3D micro-CT images in a semi-automated fashion. However, such tool must be thoroughly validated to be successfully applied in practice. Therefore, the current project aims to establish different validation methods that will evaluate the potential and accuracy of the registration tool with different samples. A successful result will highlight the sensitivity, reproducibility, and accuracy of the method to correctly identify the alignment of a 2D image in the corresponding 3D volume. In summary, with this combined experimental and computational approach, we seek to develop scalable technologies that will allow a multiscale understanding of bone remodelling and regeneration.

It is well-established that most of the metabolic processes taking place in bone span multiple spatial scales, from the cellular to the organ level. Therefore, unravelling the underlying mechanisms governing bone remodelling and regeneration requires a multiscale approach capable of connecting organ and tissue-level analysis with the cellular scale. While the former two are well-established in the field through Finite Element (FE) simulations or morphometry analysis of the structure, the latter has seen modest improvements.
In our group, we have developed a Local in vivo Environment (LivE) pipeline which combines in vivo micro-computed tomography (micro-CT) imaging, FE analysis and histological analysis to relate cell-scale to tissue-level activity. An important part of this tool allows registering 2D histological slices to 3D micro-CT images in a semi-automated fashion.
However, such tool must be thoroughly validated to be successfully applied in practice. Therefore, the current project aims to establish different validation methods that will evaluate the potential and accuracy of the registration tool with different samples. A successful result will highlight the sensitivity, reproducibility, and accuracy of the method to correctly identify the alignment of a 2D image in the corresponding 3D volume.
In summary, with this combined experimental and computational approach, we seek to develop scalable technologies that will allow a multiscale understanding of bone remodelling and regeneration.

This project aims to investigate validation methods to test a 2D-3D registration tool. The work will be done in Python, using a dataset of images available in the group.

This project aims to investigate validation methods to test a 2D-3D registration tool. The work will be done in Python, using a dataset of images available in the group.

Feel free to contact me by email (francisco.correia@hest.ethz.ch) to discuss more details of the projects and how we can align it with your interests! You will be provided with the resources, tools and support throughout your project. Francisco Correia Marques (francisco.correia@hest.ethz.ch) GLC H 29, Gloriastrasse 37/ 39, 8092 Zürich, Switzerland

Feel free to contact me by email (francisco.correia@hest.ethz.ch) to discuss more details of the projects and how we can align it with your interests! You will be provided with the resources, tools and support throughout your project.

Francisco Correia Marques (francisco.correia@hest.ethz.ch) GLC H 29, Gloriastrasse 37/ 39, 8092 Zürich, Switzerland