Large-scale bone cells identification from histology slices

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-CT imaging, FE analysis and histological analysis to relate cell-scale to tissue-level activity in mice. However, the current pipeline requires a significant amount of manual work to identify cell locations from histology slices accurately. Furthermore, as different cell types are imaged with distinct procedures, adjustments are needed to categorise each cell type successfully. Ultimately, only a limited number of the cells available can be identified, neglecting a reasonable portion of the information available in the images. The current project aims to explore automated methods to identify and localise cells in histology slices. A successful pipeline will expand our ability to quantify local cell activity and relate it to tissue-level mechanical information estimated from Finite Element simulations. 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-CT imaging, FE analysis and histological analysis to relate cell-scale to tissue-level activity in mice. However, the current pipeline requires a significant amount of manual work to identify cell locations from histology slices accurately. Furthermore, as different cell types are imaged with distinct procedures, adjustments are needed to categorise each cell type successfully. Ultimately, only a limited number of the cells available can be identified, neglecting a reasonable portion of the information available in the images.
The current project aims to explore automated methods to identify and localise cells in histology slices. A successful pipeline will expand our ability to quantify local cell activity and relate it to tissue-level mechanical information estimated from Finite Element simulations.
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 automated methods to identify and localise cells in histology slices. The work will be done in Python, using histology images available in the group.

This project aims to investigate automated methods to identify and localise cells in histology slices. The work will be done in Python, using histology 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! Francisco Correia Marques (francisco.correia@hest.ethz.ch) HCP H 22.3, Leopold-Ruzicka-Weg 4, 8093 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!

Francisco Correia Marques (francisco.correia@hest.ethz.ch) HCP H 22.3, Leopold-Ruzicka-Weg 4, 8093 Zürich, Switzerland