User-Centered Engineering of Tissue Segmentation in VR

Closed Games Engineering Bachelor Master Project Thesis Games Research Lab

Background

The vast datasets created by microscopy imaging are usually processed by automated analysis tools to identify relevant features, such as different tissue types, cell nuclei, or other structural and functional features. However, each automated analytical step needs to be validated and benchmarked. For this, scientists painstakingly markup ground truth data as a validation set. The GroundTruthXR project aims to support the mark-up process of volumetric datasets using immersive visualization tools and an intuitive user experience. Thin cell membranes are prone to image artifacts that can decrease the effectiveness of automated segmentation algorithms. This thesis/project focuses on the manual markup of cell membranes from images of pre-implantation embryos using virtual reality (VR) hardware.

Tasks

Based on the results of two preceding student projects, one aiming at segmenting nuclei, the other one on tissue membranes, your goal will be to learn about the actual workflow of the biologists that will eventually use the tool. Based on your findings in the literature, the preceding projects and the experts’ feedback, you will propose a design that covers all the users’ requirements and you will iteratively develop it - based on frequent testing and feedback by the experts.

Contact Persons at the University Würzburg

References

• Beyer, Johanna, Markus Hadwiger, and Hanspeter Pfister. 2015. “State-of-the-Art in GPU-Based Large-Scale Volume Visualization.” Comput. Graph. Forum 34 (8): 13–37. https://doi.org/10.1111/cgf.12605.
• Ganovelli, Massimiliano AND Pattanaik, Fabio AND Corsini. 2014. Introduction to Computer Graphics - a Practical Learning Approach. Boca Raton, Fla: CRC Press. https://learning.oreilly.com/library/view/introduction-to- computer/9781439852798/.
• LaViola, J. J., E. Kruijff, R. P. McMahan, D. A. Bowman, and I. Poupyrev. 2017. 3d User Interfaces: Theory and Practice. Addison-Wesley Usability and HCI Series. Addison-Wesley. https://books.google.de/books?id=ilUyjw EACAAJ.
• Mathew, B., A. Schmitz, S. Muñoz-Descalzo, N. Ansari, F. Pampaloni, E. H. K. Stelzer, and S. C. Fischer. 2015. “Robust and Automated Three-Dimensional Segmentation of Densely Packed Cell Nuclei in Different Biological Specimens with Lines-of-Sight Decomposition.” BMC Bioinformatics 16 (1). https://doi.org/10.1186/s12859-015- 0617-x.
• Roeder, A. H. K., A. Cunha, M. C. Burl, and E. M. Meyerowitz. 2012. “A Computational Image Analysis Glossary for Biologists.” Development 139 (17): 3071–80. https://doi.org/10.1242/dev.076414.