This project will build upon the specialized microscopy techniques to develop a shell composed of projected microscopy images, arranged to represent the full external surface of a sphere. This will allow us to create an atlas of the embryo’s outer surface, which in some species (e.g. Axolotl) enables us to have a novel perspective on neural development. You will build a computational tool that allows us to visualize 4D data derived from the surface of an Axolotl embryo.
What can I do before GSoC?
Build basic prototypes for this project and discuss about them with the mentors, then read these papers:
Gordon, R. (2009). Google Embryo for Building Quantitative Understanding of an Embryo As It Builds Itself. II. Progress Toward an Embryo Surface Microscope. Biological Theory, 4, 396–412.
Crawford-Young, S., Dittapongpitch, S., Gordon, R., and Harrington, K. (2018). Acquisition and reconstruction of 4D surfaces of axolotl embryos with the flipping stage robotic microscope. Biosystems, 173, 214-220.
Skills/requirements
Handling higher dimensional microscopy data (preferably also creating an API to load them as tensors for computation on the GPU). Building an intuitive GUI (or a web interface). Feature extraction (canny edges/thresholding/denoising).
Planned Effort
175 hours Mentors: Bradly Alicea (balicea@openworm.org), Susan Crawford-Young (susan.crawfordyoung@gmail.com).