GSoC 2022 Project Idea 22.2: Digital Microsphere

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.

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 (, Susan Crawford-Young (


Can you provide a Link to the data containing microscopy images so that we can try on.

Here is the data we have on Axolotl (potentially 4D): link. These are 2D images captured from different perspectives of a sphere. They rotate in space, hence the 4D data.