GSoC 2021: project idea 3.3: Digital Microsphere

To better understand the morphogenesis of the nervous system, it is necessary to develop novel techniques. 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. The source data consists of nine images per sample from different points of view, which will be projected onto the surface of a virtual sphere. This will allow us to view the surface either continuously or in a montaged fashion. The student must be proficient in Computer Vision (C++, Python) and perhaps even Topological techniques, and it will be up to the student to propose a viable solution to this problem. The following references may be helpful to the student’s application:

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(4), doi:10.1162/BIOT_a_00010

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, doi:10.1016/j.biosystems.2018.10.006

More information can be found at:

Mentors: Bradly Alicea @b.alicea , Mayukh Deb @Mayukhdeb

Tags: DevoWorm, Python, C++, microscopy, atlasing

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Hello @b.alicea @Mayukhdeb ,
I am actually interested in doing this project, how shall I proceed?

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Hi @iammarco11 , thank you for your interest. I suggest that you join our slack. We can talk there.

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