Micro-computed tomography of Geodia cydonium cortex

High resolution micro-CT scans of the cortex from different Geodia species and subsequent segmentation for quantifying spicules' number, distribution and characterizing their organisation is very labor intensive. We explore machine learning approaches to gain fast segmentations of the many thousands of individual glas spicules embedded in the in the sponge tissue. In addition to Python, we also use ImageJ and Amira for data preparation and analysis.