Segmentation and 3D Reconstruction of Glycogen Granules and Mitochondria in Microwave-fixed Brain EM

Overview

In May 2025, Ms. Maria Fernanda Veloz from the Laboratory of Prof. Pierre Magistretti, attended the Gordon Research Seminar (GRS) and Gordon Research Conference (GRC) on Volume Electron Microscopy (vEM), held in Barcelona, Spain. The meeting gathered an international community of researchers advancing the frontiers of vEM; a rapidly evolving field transforming our understanding of cellular and tissue ultrastructure through large-scale, high-resolution 3D imaging.

During the GRS, Ms. Veloz presented a poster on deep-learning–based segmentation and 3D reconstruction of glycogen granules and mitochondria in microwave-fixed brain samples. This project is part of an ongoing collaboration between the Magistretti Laboratory and Dr. Ronell Sicat from the Visualization Core Lab. By integrating advanced focused-beam microwave fixation with vEM pipelines and computational segmentation tools, the team is mapping energy-related structures in the brain at nanoscale resolution. The poster presentation was very well received by the community, sparking engaging discussions and highlighting the importance of bridging neuroscience and visualization technologies. The GRC further offered the opportunity to learn from leaders in the field, covering innovations ranging from FIB-SEM and multi-beam tomography to new computational workflows for handling large datasets.

This participation not only showcased the lab’s progress in connecting brain energy metabolism with cutting-edge imaging, but also fostered valuable feedback and collaborations within the vEM community.

Click here to download full pdf version of poster.

Text and photo c/o Ms. Veloz.