Mapping cells at scale: from tissue volumes to community challenges in vEM
January 20, 2026 @ 16:00 – 17:00 CET
Speaker: Aubrey Weigel
Project Scientist, CellMap Project Team
Howard Hughes Medical Institute, Janelia Research Campus
Abstract
Large-scale, high-resolution imaging of subcellular architecture using volume electron microscopy (vEM) unlocks new opportunities for biological discovery – but realizing this potential requires more than just data acquisition. Scalable infrastructure, robust protocols, and trained personnel are critical to extract consistent insight from these complex datasets and make them useful to the broader community. The CellMap Project Team represents a coordinated effort to scale vEM-based segmentation across six dimensions: dataset scale, biological diversity, organelle classification complexity, team training, analytical depth, and open access.
Through modular training programs, systematic quality control, and block-wise processing tools, the project has grown from individual cell volumes to tissue-scale annotation across dozens of organisms and sample types. Annotated datasets are openly shared through OpenOrganelle, providing the community with immediate access to high-resolution volumes and voxel-level segmentations. To further catalyze progress in automated segmentation, we launched the CellMap Segmentation Challenge – a large-scale, open competition featuring expertly annotated training data from over 20 eFIB-SEM datasets and more than 40 unique organelle classes.
We describe how workflows and infrastructure evolved to support this scaling effort, with a focus on designing datasets that are tailored for specific biological insight yet structured for broad reuse. By scaling people, protocols, and pipelines in parallel – and committing to open data practices – the CellMap Project Team provides a model for reproducible, high-resolution cellular mapping at scale.
Biography
Aubrey Weigel is currently a Project Scientist of the CellMap Project Team at HHMI – Janelia Research Campus. The team uses advanced imaging technologies to study the ultrastructure of subcellular organelles under both healthy and pathological conditions. Aubrey’s previous research background is in biophysics, with an emphasis in microscopy. Her formal training is in physics and engineering.
During her graduate work Aubrey was the co-discoverer of ergodicity breaking in cells along with Diego Krapf, driving a pivotal shift in the field of diffusion analysis in living systems. Throughout her postdoctoral career under the guidance of Jennifer Lippincott-Schwartz, she applied her training in physics and microscopy directly to answer biological questions. Here, Aubrey unraveled the underlying structure of the endoplasmic reticulum and revealed its complex dynamics. She also uncovered the nano-anatomy of early secretory compartments and discovered a new, dynamic organelle, responsible for delivering newly synthesized cargo from the endoplasmic reticulum to the Golgi.
Aubrey’s recent work as the leader of the Cell Organelle Segmentation in Electron Microscopy (COSEM) project includes developing an invaluable tool for cell biology – an analysis pipeline based on deep learning architectures for segmentation – allowing comprehensive reconstruction and analysis of organelles within entire cells imaged by volumetric electron microscopy. CellMap is now building upon this pipeline to generate, characterize, and discover how cells look in their native tissue environments – acting as a hub of collaborations that brings together scientists of different disciplines. Aubrey is committed to integrating her multi-disciplinary training into facilitating large-effort, collaborative, team projects to take on challenging scientific problems and sharing these resources with the broader scientific community.
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