DEVELOPMENT OF ELECTRON MICROSCOPY WORKFLOWS
The continuous development of electron workflows that are suitable to answer specific biological questions is of the utmost important as they are very diverse and compose of elements that are related to specimen preparation, data acquisition, processing and interpretation. The elements that need to be developed can be either specific pieces of instrumentation, but also specific pieces of physical modelling or theory, or chaining of existing physical tools, pieces of software or specimen preparation protocols.
There is a nonstop development of a wide variety of novel methods and instrumentation, including the automation of electron tomograms, correlative light and microscopy, integrated light and microscopy, specific vitrification methods, adaptation of focused-ion beam milling approaches, improving specific preparation and staining approaches using microwave fixation, theory for resolution measurements interpretation and quantification of acquired dataset by advanced image processing approaches including machine learning.
During the last years, the section light and electron microscopy contributed with novel instruments and methods, including TEM, energy-filtering, SEM, cryo-ET, Cryo-EM, serial Block Face SEM, Array Tomography, all with the accompanying range of specimen preparation equipment. Biological questions addressed ranged from imaging intracellular cell structures, virus replication organelles, morphological changes in mitochondria, protein structures involved with the complement pathway, the glomerulus in pieces as part of nephrology research, and more.
This research aimed at defining and shaping a workflow in terms of methods and/or instrumentation to help solve a specific biological question is often carried out in close collaboration with research groups.
Over time, some of the section’s research lines evolved into separate research groups. Check out their web-pages for more information
- Virus Replication Research Group (Montse Barcena)
- The Bionanopatterning Research Group (Thom Sharp)
- Light and Electron Microscopy Facility (Lennard Voortman, Roman Koning and Frank Faas)
CRYO ELECTRON TOMOGRAPHY AND ARTIFICIAL INTELLIGENCE
A separate research line is focused on cryo electron tomography and artificial intelligence.
Cryo electron microscopy is a 3D imaging techniques with cryo transmission electron microscopy that can resolve biological structures in the nm-scale resolution range. The technique has matured during the last decade, but the overall workflow is still in flux by continuous enhancement of instrumentation and novel approaches.
This research line is aimed at improving the overall performance of cryo electron tomography in terms of better understanding the image formation process, enhancing reconstruction algorithms, increasing the workflow throughput, attainable resolution, and/or segmentation and annotation. In several of the improvements we work on, novel automation approaches make use of artificial intelligence and machine learning.
This research line is carried out in close collaboration with the Virus Replication Group of Montse Barcena.
If you would like to collaborate on this, please do not hesitate to contact Bram Koster