Correlated light and electron microscopy

The BioEM Facility specialises in imaging structures with electron microscopy that have been imaged previously with light microscopy. These structures can be cells, parts of cells, or macromolecular complexes. The types of electron microscopy used can be serial section transmission electron microscopy, or block face scanning electron microscopy.


Maco, B., Holtmaat, A., Cantoni, M., Kreshuk, A., Straehle, C.N., Hamprecht, F.A., and Knott, G.W. (2013). Correlative in vivo 2 photon and focused ion beam scanning electron microscopy of cortical neurons. PLoS One 8, e57405.

Maco, B., Cantoni, M., Holtmaat, A., Kreshuk, A., Hamprecht, F.A., and Knott, G.W. (2014). Semiautomated correlative 3D electron microscopy of in vivo-imaged axons and dendrites. Nat Protoc 9, 1354–1366.

NeuroMorph analysis software

This project develops a set of software tools that can be used measure models of cellular structures. These models are made from serial images collected with electron microscopy.


Jorstad, A., Nigro, B., Cali, C., Wawrzyniak, M., Fua, P., and Knott, G. (2015). NeuroMorph: A Toolset for the Morphometric Analysis and Visualization of 3D Models Derived from Electron Microscopy Image Stacks. Neuroinformatics 13, 83–92.

Jorstad A., Blanc J., Knott G. (2018) NeuroMorph: A Software Toolset for 3D Analysis of Neurite Morphology and Connectivity. Frontiers in Neuroanatomy 12, 59.

3D analysis of serial EM images


Maco, B., Holtmaat, A., Jorstad, A., Fua, P., and Knott, G.W. (2014). Correlative In Vivo 2-Photon Imaging and Focused Ion Beam Scanning Electron Microscopy: 3D Analysis of Neuronal Ultrastructure. Methods Cell Biol 124, 339–361.

Preservation of cell structure

This project uses different fixation methods to explore the true architecture of the tissues and cells. Conventional fixation methods uses aldehyde fixatives, but these cause shrinkage and distortion. By exploring other methods scientists can get a better understanding of the microstructure of the natural world.


Korogod, N., Petersen, C.C., and Knott, G.W. (2015). Ultrastructural analysis of adult mouse neocortex comparing aldehyde perfusion with cryo fixation. Elife 4, e05793.