Hoogenboom Lab

Department                           Imaging Physics

Principal investigator          Jacob Hoogenboom

E-mail address                       j.p.hoogenboom@tudelft.nl

Website                                     https://www.hoogenboomlab.org/

3D “Google Maps” for biology

We want to achieve faster and automated imaging so that an entire tumour or an organ like the brain can be imaged in a “Google Maps” like fashion.

We extract information out of the data with computational methods like automated segmentation. We are interested in techniques like correlative light and electron microscopy (CLEM) as well as large volume EM using multibeam SEM.

Furthermore, we aim to better understand and optimize the techniques. We use experimental approaches and image analysis to gain insights in how to maximize the amount of information that can be extracted from a biological sample. Additionally we use electron matter simulations to create physical frameworks to understand signal generation and the interactions of electrons within a sample.

Further reading (click to link to article)

Kievits, Arent J., Duinkerken, B. H. Peter, Lane, Ryan, de Heus, Cecilia, van Beijeren Bergen en Henegouwen, Daan, Höppener, Tibbe, Wolters, Anouk H. G., Liv, Nalan, Giepmans, Ben N. G. and Hoogenboom, Jacob P.. “FAST-EM array tomography: a workflow for multibeam volume electron microscopy” Methods in Microscopy, vol. 1, no. 1, 2024, pp. 49-64. https://doi.org/10.1515/mim-2024-0005

Localization for cryo-FIB-SEM

With Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) proteins of interest can be carved out of a cell for high resolution cryo-TEM. However, finding the protein of interest inside the cell is like finding a needle in a haystack. We have developed 3D fluorescence localization to pin-point the protein for focused ion beam milling in cryogenic conditions. We are currently using this setup to investigate cell-autonomous immunity.

Further reading (click to link to article)

D. B. Boltje, R. Skoupý, C. Taisne, W. H. Evers, A. J. Jakobi, J. P. Hoogenboom, Thickness and quality controlled fabrication of fluorescence-targeted frozen-hydrated lamellae, Cell Reports Methods 5, 101004 (2025)

Superresolution E-beam calibration

Together with our colleagues at Erasmus MC, we have developed a technique to print biomolecules at very small (sub-100 nm) length scales. We use these biomolecular patterns for calibration and performance testing of super-resolution light microscopes. Projects can focus on improving the resolution and extending its application range.

Further reading (click to link to article)

S. Hari, J. Slotman, Y. Vos, C. Floris, W. A. van Cappellen, C. W. Hagen, S. Stallinga, A. Houtsmuller, and J. P. Hoogenboom, Electron-beam patterned calibration structures for superresolution fluorescence microscopy, Scientific Reports 12, 20185 (2022); C. S. Smith, J. Slotman, L. Schermelleh, N. Chakrova, S. Hari, Y. Vos, C. W. Hagen, M. Müller, W. A. van Cappellen, A. Houtsmuller, J. P. Hoogenboom, and S. Stallinga, Structured illumination microscopy with noise-controlled image reconstructions, Nature Methods 18, 821–828 (2021)  doi: 10.1038/s41592-021-01167-7

Charge visualization and mitigation in electron microscopy

High resolution electron microscopy is often not limited by diffraction or aberrations but by charge-induced image artefacts or damage. We use in-situ fluorescence microscopy in an electron microscope to visualize the diffusion of charges during electron irradiation. Projects investigate how charge diffusion is influenced for instance by electric fields or optical stimulation and how we can mitigate the occurrence of charging artefacts in electron microscopy images.