OUTPUT

Spin-off

Jacob is co-founder of Delmic, a company that was started December 2010 based on our collaborative work with the lab of Pieter Kruit in developing the SECOM integrated microscope. The company is led by our former MSc student Sander den Hoedt and Andries Effting also co-founders of Delmic.

Our work has led to over 15 patents and patent applications, most of which have been transferred to industry. We have been awarded 8 valorization grants to explore commercial or biomedical application of our techniques.

Publications

2021
C. S. Smith, J. A. Slotman, L. Schermelleh, N. Chakrova, S. Hari, Y. Vos, C. W. Hagen, M. Müller, W. A. van Cappellen, A. B. Houtsmuller, J. P. Hoogenboom, and S. Stallinga, Structured illumination microscopy with noise-controlled image reconstructions, BioRxiv, doi.org/10.1101/2021.03.11.434940 (2021)
R. Lane, Y. Vos, A. H. G. Wolters, L. van Kessel, B. N. G. Giepmans, and J. P. Hoogenboom, Optimization of negative stage bias potential for faster imaging in large-scale electron microscopy, Journal of Structural Biology: X 5, 100046 (2021)

2020
Y. Vos, R. Lane, C. J. Peddie, A. H.G. Wolters, J.P. Hoogenboom, Retarding field integrated fluorescence and electron microscope, Microscopy & Microanalysis, 27 (1), 109-120 (2020)
 M. W. H. Garming, M. Bolhuis, S. Conesa-Boj, P. Kruit, J. P. Hoogenboom, Lock-in ultrafast electron microscopy simultaneously visualizes carrier recombination and interface-mediated trapping, Journal of Physical Chemistry Letters 11, 8880−8886 (2020)
 L. Zhang, M. W. H. Garming, J. P. Hoogenboom, P. Kruit, Beam displacement and blur caused by fast electron beam deflection, Ultramicroscopy 211, 112925 (2020)
 
2019
 L. Zhang, J. P. Hoogenboom, B. Cook, P. Kruit, Photoemission sources and beam blankers for ultrafast electron microscopy Structural Dynamics 6, 051501 (2019), highlighted as Editor’s pick
 R. I. Koning*, A. Srinivasa Raja*, R. I. Lane*, A. J. Koster, J. P. Hoogenboom, Integrated light and electron microscopy, in: Correlative Imaging: Focusing on the future, L. M. Collinson and P. Verkade, John Wiley & Sons (2019) *equal contributions
 I. G. C. Weppelman, R. J. Moerland, L. Zhang, E. Kieft, P. Kruit, and J. P. Hoogenboom, Pulse length, energy spread, and temporal evolution of ultrafast electron pulses generated with a laser-triggered beam blanker, Structural Dynamics 6, 024102 (2019)
 
2018
N. Pirozzi, J. P. Hoogenboom, B. N. G. Giepmans, ColorEM: Analytical electron microscopy for element-guided identification and imaging of the building blocks of life, Histochemistry and Cell Biology 150, 509-520 (2018) cover article
T. Ando et al, The 2018 correlative microscopy techniques roadmap, Journal of Physics D: Applied Physics 51, 443001 (2018), edited by C. Eggeling, J. P. Hoogenboom, I. Schaap.
R. J. Moerland, I. G. C. Weppelman, M. Scotuzzi, J. P. Hoogenboom, Nanoscale imaging of light-matter coupling inside metal-coated nanocavities using pulsed electron beams, NanoLetters 18, 6107−6112 (2018) cover article.
 I. G. C. Weppelman, R. J. Moerland, J. P. Hoogenboom, P. Kruit, Concept and design of a beam blanker with integrated photoconductive switch for ultrafast electron microscopy, Ultramicroscopy 184, 8-17 (2018)
 
2017
L. M. Collinson, E. C. Carroll, J. P. Hoogenboom, Correlating 3D light to 3D electron microscopy for systems biology, Current Opinion in Biomedical Engineering 3, 49-55 (2017)
M. W. H. Garming, I. G. C. Weppelman, P. de Boer, F. Perona Martinez, R. Schirhagl, J. P. Hoogenboom, and R. J. Moerland, Nanoparticle discrimination based on wavelength- and lifetime-multiplexed cathodoluminescence microscopy, Nanoscale 9, 12727 (2017)
S. R. Hemelaar, P. de Boer, M. Chipaux, W. Zuidema, T. Hamoh, F. Perona Martinez, A. Nagl, J. P. Hoogenboom, B. N. G. Giepmans, R. Schirhagl, Nanodiamonds as multi-purpose labels for microscopy, Scientific Reports 7, 720 (2017)
M. Scotuzzi*, J. Kuipers*, D. I. Wensveen*, P. de Boer, C. W. Hagen, J. P. Hoogenboom**, and B. N. G. Giepmans**, Multi-color electron microscopy by element-guided identification of cells, organelles, and molecules, Scientific Reports 7, 45970 (2017)  (*shared first author, **shared last author)
M. T. Haring, N. Liv, A. C. Zonnevylle, A. C. Narvaez, L. M. Voortman, P. Kruit, and J. P. Hoogenboom, Automated sub-5nm overlay accuracy in integrated correlative fluorescence and electron microscopy using cathodoluminescence pointers, Scientific Reports 7, 43621 (2017)
 
2016
R. J. Moerland, I. G. C. Weppelman, M. W. H. Garming, P. Kruit, and J. P. Hoogenboom, Time-resolved cathodoluminescence microscopy with sub-nanosecond beam blanking for direct evaluation of the local density of states, Optics Express 24 (21), 24760-24772 (2016)
I. G. C. Weppelman, P. C. Post, C. T. H. Heerkens, C. W. Hagen, and J. P. Hoogenboom, Fabrication of narrow-gap nanostructures using electron-beam induced deposition etch masks, Microelectronic Engineering 153, 77-82 (2016)
 J. Sueters-di Meo, N. Liv, and J. P. Hoogenboom, Using advanced correlative microscopy to study complex biological samples in Encyclopedia of Analytical Chemistry, eds R.A. Meyers, John Wiley: Chichester, a9473 (2016)
R. J. Moerland and J. P. Hoogenboom, Subnanometer-accuracy optical distance ruler based on fluorescence quenching by transparent conductors, Optica 3 (2), 112 (2016), cover article
N. Liv, D. S. B. van Oosten Slingeland, J.-P. Baudoin, P. Kruit, D. W. Piston, and J. P. Hoogenboom, Electron microscopy of living cells during in-situ fluorescence microscopy, ACS Nano 10, 265-273 (2016)
 
2015
P. de Boer, J. P. Hoogenboom, and B. N. G. Giepmans, Correlated light and electron microscopy: Ultrastructure lights up!, Nature Methods 12 (6), 503 (2015)
 
2014
A. C. Narvaez, I. G. C. Weppelman, R. J. Moerland, J. P. Hoogenboom, and P. Kruit, Confocal filtering in cathodoluminescence microscopy of nanostructures, Appl. Phys. Lett. 104, 251121 (2014)
N. Liv, I. Lazić, P. Kruit, and J. P. Hoogenboom, Scanning Electron Microscopy of individual nanoparticle biomarkers in liquid, Ultramicroscopy 143, 93-99 (2014)
C. J. Peddie, N. Liv, J. P. Hoogenboom, and L. Collinson, “Integrated light and scanning electron microscopy of GFP-expressing cells” in “Methods in cell biology vol. 124”, edited by Th. Müller-Reichert and P. Verkade, Academic Press, p 363-389 (2014)
P. W. Voorneveld, L. L. Kodach, R. J. Jacobs, N. Liv, A. C. Zonnevylle, J. P. Hoogenboom, I. Biemond, H. W. Verspaget, D. W. Hommes, K. de Rooij, C. J. M. van Noesel, H. Morreau, T. van Wezel, G. J. A. Offerhaus, G. R. van den Brink, M. P. Peppelenbosch, P. ten Dijke, , and J. C. H. Hardwick, Loss of SMAD4 alters BMP signaling to promote colorectal cancer cell metastasis via activation of Rho-Rock, Gastroenterology, 147, 196-208 (2014)
 
2013
 N. Liv, A. C. Zonnevylle, A. C. Narvaez, A. P. J. Effting, P. W. Voorneveld, M. S. Lucas, J. C. Hardwick, R. A. Wepf, P. Kruit, and J. P. Hoogenboom, Simultaneous Correlative Scanning Electron and High-NA Fluorescence Microscopy, PLoS ONE 2 (8), e55707 (2013)
A. C. Zonnevylle, R. F. C. van Tol, N. Liv, A. C. Narvaez, A. P. J. Effting, P. Kruit, and J. P. Hoogenboom, Integration of a high-NA light microscope in a scanning electron microscope, J. Microscopy 252, 58-70 (2013)
A. C. Narvaez, I. G. C. Weppelman, R. J. Moerland, N. Liv, A. C. Zonnevylle, P. Kruit, and J. P. Hoogenboom, Cathodoluminescence microscopy of nanostructures on glass substrates, Optics Express 21 (24), 29968 (2013)
 
2012
W. Slingenbergh, S. K. de Boer, T. Cordes, W. R. Browne, B. L. Feringa, J. P. Hoogenboom, J. T. M. De Hosson, and W. F. van Dorp, Selective Functionalization of Tailored Nanostructures, ACS Nano 10 (6), 9214-9220 (2012)
 
2009
F. D. Stefani, J. P. Hoogenboom, and E. Barkai, Beyond quantum jumps: blinking nanoscale light emitters, Physics Today 2 (62), 34-39 (2009)
J. P. Hoogenboom, G. Sanchez-Mosteiro, G. Colas des Francs, D. Heinis, G. Legay, A. Dereux, and N. F. van Hulst, The single-molecule probe: vectorial mapping of photonic mode density in a metal mirror cavity, Nano Letters 3 (9), 1189-1195 (2009)
 
2008
J. P. Hoogenboom, J. Hernando, M. F. Garcia-Parajo, and N. F. van Hulst, Memory in single emitter fluorescence blinking reveals the dynamic character of nanoscale charge tunneling, Journal of Physical Chemistry C 9 (112), 3417-3422 (2008)
J. Hernando, J. Hoogenboom, E. van Dijk, M. Garcia-Parajo, and N. F. van Hulst, Ultrafast single-molecule photonics: Excited state dynamics in coherently coupled complexes, Journal of Luminescence 5-6 (128), 1050-1052 (2008)
 
2007
J. P. Hoogenboom, J. Hernando, E. M. H. P. van Dijk, N. F. van Hulst, and M. F. Garcia-Parajo, Power-law blinking in the fluorescence of single organic molecules, ChemPhysChem 6 (8), 823-833 (2007)
 
2006
J. P. Hoogenboom, W. K. den Otter, and H. L. Offerhaus, Accurate and unbiased estimation of power-law exponents from single-emitter blinking data, Journal of Chemical Physics (125), 204713 (2006)
J. Hernando, E. M. H. P. van Dijk, J. P. Hoogenboom, J. J. Garcia-Lopez, D. N. Reinhoudt, M. Crego-Calama, M. F. Garcia-Parajo, and N. F. van Hulst, Effect of disorder on ultrafast exciton dynamics probed by single molecule spectroscopy, Physical Review Letters (97), 216403 (2006)
R. P. A. Dullens, M. C. D. Mourad, D. G. A. L. Aarts, J. P. Hoogenboom, and W. K. Kegel, Shape-induced frustration of hexagonal order in polyhedral colloids, Physical Review Letters (96), 028304 (2006)
 
2005
A. Mulder, S. Onclin, M. Peter, J. P. Hoogenboom, H. Beijleveld, J. ter Maat, M. F. Garcia-Parajo, B. J. Ravoo, J. Huskens, N. F. van Hulst, and D. N. Reinhoudt, Molecular printboards on silicon oxide: Lithographic patterning of cyclodextrin monolayers with multivalent, fluorescent guest molecules, SMALL 2 (1), 242-253 (2005)
J. P. Hoogenboom, E. M. H. P. van Dijk, J. Hernando, N. F. van Hulst, and M. F. Garcia-Parajo, Power-law-distributed dark states are the main pathway for photobleaching of single organic molecules, Physical Review Letters 9 (95), 097401 (2005)
M. F. Garcia-Parajo, J. Hernando, G. S. Mosteiro, J. P. Hoogenboom, E. van Dijk, and N. F. van Hulst, Energy transfer in single-molecule photonic wires, ChemPhysChem 5 (6), 819-827 (2005)
 
2004
J. Kalkman, E. De Bres, A. Polman, Y. Jun, D. J. Norris, D. C. 't Hart, J. P. Hoogenboom, and A. van Blaaderen, Selective excitation of erbium in silicon-infiltrated silica colloidal photonic crystals, Journal of Applied Physics 5 (95), 2297-2302 (2004)
J. P. Hoogenboom, A. K. van Langen-Suurling, J. Romijn, and A. van Blaaderen, Epitaxial growth of a colloidal hard-sphere hcp crystal and the effects of epitaxial mismatch on crystal structure, Physical Review E (69), 051602 (2004)
J. P. Hoogenboom, C. Retif, E. de Bres, M. V. de Boer, A. K. van Langen-Suurling, J. Romijn, and A. van Blaaderen, Template-induced growth of close-packed and non-close-packed colloidal crystals during solvent evaporation, Nano Letters 2 (4), 205-208 (2004)
J. Hernando, J. P. Hoogenboom, E. M. P. H. van Dijk, J. J. Garcia-Lopez, M. Crego-Calama, D. N. Reinhoudt, M. F. Garcia-Parajo, and N. F. van Hulst, Single molecule photobleaching probes the exciton wavefunction in a multichromphoric system, Physical Review Letters (93), 236404 (2004)
 
2003
 A. van Blaaderen, J. P. Hoogenboom, D. L. J. Vossen, A. Yethiraj, A. van der Horst, K. Visscher, and M. Dogterom, Colloidal epitaxy: Playing with the boundary conditions of colloidal crystallization, Faraday Discussions (123), 107-119 (2003)
J. P. Hoogenboom, P. Vergeer, and A. van Blaaderen, A real-space analysis of colloidal crystallization in a gravitational field at a flat bottom wall, Journal of Chemical Physics 6 (119), 3371-3383 (2003)
J. P. Hoogenboom, A. K. van Langen-Suurling, J. Romijn, and A. van Blaaderen, Hard-sphere crystals with hcp and non-close packed structure grown by colloidal epitaxy, Physical Review Letters 13 (90), 138301 (2003)
 
2002
C. Strohhofer, J. P. Hoogenboom, A. van Blaaderen, and A. Polman, Highly dispersive micropatterns in ion-exchanged glass formed by ion irradiation through a mask of colloidal particles, Advanced Materials 24 (14), 1815-1818 (2002)
J. P. Hoogenboom, A. Yethiraj, A. K. van Langen-Suurling, J. Romijn, and A. van Blaaderen, Epitaxial crystal growth of charged colloids, Physical Review Letters 25 (89), 256104 (2002)
J. P. Hoogenboom, D. L. J. Vossen, C. Faivre-Moskalenko, M. Dogterom, and A. van Blaaderen, Patterning surfaces with colloidal particles using optical tweezers, Applied Physics Letters 25 (80), 4828-4830 (2002)
J. P. Hoogenboom, D. Derks, P. Vergeer, and A. van Blaaderen, Stacking faults in colloidal crystals grown by sedimentation, Journal of Chemical Physics 24 (117), 11320-11328 (2002)
 
2001
A. van Blaaderen, K. P. Velikov, J. P. Hoogenboom, D. L. J. Vossen, A. Yethiraj, R. P. A. Dullens, T. van Dillen, and A. Polman, Manipulating colloidal crystallization for photonic applications: from self-organization to do-it-yourself organization, in: Photonic crystals and light localization in the 21st century, C. M. Soukoulis, C. M. Soukoulis. Kluwer 239-251 (2001)
 
2000
J. P. Hoogenboom, H. L. Tepper, N. F. A. van der Vegt, and W. J. Briels, Transport diffusion of argon in AlPO4-5 from equilibrium molecular dynamics simulations, Journal of Chemical Physics 16 (113), 6875-6881 (2000)
 
1999
H. L. Tepper, J. P. Hoogenboom, N. F. A. van der Vegt, and W. J. Briels, Unidirectional diffusion of methane in AlPO4-5, Journal of Chemical Physics 23 (110), 11511-11516 (1999)