PhD, Stony Brook University, 1988
Presidential Faculty Fellow (White House/NSF), 1992-1997;
International Dennis Gabor Award (Hungary), 1996; Kurt Heinrich
Award (Microbeam Analysis Society), 2001; R&D 100 award
Fellow, Optical Society of America (1999), American Association
for the Advancement of Science (2002), American Physical Society
from diving, hiking, and skiing
Chris Jacobsen's research
group is focused on developing new methods in x-ray
microscopy, and applying them to interesting problems in biology,
environmental science, and materials science. Using either
diffractive optics (like Fresnel zone plates fabricated using
electron beam lithography), or lensless methods where iterative
phase retrieval methods are used to reconstruct an image from a
coherent diffraction pattern, images with a spatial resolution of
30 nm or better can be obtained. In absorption contrast, one
can combine imaging with spectroscopy to study chemical speciation
at the nanoscale, or one can use fluorescence detection to study
trace element distributions with parts-per-billion
sensitivity. We are also developing detectors and image
reconstruction algorithms that can be used to obtain quantitative
phase contrast images with hard X rays, and thus put elemental
distributions into their ultrastructural context and also go from
measurements of content to measurements of concentration (since
concentration gradients drive chemical processes). Finally,
we are interested in understanding the limitations that radiation
damage presents to x-ray microscopy studies, and in developing
both cryo instrumentation and sample preparation methods to
mitigate those limitations. These efforts require bright
x-ray beams, so we use synchrotron radiation sources at Argonne
Lab, Berkeley Lab, and elsewhere. Students in the group
explore interesting problems in optical physics and in
instrumentation, and get to broaden their perspective by working
with collaborators from other research fields like biology,
environmental science, and materials science.
Representative publications (full list
via ORCID or ResearcherID):
- C. Jacobsen, "Future challenges for x-ray microscopy," AIP
Conf. Proc. 1696, 020035 (2016). PDF.
- S. Chen, T. Paunesku, Y. Yuan, J. Deng, Q. Jin, Y.P. Hong,
D.J. Vine, B. Lai, C. Flachenecker, B. Hornberger, K. Brister,
C. Jacobsen, G.E. Woloschak, and S. Vogt, "2D/3D cryo x-ray
fluorescence imaging at the bionanoprobe at the Advanced Photon
Source," AIP Conf. Proc. 1696, 020028
- J. Deng, D.J. Vine, S. Chen, Y.S.G. Nashed, Q. Jin, T.
Peterka, S. Vogt, and C. Jacobsen, "Advances and challenges in
cryo ptychography at the Advanced Photon Source," AIP Conf.
Proc. 1696, 020030 (2016). PDF.
- Rachel Mak, Stefan M. Wild, and Chris Jacobsen, "Non-negative
matrix analysis in x-ray spectromicroscopy: choosing
regularizers," AIP Conf. Proc. 1696, 020034
- D. Yan, T. Cecil, L. Gades, C. Jacobsen, T. Madden, and A.
Miceli, "Processing of x-ray micxrocalorimeter data with pulse
shape variation using principal component analysis," Journal
of Low Temperature Physics (2016). Online.
- Kenan Li, Michael Wojcik, Leo Ocola, Ralu Divan, and Chris
Jacobsen, "Multi-layer on-chip stacked Fresnel zone plates: hard
x-ray fabrication and soft x-ray simulations," Journal of
Vacuum Science and Technology B 33, 06FD04 (2015)
[open access online].
Argonne APT 122741.
- Kenan Li and Chris Jacobsen, "Rapid calculation of paraxial
wave propagation for cylindrically symmetric optics," Journal
of the Optical Society of America A 32, 2074
Argonne APT 121760.
- Young Pyo Hong, Si Chen, and Chris Jacobsen, "A new workflow
for x-ray fluorescence tomography: MAPStoTomoPy," Proceedings
SPIE 9592, 95920W (2015) [SPIE]
- Si Chen, Junjing Deng, David J. Vine, Youssef S.G. Nashed,
Qiaoling Jin, Tom Peterka, Chris Jacobsen, and Stefan Vogt,
"Simultaneous x-ray nano-ptychographic and fluorescence
microscopy at the bionanoprobe," Proceedings SPIE 9592,
95920I (2015) [SPIE]
- Junjing Deng, David J. Vine, Si Chen, Youssef S.G. Nashed, Tom
Peterka, Rob Ross, Stefan Vogt, and Chris Jacobsen,
"Opportunities and limitations for combined fly-scan
ptychography and fluorescence microscopy," Proceedings SPIE
9592, 95920U (2015) [SPIE]
- Junjing Deng, Youssef S.G. Nashed, Si Chen, Nicholas W.
Phililips, Tom Peterka, Rob Ross, Stefan Vogt, Chris Jacobsen,
and David Vine, "Continuous motion scan ptychography:
characterization for increased speed in coherent x-ray imaging,"
Optics Express 23, 5348-5451 (2015). [open access
Argonne APT 111061.
- Junjing Deng, David J. Vine, Si Chen, Youssef S.G. Nashed,
Qiaoling Jin, Nicholas W. Phillips, Tom Peterka, Rob Ross,
Stefan Vogt, and Chris Jacobsen, "Simulataneous cryo X-ray
ptychography and fluorescence microscopy of green algae" PNAS
112, 2314-2319 (2015) [open access online].
Argonne APT 110881.
- Qiaoling Jin, Stefan Vogt, Barry Lai, Si Chen, Lydia Finney,
Sophie-Charlotte Gleber, Jesse Ward, Junjing Deng, Rachel Mak,
Nena Moonier, and Chris Jacobsen, "Ultraviolet germicidal
irradiation and its effects on elemental distributions in mouse
embryonic fibroblast cells in x-ray fluorescence analysis," PLoS
ONE 10, e0117437 (2015). [open access online].
Argonne APT 110961.
- Yue Sun, Sophie-Charlotte Gleber, Chris Jacobsen, Janos Kirz,
and Stefan Vogt, "Optimizing detector geometry for trace element
mapping by x-ray fluorescence," Ultramicroscopy 152,
44-46 (2015). [open access online]
Argonne APT 110963.
- Youssef S.G. Nashed, David J. Vine, Tom Peterka, Junjing Deng,
Rob Ross, and Chris Jacobsen, "Parallel ptychographic
reconstruction," Optics Express 22, 32082-32097
(2014). [open access online]
Argonne APT 110064.
- Francesco De Carlo, Doga Gursoy, Federica Marone, Mark Rivers,
Dilworth Y Parkinson, Faisal Khan, Nicholas Schwarz, David J
Vine, Stefan Vogt, Sophie-Charlotte Gleber, Suresh Narayanan,
Matt Newville, Tony Lanzirotti, Yue Sun, Young Pyo Hong, and
Chris Jacobsen, "Scientific Data Exchange: a schema for
HDF5-based storage of raw and analyzed data," Journal of
Synchrotron Radiation 21, 1224-1230 (2014). [PDF]
Argonne APT 78680.
- Martin D de Jonge, Christopher G Ryan, and Chris J Jacobsen,
"X-ray nanoprobes and diffraction-limited storage rings:
opportunities and challenges of fluorescence tomography of
biological specimens," Journal of Synchrotron Radiation
21, 1031-1047 (2014). [open access online]
Argonne APT 79293.
- Mirna Lerotic, Rachel Mak, Sue Wirick, Florian Meirer, and
Chris Jacobsen, "MANTiS: a program for the analysis of x-ray
spectromicroscopy data," Journal of Synchrotron Radiation
21, 1206-1212 (2014). [PDF]
Argonne APT 78672.
- Doga Gursoy, Francesco De Carlo, Xianghui Xiao, and Chris
Jacobsen, "TomoPy: a framework for the analysis of synchrotron
tomographic data," Journal of Synchrotron Radiation 21,
1188-1193 (2014). [open access online]
Argonne APT 79252.
- Rachel Mak, Mirna Lerotic, Holger Fleckenstein, Stefan Vogt,
Stefan M Wild, Sven Leyffer, Yefim Sheynkin, and Chris Jacobsen,
"Non-negative matrix analysis for effective feature extraction
in x-ray spectromicroscopy," Faraday Discussions 171,
357-371 (2014). [open access online]
Argonne APT 78674.
- Siwei Wang, Jesse Ward, Sven Leyffer, Stefan M Wild, Chris
Jacobsen, and Stefan Vogt, "Unsupervised cell identification on
multidimensional x-ray fluorescence datasets," Journal of
Synchrotron Radiation 21, 568-579 (2014). [PDF]
Argonne APT 76387
- Young Pyo Hong, Sophie-Charlotte Gleber, Thomas V O'Halloran,
Emily L Que, Reiner Bleher, Stefan Vogt, Teresa K Woodruff, and
Chris Jacobsen, "Alignment of low-dose x-ray fluorescence
tomography images using differential phase contrast," Journal
of Synchrotron Radiation 21, 229-234 (2014). [PDF]
- Si Chen, Junjing Deng, Ye Yuan, Claus Flachenecker, Rachel
Mak, Benjamin Hornberger, Qiaoling Jin, Deming Shu, Barry Lai,
Joerg Maser, Chris Roehrig, Tatjana Paunesku, Sophie-Charlotte
Gleber, David J. Vine, Lydia Finney, Jay Von Osinski, Michael
Bolbat, Ian Spink, Zhenyang Chen, Jay Steele, David Trapp, Jeff
Irwin, Michael Feser, E. Snyder, Keith Brister, Chris Jacobsen,
Gayle Woloschak, and Stefan Vogt, "The Bionanoprobe: hard x-ray
fluorescence nanoprobe with cryogenic capabilities," Journal
of Synchrotron Radiation 21, 66-75 (2014). [open
Argonne APT 78189.
- Ye Yuan, Si Chen, Tatjana Paunesku, Sophie-Charlotte Gleber,
William C. Liu, Caroline B. Doty, Rachel Mak, Junjing Deng,
Qiaoling Jin, Barry Lai, Keith Brister, Claus Flachenecker,
Chris Jacobsen, Stefan Vogt, and Gayle Woloschak, "Epidermal
Growth Factor Receptor Targeted Nuclear Delivery and
High-Resolution Whole Cell X‐ray Imaging of Fe3O4@TiO2
Nanoparticles in Cancer Cells," ACS Nano 7,
10502-10517 (2013). [open access online] Argonne APT 78486.
- Joshua Turner, Johanna Nelson, Xiaojing Huang, Jan
Steinbrener, and Chris Jacobsen, "Lensless imaging of nanoporous
glass with soft x-rays," Physics Letters A 377,
1150-1153 (2013). [PDF]
- Roger Falcone, Chris Jacobsen, Janos Kirz, Stefano Marchesini,
David Shapiro, and John Spence, "New directions in X-ray
293-318 (2011). [PDF]
- C. Holzner, M. Feser, S. Vogt, B. Hornberger, S.B. Baines, and
C. Jacobsen, "Zernike phase contrast scanning microscopy with
X-rays,” Nature Physics 6, 883-887 (2010) [PDF]
- M.D. de Jonge, C. Holzner, S.B. Baines, B.S. Twining, K.
Ignatyev, J. Diaz, D.L. Howard, D. Legnini, A. Miceli, I.
McNulty, C.J. Jacobsen, and S. Vogt, "Quantitative 3D elemental
microtomography of Cyclotella meneghiniana at 400-nm
resolution," Proceedings of the National Academy of Sciences
107, 15676-15680 (2010). [PDF]
- J. Nelson, X. Huang, J. Steinbrener, D. Shapiro, J. Kirz, S.
Marchesini, A.M. Neiman, J.J. Turner, and C. Jacobsen, "High
resolution x-ray diffraction microscopy of specifically labeled
yeast cells," Proceedings of
the National Academy of Sciences 107, 7235
- J. Steinbrener, J. Nelson, X. Huang, S. Marchesini, D.
Shapiro, J. J. Turner and C. Jacobsen, "Data preparation and
evaluation techniques for x-ray diffraction microscopy", Optics Express 18, 18598-18614, (2010).
- X. Huang, J. Nelson, J. Kirz, E. Lima, S. Marchesini, H.
Miao, A.M. Neiman, D. Shapiro, J. Steinbrener, A. Stewart, J.J.
Turner, and C. Jacobsen, "Soft x-ray diffraction microscopy of a
frozen hydrated yeast cell," Physical
Review Letters 103,
198101 (2009). [PDF]
- M. Howells, T. Beetz, H. Chapman, C. Cui, J. Holton, C.
Jacobsen, J. Kirz, E. Lima, S. Marchesini, H. Miao, D. Sayre, D.
Shapiro, J. Spence, and D. Starodub, "An assessment of the
resolution limitation due to radiation-damage in x-ray
diffraction microscopy," Journal
of Electron Spectroscopy and Related Phenomena 170, 4-12 (2009). [PDF]
- M. D. de Jonge, B. Hornberger, D. Paterson, C. Holzner, D.
Legnini, I. McNulty, C. Jacobsen, and S. Vogt, "Quantitative
phase imaging with a scanning transmission x-ray microscope," Physical Review Letters 100, 163902 (2008). [PDF]
- J. Lehmann, D. Solomon, J. Kinyangi, L. Dathe, S. Wirick, and
C. Jacobsen, "Spatial complexity of soil organic matter forms at
nanometre scales," Nature
238-242 (2008). [PDF]
- D. Shapiro, P. Thibault, T. Beetz, V. Elser, M. Howells, C.
Jacobsen, J. Kirz, E. Lima, H. Miao, A. M. Neiman, and D. Sayre,
"Biological imaging by soft x-ray diffraction microscopy," Proceedings of the National
Academy of Sciences 102,
15343-15346 (2005). [PDF]
- C.K. Boyce, M.A. Zwieniecki, G.D. Cody, C. Jacobsen, S.
Wirick, A.H. Knoll, and N. M. Holbrook, "Evolution of xylem
lignification and hydrogel transport regulation." Proceedings of the National
Academy of Sciences 101,
17555-17558 (2004). [PDF]
- J. Kirz, C. Jacobsen, and M. Howells, "Soft x-ray microscopes
and their biological applications." Quarterly Reviews of Biophysics 28, 33-130 (1995). [PDF]
I maintain a public calendar using
Microsoft Exchange at the Advanced Photon Source at Argonne National
Lab. You can view the calendar here
using a desktop computer. Unfortunately Microscoft Exchange
refuses to deliver web views of calendars to mobile devices.