Chris Jacobsen

Chris Jacobsen photo
Chris Jacobsen
PhD, Stony Brook University, 1988

Awards: 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 winner, 1999; Argonne Distinguished Fellow, 2016.
Fellow, Optical Society of America (1999), American Association for the Advancement of Science (2002), American Physical Society (2011).
Awards to students: Werner Meyer-Ilse (International X-ray Microscopy), Julian Baumert (Brookhaven Lab), Gertrude Scharf-Goldhaber (Brookhaven Lab), and Distinguished Doctoral Dissertation (Stony Brook University) awards.

Web site for my book "X-ray Microscopy" (Cambridge University Press, 2020).
X-ray Microscopy book

Research group, calendar, photos from diving, skiing etc.

Contact info:
Argonne Distinguished Fellow
Advanced Photon Source, Argonne National Laboratory
9700 S. Cass Avenue
Argonne, IL 60439-4837, USA
Office: 401-C4239
Phone +1-630-252-7960

Professor, Department of Physics & Astronomy
Northwestern University
2145 Sheridan Road
Evanston, IL 60208-3112, USA
Office: Tech F253 (Technological Institute)
Phone +1-847-467-2703

Faculty member, Graduate Program in Applied Physics
Faculty member, Chemistry of Life Processes Institute

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, Brookhaven 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 Publons):

  1. Ming Du, Doğa Gürsoy, and Chris Jacobsen, "Near, far, wherever you are: simulations on the dose efficiency of holographic and ptychographic coherent imaging," Journal of Applied Crystallography 53, 748-759 (2020). [online].
  2. Kenan Li, Sajid Ali, Michael Wojcik, Vincent De Andrade, Xiaojing Huang, Hanfei Yan, Yong S. Chu, Evgeny Nazaretski, Ajith Pattammattel, and Chris Jacobsen, "Tunable hard x-ray nanofocusing with Fresnel zone plates fabricated using deep etching," Optica 7, 410-416 (2020). [online]
  3. Doğa Gürsoy and Chris Jacobsen, "Multimodal x-ray nanotomography," MRS Bulletin 45, 272-276 (April 2020). [Online].
  4. Ming Du, Youssef S. G. Nashed, Saugat Kandel, Doğa Gürsoy, and Chris Jacobsen, "Three dimensions, two microscopes, one code: automatic differentiation for x-ray nanotomography beyond the depth of focus limit," Science Advances 6, eaay3700 (2020). [Online].
  5. Sajid Ali and Chris Jacobsen, "Effect of tilt on circular zone plate performance," Journal of the Optical Society of America A 37, 374-383 (2020). [Online].
  6. Youssef S G Nashed, Saugat Kandel, Ming Du, and Chris Jacobsen, "Learning phase retrieval with backpropagation," Microscopy and Microanalysis 25 (Supplement 2), 62-63 (2019). [online].
  7. Saugat Kandel, Siddharth Maddali, Marc Allain, Stephan O. Hruszkewycz, Chris Jacobsen, and Youssef S. G. Nashed, "Using automatic differentiation as a general framework for ptychographic reconstruction," Optics Express 27, 18653-18672 (2019). [Online].
  8. Junjing Deng, Yuan Hung Lo, Marcus Gallagher-Jones, Si Chen, Alan Pryor Jr., Qiaoling Jin, Young Pyo Hong, Youssef S. G. Nashed, Stefan Vogt, Jianwei Miao, and Chris Jacobsen, "Correlative 3D X-ray fluorescence and ptychographic tomography of frozen-hydrated green algae," Science Advances 4, eaau4548 (2018). [Online].
  9. Ming Du, Rafael Vescovi, Kamel Fezzaa, Chris Jacobsen, and Doğa Gürsoy, "X-ray tomography of extended objects: a comparison of data acquisition approaches," Journal of the Optical Society of America A 35, 1871-1879 (2018). [Online].
  10. Chris Jacobsen, "Relaxation of the Crowther criterion in multislice tomography," Optics Letters 43, 4811-4814 (2018). [online]
  11. Marc Aurele Gilles, Youssef S. G. Nashed, Ming Du, Chris Jacobsen, and Stefan M. Wild, "3D x-ray imaging of continuous objects beyond the depth of focus limit," Optica 5, 1078-1085 (2018). [online].
  12. Rafael Vescovi, Ming Du, Vincent De Andrade, William Scullin, Doğa Gürsoy, and Chris Jacobsen, "Tomosaic: efficient acquisition and reconstruction of teravoxel tomography data using limited-size synchrotron X-ray beams," Journal of Synchrotron Radiation 25, 1478-1489 (2018). [online].
  13. Kenan Li and Chris Jacobsen, "More are better, but the details matter: combinations of multiple Fresnel zone plates for improved resolution and efficiency in x-ray microscopy," Journal of Synchrotron Radiation 25, 1048-1059 (2018). [online].
  14. Ming Du and Chris Jacobsen, "Relative merits and limiting factors for x-ray and electron microscopy of thick, hydrated organic materials," Ultramicroscopy 184, 293-309 (2018). [online]. Note that there is a Corregindum in Ultramicroscopy to correct a mistake in how we treated thick background layers: online. One can see the full manuscript with the changes in blue on arXiv.
  15. Eva L. Dyer, William Gray Roncal, Judy A. Prasad, Hugo L. Fernandes, Doğa Gürsoy, Vincent De Andrade, Kamel Fezzaa, Xianghui Xiao, Joshua T. Vogelstein, Chris Jacobsen, Konrad P. Körding and Narayanan Kasthuri, "Quantifying Mesoscale Neuroanatomy Using X-Ray Microtomography," eNeuro 4, E0195-17.2017 (2017) [online].  Argonne APT 126970.
  16. Doğa Gürsoy, Young P. Hong, Kuan He, Karl Hujsak, Seunghwan Yoo, Si Chen, Yue Li, Mingyuan Ge, Lisa M. Miller, Yong S. Chu, Vincent De Andrade, Kai He, Oliver Cossairt, Aggelos K. Katsaggelos, and Chris Jacobsen, "Rapid alignment of nanotomography data using joint iterative reconstruction and reprojection," Scientific Reports 7, 11818 (2017). [online].  Argonne APT 134341.
  17. Kenan Li, Michael J. Wojcik, Ralu Divan, Leonidas E. Ocola, Bing Shi, Daniel Rosenmann, and Chris Jacobsen, "Fabrication of hard x-ray zone plates with high aspect ratio using metal-assisted chemical etching," Journal of Vacuum Science and Technology B 35, 06G901 (2017). [online]. Argonne APT 137058.
  18. Chris Jacobsen, Junjing Deng, and Youssef Nashed, "Strategies for high-throughput focused-beam ptychography," Journal of Synchrotron Radiation 24, 1078 (2017) [open access here].  Argonne APT 137255.
  19. Youssef S.G. Nashed, Tom Peterka, Junjing Deng, and Chris Jacobsen, "Distributed Automatic Differentiation for Ptychography," Procedia Computer Science 108C, 404-414 (2017) [open access here].  Argonne APT 134580.
  20. Zichao Wendy Di, Si Chen, Young Pyo Hong, Chris Jacobsen, Sven Leyffer, and Stefan M. Wild, "Joint reconstruction of x-ray fluorescence and transmission tomography," Optics Express 25, 13107-13124 (2017) [open access here].  Argonne APT 129645.
  21. Junjing Deng, Young Pyo Hong, Si Chen, Youssef S.G. Nashed, Tom Peterka, Anthony J.F. Levi, John Damoulakis, Sayan Saha, Travis Eiles, and Chris Jacobsen, "Nanoscale x-ray imaging of circuit features without wafer etching," Physical Review B 95, 104111 (2017) [open access here]. Argonne APT 134200.
  22. Junjing Deng, David J. Vine, Si Chen, Qiaoling Jin, Youssef S.G. Nashed, Tom Peterka, Stefan Vogt, and Chris Jacobsen, "X-ray ptychographic and fluorescence microscopy of frozen-hydrated cells using continuous scanning," Scientific Reports 7, 445 (2017) [open access online].  Argonne APT 134401.
  23. Kenan Li, Michael Wojcik, and Chris Jacobsen, "Multislice does it all—calculating the performance of nanofocusing x-ray optics," Optics Express 25, 1831-1846 (2017) [open access online]. Argonne APT 137058.
  24. Q. Jin, T. Paunesku, B. Lai, S.-C. Gleber, S. Chen, L. Finney, D. Vine, S. Vogt, G. Woloschak, and C. Jacobsen, "Preserving elemental content in adherent mammalian cells for analysis by synchrotron-based x-ray fluorescence microscopy," Journal of Microscopy 265, 81-93 (2017) [open access online]. Argonne APT 137607.
  25. C. Jacobsen, "Future challenges for x-ray microscopy," AIP Conf. Proc. 1696, 020035 (2016).  PDF.
  26. 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 (2016).  PDF.
  27. 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.
  28. Rachel Mak, Stefan M. Wild, and Chris Jacobsen, "Non-negative matrix analysis in x-ray spectromicroscopy: choosing regularizers," AIP Conf. Proc. 1696, 020034 (2016).  PDF.
  29. D. Yan, T. Cecil, L. Gades, C. Jacobsen, T. Madden, and A. Miceli, "Processing of x-ray microcalorimeter data with pulse shape variation using principal component analysis," Journal of Low Temperature Physics (2016).  Online.
  30. 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.
  31. 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 (2015) [PDF logoPDF]. Argonne APT 121760.
  32. Young Pyo Hong, Si Chen, and Chris Jacobsen, "A new workflow for x-ray fluorescence tomography: MAPStoTomoPy," Proceedings SPIE 9592, 95920W (2015) [SPIE] [PDF logoPDF].
  33. 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] [PDF logoPDF].
  34. 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] [PDF logoPDF].
  35. Junjing Deng, Youssef S.G. Nashed, Si Chen, Nicholas W. Phillips, 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 online].  Argonne APT 111061.
  36. 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, "Simultaneous cryo X-ray ptychography and fluorescence microscopy of green algae" PNAS 112, 2314-2319 (2015) [open access online].  Argonne APT 110881.
  37. 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.
  38. 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 onlineArgonne APT 110963.
  39. 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 onlineArgonne APT 110064.
  40. Francesco De Carlo, Doğa Gürsoy, 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 logoPDFArgonne APT 78680.
  41. 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 onlineArgonne APT 79293.
  42. 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 logoPDFArgonne APT 78672.
  43. Doğa Gürsoy, 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 onlineArgonne APT 79252.
  44. 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.
  45. 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 logoPDFArgonne APT 76387
  46. 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 logoPDF]
  47. 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 access onlineArgonne APT 78189.
  48. 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 onlineArgonne APT 78486.
  49. 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 logoPDF]
  50. Roger Falcone, Chris Jacobsen, Janos Kirz, Stefano Marchesini, David Shapiro, and John Spence, "New directions in X-ray Microscopy," Contemporary Physics 52, 293-318 (2011).  [PDF logoPDF]
  51. 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 logoPDF]
  52. 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 logoPDF]
  53. 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 (2010).  [PDF
  54. 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).   [PDF logoPDF]
  55.  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 logoPDF]
  56. 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 logoPDF]
  57. 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 logoPDF]
  58. J. Lehmann, D. Solomon, J. Kinyangi, L. Dathe, S. Wirick, and C. Jacobsen, "Spatial complexity of soil organic matter forms at nanometre scales," Nature Geoscience 1, 238-242 (2008).  [PDF logoPDF]
  59. 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 logoPDF]
  60. 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 logoPDF]
  61. J. Kirz, C. Jacobsen, and M. Howells, "Soft x-ray microscopes and their biological applications." Quarterly Reviews of Biophysics 28, 33-130 (1995).  [PDF logoPDF]

I maintain a public calendar at Argonne National Lab. You can view the calendar here.