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Dr Joe Pin-Jen Chen

Contact

Department: Electrical and Computer Engineering

Email: joe.chen@canterbury.ac.nz

Direct Dial: +64 3 3691798

Office: Link Room 503

Language: English

You just begin. You do the math. You solve one problem and the next one, and then the next. And if you solve enough problems, you get to come home.
About
Research / Creative works
Networks
Methods & Equipment

Fields of Research

  • X-ray imaging
  • X-ray free-electron laser science
  • Phase retrieval
  • Biomedical imaging
  • Computational imaging
  • Optimisation algorithms
  • Acoustic engineering
  • Quantum computing
  • Protein crystallography
  • Ultrasound

Researcher Summary

Joe's primary research is in the field of imaging, where he uses X-rays, electrons, optical light and sound waves, among other things, to look at everything from galaxies to protein molecules - with the aim of visualising our universe and understanding how things work.

He has experience in phase retrieval and X-ray diffractive imaging, exploring computational algorithms that reconstruct 3-dimensional images of proteins and viruses from X-ray diffraction data collected at synchrotrons and X-ray free-electron lasers (XFEL).

More recently, Joe is looking into applying ultrasonic ideas for biomedical and environmental applications that will hopefully go on to help many people.

Joe's other research interests include acoustic engineering, quantum optics/computing, optimisation algorithms and astrobiology.

Subject Area: Disciplines

  • Chemistry: Crystallography
  • Engineering and Technology: Electrical Engineering; Signal and Image Processing
  • Physics: Condensed Matter

Resources

  • Coherent X-ray Imaging Data Bank
  • Protein Data Bank
  • Linac Coherent Light Source (LCLS)
  • European X-ray Free-Electron Laser
  • Qiskit Quantum Computing Textbook

Research/Scholarly/Creative Works

  • Doppler D., Rabbani MT., Letrun R., Villarreal JC., Kim DH., Gandhi S., Egatz-Gomez A., Sonker M., Chen J. and Koua FHM. (2022) Co-flow injection for serial crystallography at X-ray free-electron lasers. Journal of Applied Crystallography 55: 1-13. http://dx.doi.org/10.1107/S1600576721011079. (Journal Articles)
  • Mobley BR., Schmidt KE., Chen JPJ. and Kirian RA. (2022) A Metropolis Monte Carlo algorithm for merging single-particle diffraction intensities. Acta Crystallographica Section A: Foundations and Advances 78: 200-211. http://dx.doi.org/10.1107/S2053273322001395. (Journal Articles)
  • Chen JPJ., Schmidt KE., Spence JCH. and Kirian RA. (2021) A new solution to the curved Ewald sphere problem for 3D image reconstruction in electron microscopy. Ultramicroscopy 224 http://dx.doi.org/10.1016/j.ultramic.2021.113234. (Journal Articles)
  • Chen JPJ., Donatelli JJ., Schmidt KE. and Kirian RA. (2019) Shape transform phasing of edgy nanocrystals. Acta Crystallographica Section A: Foundations and Advances 75: 239-259. http://dx.doi.org/10.1107/S205327331900113X. (Journal Articles)
  • Morgan AJ., Ayyer K., Barty A., Chen JPJ., Ekeberg T., Oberthuer D., White TA., Yefanov O. and Chapman HN. (2019) Ab initio phasing of the diffraction of crystals with translational disorder. Acta Crystallographica Section A Foundations and Advances 75(1): 25-40. http://dx.doi.org/10.1107/s2053273318015395. (Journal Articles)
  • Bajt S., Prasciolu M., Fleckenstein H., Domaracký M., Chapman HN., Morgan AJ., Yefanov O., Messerschmidt M., Du Y. and Murray KT. (2018) X-ray focusing with efficient high-NA multilayer Laue lenses. Light: Science and Applications 7(3): 17162. http://dx.doi.org/10.1038/lsa.2017.162. (Journal Articles)
  • Chen JPJ. and Kirian RA. (2018) Simultaneous retrieval of coherently illuminated defocused objects. In International Conference Image and Vision Computing New Zealand 2017-December: 1-5. http://dx.doi.org/10.1109/IVCNZ.2017.8402481. (Conference Contributions - Published)
  • Graves W., Chen J., Fromme P., Holl M. and Kyung-Han H. (2018) ASU Compact XFEL. In Proceedings of the 38th International Free-Electron Laser Conference (FEL 2017): 4. http://dx.doi.org/10.18429/JACoW-FEL2017-TUB03. (Conference Contributions - Published)
  • Kirian RA., Chen J. and Spence JCH. (2018) Phasing Serial Crystallography Data. In Boutet S; Fromme P; Hunter MS (Ed.), X-ray Free Electron Lasers: A Revolution in Structural BiologySpringer. (Chapters)
  • Wiedorn MO., Awel S., Morgan AJ., Ayyer K., Gevorkov Y., Fleckenstein H., Roth N., Adriano L., Bean R. and Beyerlein KR. (2018) Rapid sample delivery for megahertz serial crystallography at X-ray FELs. IUCrJ 5: 574-584. http://dx.doi.org/10.1107/S2052252518008369. (Journal Articles)
  • Chen JPJ. and Kirian RA. (2017) Phase retrieval in the presence of multiplicative noise. In Proceedings of SPIE - The International Society for Optical Engineering 10410 http://dx.doi.org/10.1117/12.2275182. (Conference Contributions - Published)
  • Popp D., Loh ND., Zorgati H., Ghoshdastider U., Liow LT., Ivanova MI., Larsson M., DePonte DP., Bean R. and Beyerlein KR. (2017) Flow-aligned, single-shot fiber diffraction using a femtosecond X-ray free-electron laser. Cytoskeleton 74(12): 472-481. http://dx.doi.org/10.1002/cm.21378. (Journal Articles)
  • Arnal RD., Chen JPJ., Morgan A., Bean RJ., Beyerlein KR., Yefanov O., Chapman HN. and Millane RP. (2016) Phasing XFEL diffraction data from very small crystals. St Malo, France: International Workshop on Phase Retrieval and Coherent Scattering, 7-10 Jun 2016. (Conference Contributions - Other)
  • Chen JPJ., Arnal RD., Morgan AJ., Bean RJ., Beyerlein KR., Chapman HN., Bones PJ., Millane RP. and Kirian RA. (2016) Reconstruction of an object from diffraction intensities averaged over multiple object clusters. Journal of Optics (United Kingdom) 18(11) http://dx.doi.org/10.1088/2040-8978/18/11/114003. (Journal Articles)
  • Chen JPJ. (2015) Image Reconstruction in Serial Femtosecond Nanocrystallography. Christchurch, New Zealand. University of Canterbury. (Theses / Dissertations)
  • Chen JPJ., Kirian RA., Bean RJ., Beyerlein KR., Chapman HN., Bones P., Arnal RD., Millane RP. and Spence JCH. (2015) Phase retrieval of randomly terminated finite crystals. Rovinj, Croatia: 29th European Crystallographic Meeting, 23-28 Aug 2015. (Conference Contributions - Other)
  • Chen JPJ., Kirian RA., Beyerlein KR., Bean RJ., Morgan AJ., Yefanov OM., Arnal RD., Wojtas DH., Bones PJ. and Chapman HN. (2015) Image reconstruction in serial femtosecond nanocrystallography using x-ray free-electron lasers. In Proceedings of SPIE 9600: 960002-960002. http://dx.doi.org/10.1117/12.2187610. (Conference Contributions - Published)
  • Chen J., Spence JCH. and Millane RP. (2014) Direct phasing in femtosecond nanocrystallography. I. Diffraction characteristics. Acta Crystallographica Section A: Foundations and Advancements 70(2): 143-153. http://dx.doi.org/10.1107/S2053273313032038. (Journal Articles)
  • Chen J., Spence JCH. and Millane RP. (2014) Direct phasing in femtosecond nanocrystallography. II. Phase retrieval. Acta Crystallographica Section A: Foundations and Advancements 70(2): 154-161. http://dx.doi.org/10.1107/S2053273313032725. (Journal Articles)
  • Chen JPJ. and Millane RP. (2014) Diffraction by nanocrystals II. Journal of the Optical Society of America A: Optics, Image Science, and Vision 31(8): 1730-1737. http://dx.doi.org/10.1364/JOSAA.31.001730. (Journal Articles)
  • Millane RP. and Chen J. (2014) Aspects of direct phasing in femtosecond nanocrystallography. Philosophical Transactions of the Royal Society B: Biological Sciences 369(1647) 20130498 http://dx.doi.org/10.1098/rstb.2013.0498. (Journal Articles)
  • Chen J. and Millane RP. (2013) Diffraction by nanocrystals. Journal of the Optical Society of America. A: Optics, Image Science and Vision 30(12): 2627-2634. http://dx.doi.org/10.1364/JOSAA.30.002627. (Journal Articles)
  • Chen J. and Millane RP. (2013) Diffraction by small crystals with incomplete unit cells. In IEEE Conference Proceedings IVCNZ 2013: 65-69. http://dx.doi.org/10.1109/IVCNZ.2013.6726994. (Conference Contributions - Published)
  • Chen JPJ., Spence JCH. and Millane RP. (2012) Phase retrieval in nanocrystallography. In Proceedings of SPIE - The International Society for Optical Engineering 8500: 85000I/1-12. http://dx.doi.org/10.1117/12.930930. (Conference Contributions - Published)

Affiliations

  • Institute of Physics (IOP) (Community Organisation/NGO): Associate member
  • New Zealand Association of Scientists (Professional Organisation): Member
  • Royal Society of New Zealand (RSNZ) (Professional Organisation): Member
  • Royal Society of New Zealand (RSNZ), Canterbury Branch (Professional Organisation): Member

Key Methodologies

  • X-ray free-electron lasers
  • Python (programming language)
  • Open-source software
  • X-ray crystallography
  • Serial femtosecond crystallography
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