Staff Biography-Mohamadreza Fazel, Ph.D.

Education

• Shahrekord University – B.S. (Physics) – 2006-2010
• Isfahan University of Technology — M.S. (Physics) – 2010-2013
• University of New Mexico – M.S. (Optical Engineering) – 2014-2016
• University of New Mexico – Ph.D. (Physics) – 2016-2020

Honors

• Honor student at Shahrekord University for maintaining a high GPA throughout the program, 2010
• Graduate Studies Excellence Assistantship (GSEA), University of New Mexico, 2017
• S-CAP trave; award, University of New Mexico, 2019

Research Experience

2014-2016 graduate teaching assistant, University of New Mexico

• Teaching multiple courses and introductory physics labs

2016-2020 graduate research assistant, University of New Mexico

• Training in a biophysics lab where I worked on the analysis of super-resolution single molecule localization microscopy data.
• Developed a multi-emitter localization method to pinpoint emitters within densely regions with overlapping PSFs and structured backgrounds in SMLM data
• Developed a Bayesian method to achieve nanometer localization precisions using SMLM data
• Involved in developing a comprehensive data processing and post-processing pipeline for SMLM data.
• Involved in the development of a drift correction tool as a postprocessing of SMLM data.

2020-2024 postdoctoral research scholar, Arizona State University

• Developing tools for fluorescent lifetime imaging microscopy to achieve high spatial and lifetime resolutions while learning the number of species present within the data
• Involved in developing a comprehensive methodological framework for FRET data analysis capable of inferring the number of conformational states.
• Developing a 3D tracking frameworks using aberrated PSFs.
• Developing a computational framework for spectral-FLIM data analysis capable of learning dealing with many species with overlapping spectra.

2024-presnt staff scientists, National Cancer Institute, Laboratory of Receptor Biology and Gene Expression

• Developing computational tools for the processing and post-processing of MINFLUX and DNA-PAINT data.

Professional Activities at the NCI/NIH

As a staff scientist at the optical microscopy core (OMC) in the Laboratory of Receptor Biology and Gene Expression. He has a strong interdisciplinary background in applying cutting-edge statistical machine learning methods to address problems in biophysics, fluorescence microscopy and optics. At OMC, his research is mainly focused on pattern recognition in data from advanced nanoscopy methods, such as MINFLUX and DNA-PAINT.

Invited Lectures

Invited Zoom Talk—LFD Workshop, University of California, Irvine, California, USA, November 2023.
Popular Science Talk—Science On Tap, Tempe, AZ, USA, October 2023.
Invited Zoom Talk—Physics Seminar, University of Calgary, Alberta, Canada, January 2022.
Invited Zoom Talk–Physics Colloquium, Isfahan University of Technology, Isfahan, Iran, October 2021.

Selected Publications

1. STORM: Hamidreza Heydarian, Florian Schueder, Maximilian T. Strauss, Ben van Werkhoven, Mohamadreza Fazel, Keith A. Lidke, Ralf Jungmann, Sjoerd Stallinga, Bernd Rieger, ‘Template-free 2D particle fusion in localization microscopy’. Nature Methods 09/2018; 15(10). DOI: 10.1038/s41592-018-0136-6.

2. STORM: Mohamadreza Fazel, Michael J. Wester, Hanieh Mazloom-Farsibaf, Marjolein B. M. Meddens, Alexandra Eklund, Thomas Schlichthaerle, Florian Schueder, Ralf Jungmann, Keith A. Lidke, ‘Bayesian multiple emitter fitting using reversible jump Markov chain Monte Carlo’. Scientific Reports 9, 13791 (2019). DOI: 10.1038/s41598-019-50232-x.

3. STORM: Hanieh Mazloom-Farsibaf, Farzin Farzam, Mohamadreza Fazel, Michael J. Wester, Marjolein Meddens, Keith A. Lidke, ‘Comparing lifeact and phalloidin for super-resolution imaging of actin in fixed cells’, PLoS One 16(1), e0246138 (2021). DOI:

4. STORM: Michael J. Wester, Sandeep Pallikkuth, Hanieh Mazloom-Farsibaf, Mohamadreza Fazel, David Schodt and Keith A. Lidke, ‘Robust, fiducial free drift correction for super-resolution imaging’, Scientific Reports 11, 23672 (2021). DOI: 10.1038/s41598-021-02850-7.

5. STORM: Mohamadreza Fazel, Michael J. Wester, ‘Analysis of super-resolution single molecule localization microscopy data: A tutorial’, AIP Advances 12(1):010701 (2022). DOI: 10.1063/5.0069349. (This work was featured as the most downloaded review paper from the journal in 2022).

6. FLIM: Mohamadreza Fazel, Sina Jazani, Lorenzo Scipioni, Alexander Vallmitjana, Enrico Gratton, Michelle A. Digman, and Steve Pressé, ‘High resolution fluorescence lifetime maps from minimal photon counts’, ACS Photonics (2022). DOI: 10.1021/acsphotonics.1c01936.

7. STORM: William K. Kanagy, Cédric Cleyrat, Mohamadreza Fazel, Shayna R. Lucero, Marcel P. Bruchez, Keith A. Lidke, Bridget S. Wilson, and Diane S. Lidke, ‘Docking of Syk to FcεRI is enhanced by Lyn but limited in duration by SHIP1’, Molecular Biology of the Cell (2022). DOI: 10.1091/mbc.e21-12-0603.

8. STORM: Mohamadreza Fazel, Michael J. Wester, David J. Schodt, Sebastian Restrepo Cruz, Sebastian Strauss, Florian Schueder, Thomas Schlichthaerle, Jennifer M. Gillette, Diane S. Lidke, Bernd Rieger, Ralf Jungmann, Keith A. Lidke, ‘High-Precision Estimation of Emitter Positions using Bayesian Grouping of Localizations’, Nature Communications 13 (1), 7152 (2022). DOI: 10.1038/s41467-022-34894-2.

9. FRET: Ayush Saurabh, Matthew Safar, Ioannis Sgouralis, Mohamadreza Fazel, Steve Pressé, “Single photon smFRET. I. theory and conceptual basis”, Biophysical Reports 3 (1), 100089 (2022). DOI: 10.1101/2022.07.20.500887. (This work was featured on the journal’s cover and was highlighted in the Biophysical Society website as cornerstone research).

10. FRET: Ayush Saurabh, Matthew Safar, Mohamadreza Fazel, Ioannis Sgouralis, Steve Pressé, “Single photons smFRET. II. Application to continuous illumination”, Biophysical Reports 3 (1), 100087 (2022). DOI: 10.1101/2022.07.20.500888. (This work was featured on the journal’s cover and was highlighted in the Biophysical Society website as cornerstone research).

11. FRET: Matthew Safar, Ayush Saurabh, Bidyut Sarkar, Mohamadreza Fazel, Kunihiko Ishii, Tahei Tahara, Ioannis sgouralis, Steve Pressé, “Single photon smFRET. III. Application to pulsed illumination”, Biophysical Reports 4 (1), 100088 (2023). DOI: 10.1101/2022.07.20.500892. (This work was featured on the journal’s cover and was highlighted in the Biophysical Society website as cornerstone research).

12. FLIM: Mohamadreza Fazel, Alexander Vallmitjana, Lorenzo Scipioni, Enrico Gratton, Michelle A. Digman, Steve Pressé, “Fluorescence Lifetime: Beating the IRF and interpulse window”, Biophysical Journal 122, 672-683 (2023). DOI: 10.1101/2022.09.08.507224.

13. FLIM: Mohamadreza Fazel, Sina Jazani, Lorenzo Scipioni, Alexander Vallmitjana, Songning Zhu, Enrico Gratton, Michelle A. Digman, and Steve Pressé, ‘Building Fluorescence Lifetime Maps Photon-by-photon by Leveraging Spatial Correlations’, ACS Photonics (2023). bioRxiv, DOI: 10.1101/2022.11.29.518311.

14. STORM: David J. Shodt, Michael J. Wester, Mohamadreza Fazel, Sajjad Khan, Hanieh Mazloom-Farsibaf, Sandeep Pallikkuth, Farzin Farzam, Eric A. Burns, William K. Kanagy, Derek A. Rinaldi, Elton Jhamba, Sheng Liu, Peter K. Relich, Mark J. Olah, Stanly L. Steinberg, Keith A. Lidke, “SMITE: Single Molecule Imaging Toolbox Extraordinaire (MATLAB)”, Journal of Open Source Software 8(90), 5563 (2023). DOI: 10.21105/joss.05563.

15. Fluorescence Microscopy: Mohamadreza Fazel, Kristin S. Grussmayer, Boris Ferdman, Aleksandra Radenovic, Yoav Shechtman, Jörg Enderlein, Steve Pressé, “Fluorescence Microscopy: a statistics-optics perspective”, Reviews of Modern Physics 96(2), 025003 (2024). DOI: 10.1103/RevModPhys.96.025003. (This work was featured on the journal’s cover)

Patents

1. SMT: Steve Pressé, Mohamadreza Fazel, Zeliha Kilic, “Systems and methods for simultaneous single particle tracking, phase retrieval and PSF reconstruction”, US Patent App. 18/425,056 (2024).