Current contact:

• E-mail: jakub.pospisil@uit.no
• UiT website: Jakub Pospíšil

Degrees:

• Ph.D.: 2022, Czech Technical University in Prague, Faculty of Electrical Engineering
  • Doctoral thesis: Compact structured illumination microscopy and performance evaluation in live cell super-resolution imaging
  • Supervisor: Prof. Ing. Miloš Klíma, CSc.
  • Co-supervisor: Ing. Karel Fliegel, Ph.D.

• Ing. (M.Sc.): 2015, Czech Technical University in Prague, Faculty of Electrical Engineering
  • Diploma thesis: Design of algorithm for segmentation of speech utterances in patients with Huntington’s disease
  • Supervisor: doc. Ing. Jan Rusz, Ph.D.
  • Co-supervisor: Ing. Michal Novotný, Ph.D.

Networks:

• ORCID ID: 0000-0003-3615-5752
• Scopus Author ID: 55424670500
• Google Scholar: Jakub Pospíšil

Summary:

Jakub Pospíšil was born in Jinřichův Hradec, Czech Republic in 1990. In 2015, he received his master diploma from Communications, Multimedia and Electronics program at Faculty of Electrical Engineering (FEE), Czech Technical University (CTU) in Prague.

Jakub Pospíšil defended his doctoral thesis entitled “Compact structured illumination microscopy and performance evaluation in live cell super-resolution imaging” in March 2022 at Czech technical university in Prague, Faculty of electrical engineering, Department of radioelectronics under the supervision of Prof. Miloš Klíma and Dr. Karel Fliegel. His doctoral thesis was awarded by the dean of the FEE for a prestigious dissertation.

His main area of interest is super-resolution structured illumination fluorescence microscopy (SR-SIM) image processing and analysis for applications in cell biology. He is particularly focused on the development of related advanced digital image processing algorithms.

Jakub focused on image quality assessment problem in super-resolution SIM during his Ph.D. studies, especially on the assessing resolution in super-resolution reconstructed images. The work is conducted in close cooperation with Laboratoire d’Optique Biomédicale (Prof. Theo Lasser), EPFL, Switzerland, BioFrontiers (Dr. Guy Hagen), University of Colorado, Colorado Springs, USA, and Biomolecular Photonics (Prof. Thomas Huser), Bielefeld University, Germany.

In September 2018, Jakub joined the Innovative Training Network (ITN) project DeLIVER under the supervision of Prof. Thomas Huser, University Bielefeld, Germany. His main research objective in DeLIVER project is the development of high-speed structured illumination microscopy with instant, GPU-based image reconstruction. To this end, he utilizes compact fiber-optic interferometers to generate interference patterns at rates of 60 Hz or more. These patterns are used as excitation patterns for SR-SIM.  He also extends the existing open-source SR-SIM image reconstruction software SIMToolbox. Once the development of these SR-SIM platforms is completed, he will characterize the structure and dynamics of fenestrated cells from isolated mice, rats and humans. To obtain even higher spatial resolution below 100 nm, he will also attempt to implement nonlinear SIM image reconstruction.

In July 2022, Jakub joined the Vascular Biology Research Group (VBRG), Department of Medical Biology, UiT The Arctic University of Norway where he works as a postdoctoral research fellow. His current research involves developing super-resolution microscopy methods for the study of liver sinusoidal endothelial cells (LSECs).

Participation on projects

• The Research council of Norway, No. 325446, project “Pack a pill in a PACA: PACA nanomedicines for targeting age-related changes in liver endothelium to prevent age-related diseases” (2022-2026)
• European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement, No. 766181, project “DeLIVER” (2018-2022)
• Ministry of Industry and Trade, No. FV20548, “Videodetection of persons in tunnels in real-time” (2017-2018)
• Czech Science Foundation, No. GA17-05840S, “Multicriteria optimization of shift-variant imaging system models”
• Student grant agency of CTU in Prague, No. SGS18/141/OHK3/2T/13, “Analysis and advanced algorithms for ultra-wide imaging systems”
• Student grant agency of CTU in Prague, No. SGS16/167/OHK3/2T/13, “Algorithms for video-sequenced live cell super-resolution microscopy”

List of Publications

2021

• J. Pospíšil, G. Wiebusch, K. Fliegel, M. Klíma, T. Huser, “Highly compact and cost-effective 2-beam super-resolution structured illumination microscope based on all-fiber optic components,” Optics Express. 2021, 29(8), 11833-11844. ISSN 1094-4087.
• C. Pilger, J. Pospíšil, M. Müller, M. Ruoff, M. Schütte, H. Spiecker, T. Huser, “Super-resolution fluorescence microscopy by line-scanning with an unmodified two-photon microscope,” Phil. Trans. R. Soc. A. 2021, 379(20200300), 1–11. ISSN 1364-503X.

2019

• J. Pospíšil, T. Lukeš, J. Bendesky, K. Fliegel, K. Spendier, G. M. Hagen, “Imaging tissues and cells beyond the diffraction limit with structured illumination microscopy and Bayesian image reconstruction,” GigaScience. 2019, 8(1), 1-12. ISSN 2047-217X.

2018

• T. Lukeš, J. Pospíšil, K. Fliegel, T. Lasser, G. M. Hagen, “Quantitative super-resolution single molecule microscopy dataset of YFP-tagged growth factor receptors,” GigaScience. 2018, 7(3), 1-10. ISSN 2047-217X.
• P. Janout, J. Pospíšil, K. Fliegel, M. Klíma, P. Páta, “Interpolation methods for the improvement of the point spread function estimation,” In: 2018 28th International Conference Radioelektronika. IEEE (Institute of Electrical and Electronics Engineers), 2018. ISBN 978-1-5386-2485-2.
• J. Pospíšil, K. Fliegel, J. Švihlík, M. Klíma, “Comparison of resolution estimation methods in optical microscopy,” In: Proceedings Volume 10752 – Applications of Digital Image Processing XLI. Bellingham: SPIE, 2018. SPIE PROCEEDINGS. vol. 10752. ISSN 1996-756X. ISBN 9781510620766.
• A. Willème, S. Mahmoudpour, I. Viola, K. Fliegel, J. Pospíšil, T. Ebrahimi, P. Schelkens, A. Descampe, et al. “Overview of the JPEG XS core coding system subjective evaluations,” In: Proceedings Volume 10752 – Applications of Digital Image Processing XLI. Bellingham: SPIE, 2018. p. 107521M-1-107521M-12. SPIE PROCEEDINGS. vol. 10752. ISSN 0277-786X. ISBN 9781510620759.

2017

• J. Pospíšil, K. Fliegel, M. Klíma, “Phase estimation of illumination pattern in structured illumination microscopy,” in 2017 27th International Conference Radioelektronika (RADIOELEKTRONIKA). Brno: VUT v Brně, FEKT, Ústav radioelektroniky, 2017. pp. 174-177. ISBN 978-1-5090-4591-4.
• J. Pospíšil, K. Fliegel, M. Klíma, “Analysis of image reconstruction artifacts in structured illumination microscopy,” in Applications of Digital Image Processing XL. Bellingham: SPIE, 2017. pp. 1039632-1-1039632-13. Proceedings of SPIE. ISSN 0277-786X. ISBN 978-1-5106-1249-5.
• J. Pospíšil, K. Fliegel, M. Klíma, “Assessing resolution in live cell structured illumination microscopy“, in Photonics, Devices, and Systems VII. Bellingham: SPIE, 2017. pp. 106030D-1-106030D-7. Proceedings of SPIE. vol. 10603. ISSN 0277-786X. ISBN 978-1-5106-1702-5.

2015

• M. Novotný, J. Pospíšil, R. Čmejla, J. Rusz, “Automatic detection of voice onset time in dysarthric speech“, in 2015 IEEE International Conference on Acoustics, Speech, and Signal Processing – Proceedings. New Jersey: IEEE Signal Processing Society, 2015. p. 4340-4344. ISSN 1520-6149. ISBN 978-1-4673-6997-8.