Dr. Guy Hagen, Research Associate,
University of Colorado, Colorado Springs
Dr. Guy Hagen, Research Associate from the University of Colorado, Colorado Springs creates high performance image reconstruction methods and open-source software to process super-resolution microscopy data. In 2014 Dr. Hagen released ThunderSTORM, an ImageJ plug-in for automated processing of photo-activated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM) data.1 In 2016, he introduced SIMToolbox, a MATLAB toolbox for processing SIM data. It has the flexibility to process 2D and 3D images, including both optical sectioning and super-resolution applications, and can be used on data acquired from commercial systems.2 SIMToolbox also includes maximum a posteriori probability estimation (MAP-SIM), a super-resolution restoration method that suppresses out of focus light, improves spatial resolution, and reduces reconstruction artifacts.3 Dr. Hagen is currently developing live cell imaging using SIM, and is continuing to develop data analysis methods for super-resolution microscopy.
SIM is a widefield fluorescence technique that uses illumination patterns with high spatial frequency to illuminate samples. Algorithms applied to a combination of images taken with different phases and orientation of the illumination pattern are used to reconstruct a high-resolution image. Reconstruction of images routinely requires many images per focal plane. Fluorescent signals need to withstand photobleaching and the acquisition rate must be fast enough to observe live cell dynamics.
Imaging twice as fast with the Prime 95B [Scientific CMOS camera] is a great advantage. The reduction of pixel-to-pixel variance and the reduction of visible column structure in the camera greatly improves our results.
- Ovesný, M., Krížek, P., Borkovec, J., Švindrych, Z., and Hagen, G. M. ThunderSTORM: a comprehensive ImageJ plugin for PALM and STORM data analysis and super-resolution imaging. Bioinformatics (2014), doi: 10.1093/bioinformatics/btu202
- Krížek P, LukeŠ T, Ovesný M, Fliegel K, Hagen GM. (2016). SIMToolbox: a MATLAB toolbox for structured illumination fluorescence microscopy. Bioinformatics (2016), doi: 10.1093/bioinformatics/btv576
- LukeŠ T, Krížek P, Švindrych Z, Benda J, Ovesný M, Fliegel K, Klíma M, Hagen GM. Three-dimensional super resolution structured illumination microscopy with maximum a posteriori probability image estimation. Opt Express (2014), doi: 10.1364/OE.22.029805