An LED-Based structured illumination microscope using a digital micromirror device and GPU accelerated image reconstruction

Musa Aydın; Yiğit Uysallı; Ekin Özgönül; Berna Morova; Fatmanur Tiryaki; Elif Nur Firat-Karalar; Buket Doğan; Alper Kiraz

doi:10.1371/journal.pone.0273990

An LED-Based structured illumination microscope using a digital micromirror device and GPU accelerated image reconstruction

PLoS One. 2022 Sep 9;17(9):e0273990. doi: 10.1371/journal.pone.0273990. eCollection 2022.

Authors

Musa Aydın¹, Yiğit Uysallı², Ekin Özgönül², Berna Morova^{2

3}, Fatmanur Tiryaki⁴, Elif Nur Firat-Karalar^{4

5}, Buket Doğan⁶, Alper Kiraz^{2

3

7}

Affiliations

¹ Department of Computer Engineering, Fatih Sultan Mehmet Vakif University, Istanbul, Turkey.
² Department of Physics, Koç University, Istanbul, Turkey.
³ KUTTAM, Koç University Research Center for Translational Medicine, Istanbul, Turkey.
⁴ Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey.
⁵ School of Medicine, Koç University, Istanbul, Turkey.
⁶ Department of Computer Engineering, Marmara University, Istanbul, Turkey.
⁷ Department of Electrical and Electronics Engineering, Koç University, Istanbul, Turkey.

Abstract

When combined with computational approaches, fluorescence imaging becomes one of the most powerful tools in biomedical research. It is possible to achieve resolution figures beyond the diffraction limit, and improve the performance and flexibility of high-resolution imaging systems with techniques such as structured illumination microscopy (SIM) reconstruction. In this study, the hardware and software implementation of an LED-based super-resolution imaging system using SIM employing GPU accelerated parallel image reconstruction is presented. The sample is illuminated with two-dimensional sinusoidal patterns with various orientations and lateral phase shifts generated using a digital micromirror device (DMD). SIM reconstruction is carried out in frequency space using parallel CUDA kernel functions. Furthermore, a general purpose toolbox for the parallel image reconstruction algorithm and an infrastructure that allows all users to perform parallel operations on images without developing any CUDA kernel code is presented. The developed image reconstruction algorithm was run separately on a CPU and a GPU. Two different SIM reconstruction algorithms have been developed for the CPU as mono-thread CPU algorithm and multi-thread OpenMP CPU algorithm. SIM reconstruction of 1024 × 1024 px images was achieved in 1.49 s using GPU computation, indicating an enhancement by ∼28 and ∼20 in computation time when compared with mono-thread CPU computation and multi-thread OpenMP CPU computation, respectively.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Image Processing, Computer-Assisted / methods
Lighting*
Microscopy*
Software

Grants and funding

Funded studies This work was supported by Marmara University Scientific Research Projects Coordination Unit (Project Number: FEN-C-DRP-110618-) and TÜBİTAK (Grant No. 118F529). A. Kiraz acknowledges partial support from the Turkish Academy of Sciences (TÜBA). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.