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

dc.contributor.coauthorAydın, Musa
dc.contributor.coauthorDoğan, Buket
dc.contributor.departmentDepartment of Electrical and Electronics Engineering
dc.contributor.departmentDepartment of Molecular Biology and Genetics
dc.contributor.departmentDepartment of Physics
dc.contributor.departmentGraduate School of Sciences and Engineering
dc.contributor.departmentKUTTAM (Koç University Research Center for Translational Medicine)
dc.contributor.departmentSchool of Medicine
dc.contributor.kuauthorKaralar, Elif Nur Fırat
dc.contributor.kuauthorKiraz, Alper
dc.contributor.kuauthorMorova, Berna
dc.contributor.kuauthorÖzgönül, Ekin
dc.contributor.kuauthorUysallı, Yiğit
dc.contributor.schoolcollegeinstituteCollege of Engineering
dc.contributor.schoolcollegeinstituteCollege of Sciences
dc.contributor.schoolcollegeinstituteGRADUATE SCHOOL OF SCIENCES AND ENGINEERING
dc.contributor.schoolcollegeinstituteResearch Center
dc.contributor.schoolcollegeinstituteSCHOOL OF MEDICINE
dc.date.accessioned2024-11-09T13:09:17Z
dc.date.issued2022
dc.description.abstractWhen 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 superresolution 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.
dc.description.fulltextYES
dc.description.indexedbyWOS
dc.description.indexedbyScopus
dc.description.indexedbyPubMed
dc.description.issue9
dc.description.openaccessYES
dc.description.publisherscopeInternational
dc.description.sponsoredbyTubitakEuTÜBİTAK
dc.description.sponsorshipScientific and Technological Research Council of Turkey (TÜBİTAK)
dc.description.sponsorshipMarmara University Scientific Research Projects Coordination Unit
dc.description.sponsorshipTurkish Academy of Sciences (TÜBA)
dc.description.versionPublisher version
dc.description.volume17
dc.identifier.doi10.1371/journal.pone.0273990
dc.identifier.embargoNO
dc.identifier.filenameinventorynoIR03270
dc.identifier.issn1932-6203
dc.identifier.quartileQ2
dc.identifier.scopus2-s2.0-85137696430
dc.identifier.urihttps://doi.org/10.1371/journal.pone.0273990
dc.identifier.wos892051000079
dc.keywordsAlgorithms
dc.keywordsImage processing, Computer-assisted
dc.keywordsLighting
dc.keywordsMicroscopy
dc.keywordsSoftware
dc.language.isoeng
dc.publisherPublic Library of Science
dc.relation.grantno118F529
dc.relation.grantnoFEN-C-DRP-110618
dc.relation.ispartofPlos One
dc.relation.urihttp://cdm21054.contentdm.oclc.org/cdm/ref/collection/IR/id/10830
dc.subjectScience and technology
dc.titleAn LED-Based structured illumination microscope using a digital micromirror device and GPU accelerated image reconstruction
dc.typeJournal Article
dspace.entity.typePublication
local.contributor.kuauthorKiraz, Alper
local.contributor.kuauthorKaralar, Elif Nur Fırat
local.contributor.kuauthorMorova, Berna
local.contributor.kuauthorUysallı, Yiğit
local.contributor.kuauthorÖzgönül, Ekin
local.publication.orgunit1GRADUATE SCHOOL OF SCIENCES AND ENGINEERING
local.publication.orgunit1College of Engineering
local.publication.orgunit1SCHOOL OF MEDICINE
local.publication.orgunit1College of Sciences
local.publication.orgunit1Research Center
local.publication.orgunit2KUTTAM (Koç University Research Center for Translational Medicine)
local.publication.orgunit2Department of Physics
local.publication.orgunit2Department of Electrical and Electronics Engineering
local.publication.orgunit2Department of Molecular Biology and Genetics
local.publication.orgunit2School of Medicine
local.publication.orgunit2Graduate School of Sciences and Engineering
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