Open-source microscope add-on for structured illumination microscopy
Status PubMed-not-MEDLINE Jazyk angličtina Země Anglie, Velká Británie Médium electronic
Typ dokumentu časopisecké články
Grantová podpora
18330.1 PFNM-NM
Kommission für Technologie und Innovation (Commission for Technology and Innovation)
205320_152675
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)
ERC-2017-CoG; InCell.),
EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
PubMed
38378733
PubMed Central
PMC10879112
DOI
10.1038/s41467-024-45567-7
PII: 10.1038/s41467-024-45567-7
Knihovny.cz E-zdroje
- Publikační typ
- časopisecké články MeSH
Super-resolution techniques expand the abilities of researchers who have the knowledge and resources to either build or purchase a system. This excludes the part of the research community without these capabilities. Here we introduce the openSIM add-on to upgrade existing optical microscopes to Structured Illumination super-resolution Microscopes (SIM). The openSIM is an open-hardware system, designed and documented to be easily duplicated by other laboratories, making super-resolution modality accessible to facilitate innovative research. The add-on approach gives a performance improvement for pre-existing lab equipment without the need to build a completely new system.
BioFrontiers Center University of Colorado Colorado Springs Colorado Springs CO USA
Center for Innovation in Global Health Stanford University Stanford CA USA
Department of Medical Biology UiT The Arctic University of Norway Tromsø Norway
Faculty of Electrical Engineering Czech Technical University Prague Prague Czech Republic
School of Engineering Swiss Federal Institute of Technology Lausanne Switzerland
School of Life Sciences Swiss Federal Institute of Technology Lausanne Switzerland
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Schermelleh L, et al. Super-resolution microscopy demystified. Nat. Cell Biol. 2019;21:72–84. doi: 10.1038/s41556-018-0251-8. PubMed DOI
Brown JWP, et al. Single-molecule detection on a portable 3D-printed microscope. Nat. Commun. 2019;10:5662. doi: 10.1038/s41467-019-13617-0. PubMed DOI PMC
Gustafsson MGL. Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J. Microsc. 2000;198:82–87. doi: 10.1046/j.1365-2818.2000.00710.x. PubMed DOI
Coltharp C, Xiao J. Superresolution microscopy for microbiology. Cell. Microbiol. 2012;14:1808–1818. doi: 10.1111/cmi.12024. PubMed DOI PMC
Shao L, Kner P, Rego EH, Gustafsson MGL. Super-resolution 3D microscopy of live whole cells using structured illumination. Nat. Methods. 2011;8:1044–1046. doi: 10.1038/nmeth.1734. PubMed DOI
Demmerle J, et al. Strategic and practical guidelines for successful structured illumination microscopy. Nat. Protoc. 2017;12:988–1010. doi: 10.1038/nprot.2017.019. PubMed DOI
Hell SW, Wichmann J. Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy. Opt. Lett. 1994;19:780. doi: 10.1364/OL.19.000780. PubMed DOI
Betzig E, et al. Imaging intracellular fluorescent proteins at nanometer resolution. Science. 2006;313:1642–1645. doi: 10.1126/science.1127344. PubMed DOI
Rust MJ, Bates M, Zhuang X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM) Nat. Methods. 2006;3:793–796. doi: 10.1038/nmeth929. PubMed DOI PMC
Marx V. Microscopy: OpenSPIM 2.0. Nat. Methods. 2016;13:979–982. doi: 10.1038/nmeth.4070. PubMed DOI
Girstmair J, et al. Light-sheet microscopy for everyone? Experience of building an OpenSPIM to study flatworm development. BMC Developmental Biol. 2016;16:22. doi: 10.1186/s12861-016-0122-0. PubMed DOI PMC
Pitrone PG, et al. OpenSPIM: an open-access light-sheet microscopy platform. Nat. Methods. 2013;10:598–599. doi: 10.1038/nmeth.2507. PubMed DOI PMC
Sharkey JP, Foo DCW, Kabla A, Baumberg JJ, Bowman RW. A one-piece 3D printed flexure translation stage for open-source microscopy. Rev. Sci. Instrum. 2016;87:025104. doi: 10.1063/1.4941068. PubMed DOI
Diederich, B. et al. UC2 – A 3D-printed General-Purpose Optical Toolbox for Microscopic Imaging. in Imaging and Applied Optics ITh3B.5 (2019).
Martens KJA, et al. Visualisation of dCas9 target search in vivo using an open-microscopy framework. Nat. Commun. 2019;10:3552. doi: 10.1038/s41467-019-11514-0. PubMed DOI PMC
Hannebelle, M. T. M. & Raeth, E. openSIM webpage. Open-source microscope add-on for structured illumination microscopy. https://opensim.notion.site/ (2024). PubMed
Kner P, Chhun BB, Griffis ER, Winoto L, Gustafsson MGL. Super-resolution video microscopy of live cells by structured illumination. Nat. Methods. 2009;6:339–342. doi: 10.1038/nmeth.1324. PubMed DOI PMC
Förster R, et al. Simple structured illumination microscope setup with high acquisition speed by using a spatial light modulator. Opt. Express. 2014;22:20663–20677. doi: 10.1364/OE.22.020663. PubMed DOI
Lu-Walther H-W, et al. fastSIM: a practical implementation of fast structured illumination microscopy. Methods Appl. Fluoresc. 2015;3:014001. doi: 10.1088/2050-6120/3/1/014001. PubMed DOI
Fiolka R, Shao L, Rego EH, Davidson MW, Gustafsson MGL. Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination. Proc. Natl Acad. Sci. 2012;109:5311–5315. doi: 10.1073/pnas.1119262109. PubMed DOI PMC
Křížek P, Lukeš T, Ovesný M, Fliegel K, Hagen GM. SIMToolbox: a MATLAB toolbox for structured illumination fluorescence microscopy. Bioinformatics. 2016;32:318–320. doi: 10.1093/bioinformatics/btv576. PubMed DOI
Leitao SM, et al. Time-resolved scanning ion conductance microscopy for three-dimensional tracking of nanoscale cell surface dynamics. ACS Nano. 2021;15:17613–17622. doi: 10.1021/acsnano.1c05202. PubMed DOI PMC
Gustafsson MGL, et al. Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination. Biophys. J. 2008;94:4957–4970. doi: 10.1529/biophysj.107.120345. PubMed DOI PMC
Křížek P, Raška I, Hagen GM. Flexible structured illumination microscope with a programmable illumination array. Opt. Express. 2012;20:24585. doi: 10.1364/OE.20.024585. PubMed DOI
Lukeš T, et al. Three-dimensional super-resolution structured illumination microscopy with maximum a posteriori probability image estimation. Opt. Express. 2014;22:29805. doi: 10.1364/OE.22.029805. PubMed DOI
Pospíšil J, et al. Imaging tissues and cells beyond the diffraction limit with structured illumination microscopy and Bayesian image reconstruction. GigaScience. 2019;8:giy126. doi: 10.1093/gigascience/giy126. PubMed DOI PMC
Schlichenmeyer TC, Wang M, Elfer KN, Brown JQ. Video-rate structured illumination microscopy for high-throughput imaging of large tissue areas. Biomed. Opt. Express, BOE. 2014;5:366–377. doi: 10.1364/BOE.5.000366. PubMed DOI PMC
Heintzmann, R. Structured illumination methods. in Handbook of Biological Confocal Microscopy 265–279 (Springer, 2006).
Rego E, Shao L. Practical structured illumination microscopy. Methods Mol. Biol. (Clifton, N. J.) 2015;1251:175–192. doi: 10.1007/978-1-4939-2080-8_10. PubMed DOI
Křížek, P. & Hagen, G. Spatial light modulators in fluorescence microscopy. In Microscopy: Science, Technology, Applications and Education 1366–1377 (2010).
Heintzmann, R. & Cremer, C. Laterally modulated excitation microscopy: Improvement of resolution by using a diffraction grating. Proc. SPIE3568, (1999).
Goodmann, J. W. Frequency Analysis of Optical Imaging Systems. In Introduction to Fourrier Optics (1996).
Sandmeyer A, et al. Cost-effective live cell structured illumination microscopy with video-rate imaging. ACS Photonics. 2021;8:1639–1648. doi: 10.1021/acsphotonics.0c01937. DOI
Dan D, et al. DMD-based LED-illumination Super-resolution and optical sectioning microscopy. Sci. Rep. 2013;3:1116. doi: 10.1038/srep01116. PubMed DOI PMC
Li, M. et al. Structured illumination microscopy using digital micromirror device and coherent light source. in Optics in Health Care and Biomedical Optics X vol. 11553 1155313 (SPIE, 2020).
Aydın M, et al. An LED-Based structured illumination microscope using a digital micromirror device and GPU accelerated image reconstruction. PLOS ONE. 2022;17:e0273990. doi: 10.1371/journal.pone.0273990. PubMed DOI PMC
Neil MaA, Juškaitis R, Wilson T. Method of obtaining optical sectioning by using structured light in a conventional microscope. Opt. Lett., OL. 1997;22:1905–1907. doi: 10.1364/OL.22.001905. PubMed DOI
Chen X, et al. Superresolution structured illumination microscopy reconstruction algorithms: a review. Light Sci. Appl. 2023;12:172. doi: 10.1038/s41377-023-01204-4. PubMed DOI PMC
Yin X, et al. Niche-independent high-purity cultures of Lgr5+ intestinal stem cells and their progeny. Nat. Methods. 2014;11:106–112. doi: 10.1038/nmeth.2737. PubMed DOI PMC
Gjorevski N, et al. Designer matrices for intestinal stem cell and organoid culture. Nature. 2016;539:560–564. doi: 10.1038/nature20168. PubMed DOI
Kimmel CB, Ballard WW, Kimmel SR, Ullmann B, Schilling TF. Stages of embryonic development of the zebrafish. Dev. Dyn. 1995;203:253–310. doi: 10.1002/aja.1002030302. PubMed DOI
Herrgen L, Schröter C, Bajard L, Oates AC. Multiple embryo time-lapse imaging of zebrafish development. Methods Mol. Biol. 2009;546:243–254. doi: 10.1007/978-1-60327-977-2_15. PubMed DOI
Hannebelle, M. T. M. & Raeth, E. openSIM Zenodo repository. Open-source microscope add-on for structured illumination microscopy10.5281/zenodo.10067217 (2024). PubMed
Schindelin J, et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods. 2012;9:676–682. PubMed PMC
Barthel, K. U. 3D-Data Representation with Image J. (2006).
Hannebelle, M. T. M. & Raeth, E. openSIM GitHub repository. Open-source microscope add-on for structured illumination microscopy10.5281/zenodo.10470689 (2024). PubMed