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Olevsko I, Szederkenyi K, Corridon J, Au A, Delhomme B, Bastien T, Fernandes J, Yip C, Oheim M, Salomon A. A simple, inexpensive and multi-scale 3-D fluorescent test sample for optical sectioning microscopies. Microsc Res Tech 2021; 84:2625-2635. [PMID: 34008289 DOI: 10.1002/jemt.23813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/05/2021] [Accepted: 04/27/2021] [Indexed: 11/11/2022]
Abstract
Fluorescence standards allow for quality control and for the comparison of data sets across instruments and laboratories in applications of quantitative fluorescence. For example, users of microscopy core facilities can expect a homogenous and time-invariant illumination and an uniform detection sensitivity, which are prerequisites for imaging analysis, tracking or fluorimetric pH or Ca2+ -concentration measurements. Similarly, confirming the three-dimensional (3-D) resolution of optical sectioning microscopes calls for a regular calibration with a standardized point source. The test samples required for such measurements are typically different ones, they are often expensive and they depend much on the very microscope technique used. Similarly, the ever-increasing choice among microscope techniques and geometries increases the demand for comparison across instruments. Here, we advocate and demonstrate the multiple uses of a surprisingly versatile and simple 3-D test sample that can complement existing and much more expensive calibration samples: commercial tissue paper labeled with a fluorescent highlighter pen. We provide relevant sample characteristics and show examples ranging from the sub-μm to cm scale, acquired on epifluorescence, confocal, image scanning, two-photon (2P) and light-sheet microscopes.
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Affiliation(s)
- Ilya Olevsko
- Department of Chemistry, Bar-Ilan University, Institute of Nanotechnology and Advanced Materials (BINA), Ramat-Gan, Israel
| | - Kaitlin Szederkenyi
- Université de Paris, CNRS, SPPIN - Saints-Pères Paris Institute for the Neurosciences, Paris, France.,University of Toronto, Donnelly Centre for Cellular & Biomolecular Research, Toronto, Ontario, Canada
| | - Jennifer Corridon
- Université de Paris, CNRS UMS 2009, INSERM US 36, BioMedTech Facilities, Paris, France.,Université de Paris, Service Commun de Microscopie (SCM), Paris, France
| | - Aaron Au
- University of Toronto, Donnelly Centre for Cellular & Biomolecular Research, Toronto, Ontario, Canada
| | - Brigitte Delhomme
- Université de Paris, CNRS, SPPIN - Saints-Pères Paris Institute for the Neurosciences, Paris, France
| | - Thierry Bastien
- Université de Paris, CNRS UMS 2009, INSERM US 36, BioMedTech Facilities, Paris, France.,Université de Paris, Plateforme de Prototypage, Paris, France
| | - Julien Fernandes
- UTechS Photonic BioImaging, C2RT, Institut Pasteur, Paris, France
| | - Christopher Yip
- University of Toronto, Donnelly Centre for Cellular & Biomolecular Research, Toronto, Ontario, Canada
| | - Martin Oheim
- Université de Paris, CNRS, SPPIN - Saints-Pères Paris Institute for the Neurosciences, Paris, France.,Université de Paris, CNRS UMS 2009, INSERM US 36, BioMedTech Facilities, Paris, France.,Université de Paris, Service Commun de Microscopie (SCM), Paris, France
| | - Adi Salomon
- Department of Chemistry, Bar-Ilan University, Institute of Nanotechnology and Advanced Materials (BINA), Ramat-Gan, Israel.,Université de Paris, CNRS, SPPIN - Saints-Pères Paris Institute for the Neurosciences, Paris, France
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Lam F, Cladière D, Guillaume C, Wassmann K, Bolte S. Super-resolution for everybody: An image processing workflow to obtain high-resolution images with a standard confocal microscope. Methods 2016; 115:17-27. [PMID: 27826080 DOI: 10.1016/j.ymeth.2016.11.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 11/29/2022] Open
Abstract
In the presented work we aimed at improving confocal imaging to obtain highest possible resolution in thick biological samples, such as the mouse oocyte. We therefore developed an image processing workflow that allows improving the lateral and axial resolution of a standard confocal microscope. Our workflow comprises refractive index matching, the optimization of microscope hardware parameters and image restoration by deconvolution. We compare two different deconvolution algorithms, evaluate the necessity of denoising and establish the optimal image restoration procedure. We validate our workflow by imaging sub resolution fluorescent beads and measuring the maximum lateral and axial resolution of the confocal system. Subsequently, we apply the parameters to the imaging and data restoration of fluorescently labelled meiotic spindles of mouse oocytes. We measure a resolution increase of approximately 2-fold in the lateral and 3-fold in the axial direction throughout a depth of 60μm. This demonstrates that with our optimized workflow we reach a resolution that is comparable to 3D-SIM-imaging, but with better depth penetration for confocal images of beads and the biological sample.
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Affiliation(s)
- France Lam
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Core Facilities - Institut de Biologie Paris Seine (IBPS), 75005 Paris, France
| | - Damien Cladière
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratory of Developmental Biology - Institut de Biologie Paris Seine (IBPS), 75005 Paris, France
| | - Cyndélia Guillaume
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Core Facilities - Institut de Biologie Paris Seine (IBPS), 75005 Paris, France
| | - Katja Wassmann
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratory of Developmental Biology - Institut de Biologie Paris Seine (IBPS), 75005 Paris, France
| | - Susanne Bolte
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Core Facilities - Institut de Biologie Paris Seine (IBPS), 75005 Paris, France.
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Sun H, Aidun CK, Egertsdotter U. Possible effect from shear stress on maturation of somatic embryos of Norway spruce (Picea abies). Biotechnol Bioeng 2011; 108:1089-99. [PMID: 21449024 DOI: 10.1002/bit.23040] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Revised: 12/01/2010] [Accepted: 12/09/2010] [Indexed: 01/07/2023]
Abstract
Somatic embryogenesis is the only method with the potential for industrial scale clonal propagation of conifers. Implementation of the method has so far been hampered by the extensive manual labor required for development of the somatic embryos into plants. The utilization of bioreactors is limited since the somatic embryos will not mature and germinate under liquid culture conditions. The negative effect on mature embryo yields from liquid culture conditions has been previously described. We have described the negative effects of shear stress on the development of early stage somatic embryos (proembryogenic masses; PEMs) at shear stresses of 0.086 and 0.14 N/m(2). In the present study, additional flow rates were studied to determine the effects of shear stress at lower rates resembling shear stress in a suspension culture flask. The results showed that shear stress at 0.009, 0.014, and 0.029 N/m(2) inhibited the PEM expansions comparing with the control group without shear stress. This study also provides validation for the cross-correlation method previously developed to show the effect of shear stress on early stage embryo suspensor cell formation and polarization. Furthermore, shear stress was shown to positively affect the uptake of water into the cells. The results indicate that the plasmolyzing effect from macromolecules added to liquid culture medium to stimulate maturation of the embryos are affected by liquid culture conditions and thus can affect the conversion of PEMs into mature somatic embryos.
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Affiliation(s)
- Hong Sun
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia
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De Mey JR, Kessler P, Dompierre J, Cordelières FP, Dieterlen A, Vonesch JL, Sibarita JB. Fast 4D Microscopy. Methods Cell Biol 2008; 85:83-112. [PMID: 18155460 DOI: 10.1016/s0091-679x(08)85005-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Many cellular processes involve fast movements of weakly labeled cellular structures in all directions, which should be recorded in 3D time-lapse microscopy (4D microscopy). This chapter introduces fast 4D imaging, which is used for sampling the cell's volume by collecting focal planes in time-lapse mode as rapidly as possible, without perturbing the sample by strong illumination. The final images should contain sufficient contrast allowing for the isolation of structures of interest by segmentation and the analysis of their intracellular movements by tracking. Because they are the most sensitive, systems using wide-field microscopy and deconvolution techniques are discussed in greater depth. We discuss important points to consider, including system components and multifunctionality, spatial resolution and sampling conditions, and mechanical and optical stability and how to test for it. We consider image formation using high numerical aperture optics and discuss the influence of optical blur and noise on image formation of living cells. Spherical aberrations, their consequences for axial image quality, and their impact on the success of deconvolution of low intensity image stacks are explained in detail. Simple protocols for acquiring and treating point spread functions (PSFs) and live cells are provided. A compromise for counteracting spherical aberration involving the use of a kit of immersion oils for PSF and cell acquisition is illustrated. Recommendations for evaluating acquisition conditions and deconvolution parameters are given. Finally, we discuss future developments based on the use of adaptive optics which will push back many of today's limits.
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Affiliation(s)
- J R De Mey
- Ecole Supérieure de Biotechnologie de Strasbourg, UMR-7175 CNRS/Université Louis Pasteur (Strasbourg I), BP10413, 67412 IllKIRCH Cedex, France
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Lehmussola A, Ruusuvuori P, Selinummi J, Huttunen H, Yli-Harja O. Computational framework for simulating fluorescence microscope images with cell populations. IEEE TRANSACTIONS ON MEDICAL IMAGING 2007; 26:1010-6. [PMID: 17649914 DOI: 10.1109/tmi.2007.896925] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Fluorescence microscopy combined with digital imaging constructs a basic platform for numerous biomedical studies in the field of cellular imaging. As the studies relying on analysis of digital images have become popular, the validation of image processing methods used in automated image cytometry has become an important topic. Especially, the need for efficient validation has arisen from emerging high-throughput microscopy systems where manual validation is impractical. We present a simulation platform for generating synthetic images of fluorescence-stained cell populations with realistic properties. Moreover, we show that the synthetic images enable the validation of analysis methods for automated image cytometry and comparison of their performance. Finally, we suggest additional usage scenarios for the simulator. The presented simulation framework, with several user-controllable parameters, forms a versatile tool for many kinds of validation tasks, and is freely available at http://www.cs.tut.fi/sgn/csb/simcep.
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Affiliation(s)
- Antti Lehmussola
- Institute of Signal Processing, Tampere University of Technology, FI-33101 Tampere, Finland
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