3
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Senft RA, Diaz-Rohrer B, Colarusso P, Swift L, Jamali N, Jambor H, Pengo T, Brideau C, Llopis PM, Uhlmann V, Kirk J, Gonzales KA, Bankhead P, Evans EL, Eliceiri KW, Cimini BA. A biologist's guide to planning and performing quantitative bioimaging experiments. PLoS Biol 2023; 21:e3002167. [PMID: 37368874 PMCID: PMC10298797 DOI: 10.1371/journal.pbio.3002167] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023] Open
Abstract
Technological advancements in biology and microscopy have empowered a transition from bioimaging as an observational method to a quantitative one. However, as biologists are adopting quantitative bioimaging and these experiments become more complex, researchers need additional expertise to carry out this work in a rigorous and reproducible manner. This Essay provides a navigational guide for experimental biologists to aid understanding of quantitative bioimaging from sample preparation through to image acquisition, image analysis, and data interpretation. We discuss the interconnectedness of these steps, and for each, we provide general recommendations, key questions to consider, and links to high-quality open-access resources for further learning. This synthesis of information will empower biologists to plan and execute rigorous quantitative bioimaging experiments efficiently.
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Affiliation(s)
- Rebecca A. Senft
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Barbara Diaz-Rohrer
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Pina Colarusso
- Live Cell Imaging Laboratory, University of Calgary, Calgary, Alberta, Canada
| | - Lucy Swift
- Live Cell Imaging Laboratory, University of Calgary, Calgary, Alberta, Canada
| | - Nasim Jamali
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Helena Jambor
- National Center for Tumor Diseases, University Cancer Center, NCT-UCC, Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden, Dresden, Germany
| | - Thomas Pengo
- Informatics Institute, University of Minnesota Twin Cities, Minneapolis, Minnesota, United States of America
| | - Craig Brideau
- Live Cell Imaging Laboratory, University of Calgary, Calgary, Alberta, Canada
| | - Paula Montero Llopis
- MicRoN Core, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Virginie Uhlmann
- European Bioinformatic Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Jason Kirk
- Optical Imaging & Vital Microscopy Core, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kevin Andrew Gonzales
- Mammalian Cell Biology and Development, Rockefeller University, New York, New York, United States of America
| | - Peter Bankhead
- Edinburgh Pathology, Centre for Genomic and Experimental Medicine, and CRUK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Edward L. Evans
- Morgridge Institute and University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kevin W. Eliceiri
- Morgridge Institute and University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Beth A. Cimini
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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5
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Luo Y, Chu CH, Vyas S, Kuo HY, Chia YH, Chen MK, Shi X, Tanaka T, Misawa H, Huang YY, Tsai DP. Varifocal Metalens for Optical Sectioning Fluorescence Microscopy. NANO LETTERS 2021; 21:5133-5142. [PMID: 34097419 DOI: 10.1021/acs.nanolett.1c01114] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fluorescence microscopy with optical sectioning capabilities is extensively utilized in biological research to obtain three-dimensional structural images of volumetric samples. Tunable lenses have been applied in microscopy for axial scanning to acquire multiplane images. However, images acquired by conventional tunable lenses suffer from spherical aberration and distortions. Here, we design, fabricate, and implement a dielectric Moiré metalens for fluorescence imaging. The Moiré metalens consists of two complementary phase metasurfaces, with variable focal length, ranging from ∼10 to ∼125 mm at 532 nm by tuning mutual angles. In addition, a telecentric configuration using the Moiré metalens is designed for high-contrast multiplane fluorescence imaging. The performance of our system is evaluated by optically sectioned images obtained from HiLo illumination of fluorescently labeled beads, as well as ex vivo mice intestine tissue samples. The compact design of the varifocal metalens may find important applications in fluorescence microscopy and endoscopy for clinical purposes.
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Affiliation(s)
- Yuan Luo
- Institute of Medical Device and Imaging, National Taiwan University, Taipei 10051, Taiwan
- YongLin Institute of Health, National Taiwan University, Taipei 10672, Taiwan
- Institute of Biomedical Engineering, National Taiwan University, Taipei 10051, Taiwan
| | - Cheng Hung Chu
- Institute of Medical Device and Imaging, National Taiwan University, Taipei 10051, Taiwan
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
- Innovative Photon Manipulation Research Team, RIKEN Center for Advanced Photonics, Saitama 351-0198, Japan
| | - Sunil Vyas
- Institute of Medical Device and Imaging, National Taiwan University, Taipei 10051, Taiwan
| | - Hsin Yu Kuo
- Institute of Medical Device and Imaging, National Taiwan University, Taipei 10051, Taiwan
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Yu Hsin Chia
- Institute of Medical Device and Imaging, National Taiwan University, Taipei 10051, Taiwan
- Institute of Biomedical Engineering, National Taiwan University, Taipei 10051, Taiwan
| | - Mu Ku Chen
- Department of Electronic and Information Engineering, The Hong Kong Polytechnic University, Kowloon 999077, Hong Kong
| | - Xu Shi
- Research Institute for Electronic Science Hokkaido University, Sapporo 001-0021, Japan
| | - Takuo Tanaka
- Innovative Photon Manipulation Research Team, RIKEN Center for Advanced Photonics, Saitama 351-0198, Japan
- Metamaterial Laboratory, RIKEN Cluster for Pioneering Research, Saitama 351-0198, Japan
- Institute of Post-LED Photonics, Tokushima University, Tokushima 770-8506, Japan
| | - Hiroaki Misawa
- Research Institute for Electronic Science Hokkaido University, Sapporo 001-0021, Japan
| | - Yi-You Huang
- Institute of Biomedical Engineering, National Taiwan University, Taipei 10051, Taiwan
- Department of Biomedical Engineering, National Taiwan University Hospital, Taipei 100225, Taiwan
| | - Din Ping Tsai
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
- Department of Electronic and Information Engineering, The Hong Kong Polytechnic University, Kowloon 999077, Hong Kong
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7
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McDonald AD, Jones BJP, Nygren DR, Adams C, Álvarez V, Azevedo CDR, Benlloch-Rodríguez JM, Borges FIGM, Botas A, Cárcel S, Carrión JV, Cebrián S, Conde CAN, Díaz J, Diesburg M, Escada J, Esteve R, Felkai R, Fernandes LMP, Ferrario P, Ferreira AL, Freitas EDC, Goldschmidt A, Gómez-Cadenas JJ, González-Díaz D, Gutiérrez RM, Guenette R, Hafidi K, Hauptman J, Henriques CAO, Hernandez AI, Hernando Morata JA, Herrero V, Johnston S, Labarga L, Laing A, Lebrun P, Liubarsky I, López-March N, Losada M, Martín-Albo J, Martínez-Lema G, Martínez A, Monrabal F, Monteiro CMB, Mora FJ, Moutinho LM, Muñoz Vidal J, Musti M, Nebot-Guinot M, Novella P, Palmeiro B, Para A, Pérez J, Querol M, Repond J, Renner J, Riordan S, Ripoll L, Rodríguez J, Rogers L, Santos FP, Dos Santos JMF, Simón A, Sofka C, Sorel M, Stiegler T, Toledo JF, Torrent J, Tsamalaidze Z, Veloso JFCA, Webb R, White JT, Yahlali N. Demonstration of Single-Barium-Ion Sensitivity for Neutrinoless Double-Beta Decay Using Single-Molecule Fluorescence Imaging. PHYSICAL REVIEW LETTERS 2018; 120:132504. [PMID: 29694208 DOI: 10.1103/physrevlett.120.132504] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/02/2018] [Indexed: 06/08/2023]
Abstract
A new method to tag the barium daughter in the double-beta decay of ^{136}Xe is reported. Using the technique of single molecule fluorescent imaging (SMFI), individual barium dication (Ba^{++}) resolution at a transparent scanning surface is demonstrated. A single-step photobleach confirms the single ion interpretation. Individual ions are localized with superresolution (∼2 nm), and detected with a statistical significance of 12.9σ over backgrounds. This lays the foundation for a new and potentially background-free neutrinoless double-beta decay technology, based on SMFI coupled to high pressure xenon gas time projection chambers.
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Affiliation(s)
- A D McDonald
- Department of Physics, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - B J P Jones
- Department of Physics, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - D R Nygren
- Department of Physics, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - C Adams
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - V Álvarez
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - C D R Azevedo
- Institute of Nanostructures, Nanomodelling and Nanofabrication (i3N), Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - J M Benlloch-Rodríguez
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - F I G M Borges
- LIP, Department of Physics, University of Coimbra, P-3004 516 Coimbra, Portugal
| | - A Botas
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - S Cárcel
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - J V Carrión
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - S Cebrián
- Laboratorio de Física Nuclear y Astropartículas, Universidad de Zaragoza, Calle Pedro Cerbuna, 12, 50009 Zaragoza, Spain
| | - C A N Conde
- LIP, Department of Physics, University of Coimbra, P-3004 516 Coimbra, Portugal
| | - J Díaz
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - M Diesburg
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - J Escada
- LIP, Department of Physics, University of Coimbra, P-3004 516 Coimbra, Portugal
| | - R Esteve
- Instituto de Instrumentación para Imagen Molecular (I3M), Centro Mixto CSIC-Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - R Felkai
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - L M P Fernandes
- LIBPhys, Physics Department, University of Coimbra, Rua Larga, 3004-516 Coimbra, Portugal
| | - P Ferrario
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - A L Ferreira
- Institute of Nanostructures, Nanomodelling and Nanofabrication (i3N), Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - E D C Freitas
- LIBPhys, Physics Department, University of Coimbra, Rua Larga, 3004-516 Coimbra, Portugal
| | - A Goldschmidt
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, California 94720, USA
| | - J J Gómez-Cadenas
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - D González-Díaz
- Instituto Gallego de Física de Altas Energías, Univ. de Santiago de Compostela, Campus sur, Rúa Xosé María Suárez Núñez, s/n, 15782 Santiago de Compostela, Spain
| | - R M Gutiérrez
- Centro de Investigación en Ciencias Básicas y Aplicadas, Universidad Antonio Nariño, Sede Circunvalar, Carretera 3 Este No. 47 A-15, Bogotá, Colombia
| | - R Guenette
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - K Hafidi
- Argonne National Laboratory, Argonne Illinois 60439, USA
| | - J Hauptman
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011-3160, USA
| | - C A O Henriques
- LIBPhys, Physics Department, University of Coimbra, Rua Larga, 3004-516 Coimbra, Portugal
| | - A I Hernandez
- Centro de Investigación en Ciencias Básicas y Aplicadas, Universidad Antonio Nariño, Sede Circunvalar, Carretera 3 Este No. 47 A-15, Bogotá, Colombia
| | - J A Hernando Morata
- Instituto Gallego de Física de Altas Energías, Univ. de Santiago de Compostela, Campus sur, Rúa Xosé María Suárez Núñez, s/n, 15782 Santiago de Compostela, Spain
| | - V Herrero
- Instituto de Instrumentación para Imagen Molecular (I3M), Centro Mixto CSIC-Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - S Johnston
- Argonne National Laboratory, Argonne Illinois 60439, USA
| | - L Labarga
- Departamento de Física Teórica, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain
| | - A Laing
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - P Lebrun
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - I Liubarsky
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - N López-March
- Department of Physics, University of Texas at Arlington, Arlington, Texas 76019, USA
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - M Losada
- Centro de Investigación en Ciencias Básicas y Aplicadas, Universidad Antonio Nariño, Sede Circunvalar, Carretera 3 Este No. 47 A-15, Bogotá, Colombia
| | - J Martín-Albo
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - G Martínez-Lema
- Instituto Gallego de Física de Altas Energías, Univ. de Santiago de Compostela, Campus sur, Rúa Xosé María Suárez Núñez, s/n, 15782 Santiago de Compostela, Spain
| | - A Martínez
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - F Monrabal
- Department of Physics, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - C M B Monteiro
- LIBPhys, Physics Department, University of Coimbra, Rua Larga, 3004-516 Coimbra, Portugal
| | - F J Mora
- Instituto de Instrumentación para Imagen Molecular (I3M), Centro Mixto CSIC-Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - L M Moutinho
- Institute of Nanostructures, Nanomodelling and Nanofabrication (i3N), Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - J Muñoz Vidal
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - M Musti
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - M Nebot-Guinot
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - P Novella
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - B Palmeiro
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - A Para
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - J Pérez
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - M Querol
- Instituto de Instrumentación para Imagen Molecular (I3M), Centro Mixto CSIC-Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - J Repond
- Argonne National Laboratory, Argonne Illinois 60439, USA
| | - J Renner
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - S Riordan
- Argonne National Laboratory, Argonne Illinois 60439, USA
| | - L Ripoll
- Escola Politècnica Superior, Universitat de Girona, Av. Montilivi, s/n, 17071 Girona, Spain
| | - J Rodríguez
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - L Rogers
- Department of Physics, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - F P Santos
- LIP, Department of Physics, University of Coimbra, P-3004 516 Coimbra, Portugal
| | - J M F Dos Santos
- LIBPhys, Physics Department, University of Coimbra, Rua Larga, 3004-516 Coimbra, Portugal
| | - A Simón
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - C Sofka
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - M Sorel
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - T Stiegler
- Department of Physics and Astronomy, Texas A&M University, College Station, Texas 77843-4242, USA
| | - J F Toledo
- Instituto de Instrumentación para Imagen Molecular (I3M), Centro Mixto CSIC-Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - J Torrent
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - Z Tsamalaidze
- Joint Institute for Nuclear Research (JINR), Joliot-Curie 6, 141980 Dubna, Russia
| | - J F C A Veloso
- Institute of Nanostructures, Nanomodelling and Nanofabrication (i3N), Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - R Webb
- Department of Physics and Astronomy, Texas A&M University, College Station, Texas 77843-4242, USA
| | - J T White
- Department of Physics and Astronomy, Texas A&M University, College Station, Texas 77843-4242, USA
| | - N Yahlali
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
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