Public Protocols
All protocols are available on protocols.io
2025
27th of January
Authors:
Nathalie Gaudreault1, Luis-Francisco Acevedo-Hueso2, Rizwan Ali3, Sergiy V Avilov4, Steve Bagley5, Rodrigo R Bammann6, Fabio Barachati7, Laszlo Barna8, Valeria Berno9, Cristina Bertocchi10, Veronika Boczonadi11, Ulrike Boehm12, Manel Bosch13, Craig Brideau14, Mariana T Carvalho15, Nabanita Chatterjee16, Pina Colarusso17, Richard Cole18, Nasser Darwish-Miranda19, Suat Dervish20, Ralf Dietzel21, Sam Duwé22, Frank Eismann23, Orestis Faklaris24, Andreas Felscher25, Zannatul Ferdous26, Thomas Guilbert27, Manfred Gonnert28, David Grunwald29, Tingting Gu30, Birgit Hoffmann31, Marcel Kirchner32, Ayse Aslihan Koksoy33, Gabriel Krens19, Alex J Laude11, Jeffrey M LeDue34, Penghuan Liu35, Pascal Lorentz36, Gabriel GGM G Martins37, Valeria.MezzanoRobinson38, Miso Mitkovski39, Glyn Nelson11, Michael S Nelson40, Roland Nitschke41, Alex L Payne-Dwyer42, Jaime Arturo Pimentel Cabrera43, Santosh Podder44, Britta Schroth-Diez45, Stanley Schwartz46, Ronian Siew47, Sathya Srinivasan48, Roland Thuenauer49, Kees van der Oord50, Douglas J Taatjes51, Chloë van Oostende-Triplet52, Tse-Luen Wee53, Kurt R Weiss54, Laurent Gelman
1Allen Institute for Cell Science, Seattle, WA, USA; 2Quantum Medical Diagnostics; 3King Abdullah International Medical Research Center/ King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Saudi Arabia; 4Max Planck Institute of Immunobiology and Epigenetics; 5Cancer Research UK Manchester Institute, UK; 6Scientifica; 7PicoQuant GmbH; 8Addiction and Neuroplasticity Lab, Department of Psychological and Brain Sciences, Indiana University Bloomington; 9Milano, Italy; 10Pontificia Universidad Católica de Chile, Chile; 11Newcastle University, BioImaging Unit, UK; 12Carl Zeiss AG, Oberkochen, Germany; 13Scientific and Technological Centers, Universitat de Barcelona (CCiTUB), Spain; 14University of Calgary, Canada; 15INL – International Iberian Nanotechnology Laboratory; 16UNIVERSITY OF GOTHENBURG Centre for Cellular Imaging – Core Facilities Sahlgrenska Academy, Sweden; 17Live Cell Imaging Laboratory, Snyder Institute of Chronic Diseases, University of Calgary, Canada; 18New York State Dept of Health,Wadsworth Center; 19Institute of Science and Technology Austria; 20Westmead Cytometry, Imaging, & Electron Microscopy, Sydney, Australia; 21Omicron Laserage Laserprodukte GmbH, Germany; 22Advanced Optical Microscopy Centre; 23Carl Zeiss Microscopy GmbH, Germany; 24MRI, Biocampus, University of Montpellier, CNRS, INSERM, Montpellier, France; 25Coherent GmbH & Co.KG; 26Hokkaido University; 27Institut Cochin, Inserm, France; 28Thorlabs GmbH; 29UMass Chan Medical School; 30University of Oklahoma; 31University Hospital Jena, Biomolecular Photonics Group; 32Max Planck Institute for Biology of Ageing, Germany; 33MD Anderson Cancer Center; 34University of British Columbia, Canada; 35Key Laboratory for Modern Measurement Technology and Instruments of Zhejiang Province, China Jiliang University, Hangzhou, China; 36Department of Biomedicine, University of Basel, Zwitzerland; 37GIMM – Gulbenkian Institute for Molecular Medicine; 38Experimental Pathology, NYU Sch. Of Medicine, USA; 39Max Planck Institute for Multidisciplinary Sciences; 40Department of Biomedical Engineering, University of Wisconsin – Madison, USA; 41Life Imaging Center and Signalling Research Centres CIBSS and BIOSS, University of Freiburg, Germany; 42School of Physics, University of York,; 43Instituto de Biotecnología. Universidad Nacional Autónoma de México; 44Indian Institute of Science Education and Research (IISER) Pune; 45Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany; 46ISO International Standards Organization TC172 SC5; 47Venture Biotech Modules Business; 48Oregon National Primate Research Center (ONPRC, OHSU West Campus), USA; 49Leibniz Institute for Experimental Virology (HPI), Germany; 50Nikon Europe BV; 51Microscopy Imaging Center, University of Vermont, Burlington, VT USA; 52Cell Biology and Image Acquisition Core Facility, University of Ottawa, Canada; 53Cold Spring Harbor Laboratory, USA; 54UW Madison Biochemistry Dept.; 55Friedrich Miescher Institute for Biomedical Research, Switzerland
DOI: dx.doi.org/10.17504/protocols.io.n2bvj3m45lk5/v1
2025
13th of January
Authors:
David McFadden1, Laszlo Barna2, Luis-Francisco Acevedo-Hueso3, Sergiy V Avilov4, Gert-Jan Bakker5, Sebastian Beer6, Ivan Belyaev7, Valeria Berno8, Mariana T Carvalho9, Yann Cesbron10, Catalin Chiritescu11, Orestis Faklaris12, Nathalie Gaudreault13, David Grunwald14, Thomas Guilbert15, Mathias Hammer16, Rainer Heintzmann17, Gerhard Holst18, Ayse Aslihan Koksoy19, Gabriel G Martins20, Glyn Nelson21, Roland Nitschke22, Alex L Payne-Dwyer23, Santosh Podder24, Sathya Srinivasan25, Kees van der Oord26, Andre Zeug27, Britta Schroth-Diez28
David McFadden1, Laszlo Barna2, Luis-Francisco Acevedo-Hueso3, Sergiy V Avilov4, Gert-Jan Bakker5, Sebastian Beer6, Ivan Belyaev7, Valeria Berno8, Mariana T Carvalho9,
1Friedrich Schiller University Jena; 2Institute of Experimental Medicine, Budapest; 3Neuro-AI Monitoring and Quantum Medical Diagnostics; 4Max Planck Institute of Immunobiology and Epigenetics; 5Radboud University Medical Center, Medical BioSciences department, Nijmegen, the Netherlands; 6Hamamatsu Photonics Deutschland GmbH; 7The Microverse cluster, Friedrich Schiller University Jena; 8ALEMBIC Advanced Light and Electron Microscopy BioImaging Center, San Raffaele Scientific Institute; 9INL – International Iberian Nanotechnology Laboratory; 10Institute of Science and Technology Austria; 11Phi Optics; 12MRI, Biocampus, University of Montpellier, CNRS, INSERM, Montpellier, France; 13Allen Institute for Cell Science, Seattle, WA, USA; 14UMass Chan Medical School; 15Institut Cochin, INSERM U1016, CNRS UMR 8104, Université Paris Cité, Paris, France; 16UMass Chan Medical School, RNA Therapeutics Institute, Worcester, MA, USA; 17Leibniz Institute of Photonic Technology; 18Excelitas PCO GmbH; 19MD Anderson Cancer Center; 20Gulbenkian Institute for Molecular Medicine; 21Newcastle University, BioImaging Unit, UK; 22Life Imaging Center, University of Freiburg, Germany; 23School of Physics Engineering and Technology, University of York, UK; 24Indian Institute of Science Education and Research (IISER) Pune; 25ONPRC; 26Nikon Europe BV; 27Cellular Neurophysiology, Hannover Medical School, Hannover, Germany; 28Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
DOI: dx.doi.org/10.17504/protocols.io.14egn61pyl5d/v1
1. Introduction – Background and Aims
Authors:
Gert-Jan Bakker1, Mathias Hammer2, Luis-Francisco Acevedo-Hueso3, Sergiy V Avilov4, Laszlo Barna5, Sebastian Beer6, Valeria Berno7, Yann Cesbron8, Orestis Faklaris9, Nathalie Gaudreault10, David Grunwald2, Rainer Heintzmann11, Gerhard Holst12, Ayse Aslihan Koksoy13, Glyn Nelson14, Roland Nitschke15, Alex L Payne-Dwyer16, Britta Schroth-Diez17, Sathya Srinivasan18, Kees van der Oord19, Andre Zeug20, David McFadden21
1Radboud University Medical Center, Medical BioSciences department, Nijmegen, the Netherlands; 2UMass Chan Medical School, RNA Therapeutics Institute, Worcester, MA, USA; 3Neuro-AI Monitoring and Quantum Medical Diagnostics; 4Max Planck Institute of Immunobiology and Epigenetics; 5Institute of Experimental Medicine, Budapest; 6Hamamatsu Photonics Deutschland GmbH; 7ALEMBIC Advanced Light and Electron Microscopy BioImaging Center, San Raffaele Scientific Institute; 8Institute of Science and Technology Austria; 9MRI, Biocampus, University of Montpellier, CNRS, INSERM, Montpellier, France; 10Allen Institute for Cell Science, Seattle, WA, USA; 11Leibniz Institute of Photonic Technology; 12Excelitas PCO GmbH; 13MD Anderson Cancer Center; 14Newcastle University, BioImaging Unit, UK; 15Life Imaging Center, University of Freiburg, Germany; 16School of Physics Engineering and Technology, University of York, UK; 17Max Planck Insitute of Molecular Cell Biology and Genetics, Dresden, Germany; 18ONPRC; 19Nikon Europe BV; 20Cellular Neurophysiology, Hannover Medical School, Hannover, Germany; 21Friedrich Schiller University Jena
DOI: dx.doi.org/10.17504/protocols.io.eq2lyw5mevx9/v1
2. Sample Preparation – An Easy-to-Prepare Sample Slide
Authors:
Valeria Berno1, Kees van der Oord2, Luis-Francisco Acevedo-Hueso3, Laszlo Barna4, Sebastian Beer5, Yann Cesbron6, Orestis Faklaris7, Nathalie Gaudreault8, David Grunwald9, Mathias Hammer9, Rainer Heintzmann10, Ayse Aslihan Koksoy11, David McFadden12, Glyn Nelson13, Roland Nitschke14, Santosh Podder15, Britta Schroth-Diez16, Sathya Srinivasan17, Andre Zeug18, Gert-Jan Bakker19
1ALEMBIC Advanced Light and Electron Microscopy BioImaging Center, San Raffaele Scientific Institute; 2Nikon Europe BV; 3Neuro-AI Monitoring and Quantum Medical Diagnostics; 4Institute of Experimental Medicine, Budapest; 5Hamamatsu Photonics Deutschland GmbH; 6Institute of Science and Technology Austria; 7MRI, Biocampus, University of Montpellier, CNRS, INSERM, Montpellier, France; 8Allen Institute for Cell Science, Seattle, WA, USA; 9UMass Chan Medical School, RNA Therapeutics Institute, Worcester, MA, USA; 10Leibniz Institute of Photonic Technology; 11MD Anderson Cancer Center; 12Friedrich Schiller University Jena; 13Newcastle University, BioImaging Unit, UK; 14Life Imaging Center and Signalling Research Centres CIBSS and BIOSS, University of Freiburg, Germany; 15Indian Institute of Science Education and Research (IISER) Pune; 16Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany; 17ONPRC; 18Cellular Neurophysiology, Hannover Medical School, Hannover, Germany; 19Radboud University Medical Center, Medical BioSciences department, Nijmegen, the Netherlands
DOI: dx.doi.org/10.17504/protocols.io.x54v92b91l3e/v1
3. Data Generation – Systems with an Area Detector
Authors:
Mathias Hammer1, Britta Schroth-Diez2, Luis-Francisco Acevedo-Hueso3, Gert-Jan Bakker4, Laszlo Barna5, Sebastian Beer6, Valeria Berno7, Yann Cesbron8, Orestis Faklaris9, Nathalie Gaudreault10, Thomas Guilbert11, Rainer Heintzmann12, Gabriel G Martins13, David McFadden14, Glyn Nelson15, Roland Nitschke16, Kees van der Oord17, Sathya Srinivasan18, Andre Zeug19, David Grunwald20
1UMASS Chan Medical School, RNA Therapeutics Institute, Worcester, MA, USA; 2Max Planck Insitute of Molecular Cell Biology and Genetics, Dresden, Germany; 3Neuro-AI Monitoring and Quantum Medical Diagnostics; 4Radboud University Medical Center, Medical BioSciences department, Nijmegen, the Netherlands; 5Institute of Experimental Medicine, Budapest; 6Hamamatsu Photonics Deutschland GmbH; 7ALEMBIC Advanced Light and Electron Microscopy BioImaging Center, San Raffaele Scientific Institute; 8Institute of Science and Technology Austria; 9MRI, Biocampus, University of Montpellier, CNRS, INSERM, Montpellier, France; 10Allen Institute for Cell Science, Seattle, WA, USA; 11Institut Cochin, INSERM U1016, CNRS UMR 8104, Université Paris Cité, Paris, France; 12Leibniz Institute of Photonic Technology; 13Gulbenkian Institute for Molecular Medicine; 14Friedrich Schiller University Jena; 15Newcastle University, BioImaging Unit, UK; 16Life Imaging Center, University of Freiburg, Germany; 17Nikon Europe BV; 18ONPRC; 19Cellular Neurophysiology, Hannover Medical School, Hannover, Germany; 20UMass Chan Medical School, RNA Therapeutics Institute, Worcester, MA, USA
DOI: dx.doi.org/10.17504/protocols.io.bp2l62eorgqe/v1
4. Data Generation – Systems with a Point Detector
Authors:
Andre Zeug1, Valeria Berno2, Luis-Francisco Acevedo-Hueso3, Gert-Jan Bakker4, Mariana T Carvalho5, Yann Cesbron6, Orestis Faklaris7, Ayse Aslihan Koksoy8, Gabriel G Martins9, David McFadden10, Glyn Nelson11, Roland Nitschke12, Britta Schroth-Diez13, Sathya Srinivasan14, Kees van der Oord15
1Cellular Neurophysiology, Hannover Medical School, Hannover, Germany; 2ALEMBIC Advanced Light and Electron Microscopy BioImaging Center, San Raffaele Scientific Institute; 3Neuro-AI Monitoring and Quantum Medical Diagnostics; 4Radboud University Medical Center, Medical BioSciences department, Nijmegen, the Netherlands; 5INL – International Iberian Nanotechnology Laboratory; 6Institute of Science and Technology Austria; 7MRI, Biocampus, University of Montpellier, CNRS, INSERM, Montpellier, France; 8MD Anderson Cancer Center; 9Gulbenkian Institute for Molecular Medicine; 10Friedrich Schiller University Jena; 11Newcastle University, BioImaging Unit, UK; 12Life Imaging Center and Signalling Research Centres CIBSS and BIOSS, University of Freiburg, Germany; 13Max Planck Insitute of Molecular Cell Biology and Genetics, Dresden, Germany; 14ONPRC; 15Nikon Europe BV
DOI: dx.doi.org/10.17504/protocols.io.j8nlk8176l5r/v1
5. Analysis – Characterization of the Photon Conversion Factor, Noise, and Dynamic Range
Authors:
David McFadden1, Kees van der Oord2, Luis-Francisco Acevedo-Hueso3, Sergiy V Avilov4, Gert-Jan Bakker5, Ivan Belyaev6, Valeria Berno7, Mariana T Carvalho8, Yann Cesbron9, Catalin Chiritescu10, Orestis Faklaris11, Glyn Nelson12, Roland Nitschke13, Britta Schroth-Diez14, Sathya Srinivasan15, Andre Zeug16, Rainer Heintzmann1
1Friedrich Schiller University Jena, Jena, Germany; 2Nikon Europe BV; 3Neuro-AI Monitoring and Quantum Medical Diagnostics; 4Max Planck Institute of Immunobiology and Epigenetics; 5Radboud University Medical Center, Medical BioSciences department, Nijmegen, the Netherlands; 6The Microverse cluster, Friedrich Schiller University Jena; 7ALEMBIC Advanced Light and Electron Microscopy BioImaging Center, San Raffaele Scientific Institute; 8INL – International Iberian Nanotechnology Laboratory; 9Institute of Science and Technology Austria; 10Phi Optics; 11MRI, Biocampus, University of Montpellier, CNRS, INSERM, Montpellier, France; 12Newcastle University, BioImaging Unit, UK; 13Life Imaging Center and Signalling Research Centres CIBSS and BIOSS, University of Freiburg, Germany; 14Max Planck Insitute of Molecular Cell Biology and Genetics, Dresden, Germany; 15ONPRC; 16Cellular Neurophysiology, Hannover Medical School, Hannover, Germany
DOI: dx.doi.org/10.17504/protocols.io.rm7vzjew2lx1/v1
2022
19th of October
Monitoring the point spread function for quality control of confocal microscopes
Authors:
Glyn Nelson1, Ioannis Alexopoulos2, Maria Azevedo3, Fabio Barachati4, Yury Belyaev5, Mariana T Carvalho6, Yann Cesbron7, Aurelien Dauphin8, Alexander D Corbett9, Ian M Dobbie10, Laurent Gelman11, Nadia Halidi12, Xiang Hao13, Hella Hartmann14, Rainer Heintzmann15, Peter Hemmerich16, Marcel Kirchner17, Judith Lacoste18, Penghuan Liu19, Laure lantard20, Claire A Mitchell21, Tobias Müller22, Kees van der Oord23, Alex L Payne-Dwyer24, Santosh Podder25, Rachid Rezgui26, Sandra Ritz27, Stanley Schwartz28, Michael J Shaw29, Tse-Luen Wee30, Roland Nitschke31, Orestis Faklaris32
1Bioimaging Unit, Newcastle University, UK; 2Multiscale Imaging Platform, Institute for Lung Health, Justus Liebig Universität Gießen; 3i3S – Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal; 4PicoQuant GmbH; 5Microscopy Imaging Center (MIC), University of Bern, Bern, Switzerland; 6INL – International Iberian anotechnology Laboratory; 7Institute of Science and Technology Austria, Klosterneuburg, Austria; 8Unite Genetique et Biologie du Développement U934, PICT-IBiSA, Institut Curie, INSERM, CNRS, PSL Research University, Paris, 75005, France; 9University of Exeter; 10Johns Hopkins University; 11Friedrich Miescher Institute for Biomedical Research; 12Centre for Genomic Regulation; 13Zhejiang University, Hangzhou 310027, China; 14TU Dresden, CMCB; 15Leibniz Institute of Photonic Technology; 16Leibniz Institute on Aging, Core Facility Imaging, Jena, Germany; 17Max Planck Institute , Koln; 18MIA Cellavie Inc.; 19College of Optical and Electronic Technology, China Jiliang Univeristy, Hangzhou, hina; 20Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; 21Beatson Advanced Imaging Resource, The Beatson Institute for Cancer Research, Glasgow, UK; 22IMP, Vienna; 23Nikon Europe BV; 24School of Physics, Engineering and Technology, University of York, UK; 25Indian Institute of Science Education and Research (IISER) Pune; 26New York University, Abu Dhabi; 27Institute of Molecular Biology gGmbH (IMB); 28ISO International Standards Organization TC172 SC5; 29National Physical Laboratory; 30Cold Spring Harbor Laboratory; 31Life Imaging Center, University of Freiburg, Germany; 32MRI, Biocampus, University of Montpellier, CNRS, INSERM, Montpellier, France
DOI: dx.doi.org/10.17504/protocols.io.bp2l61ww1vqe/v1
2023
19th of October
Repeatability of the XY positioning of motorized xy-tables of light microscopes
Authors:
Mariana T Carvalho1, Hans Fried2, Stuart Jarvis3, Claire A Mitchell4, Roland Nitschke5, Kees van der Oord6, Arnd Rühl7, Stanley Schwartz8, Martin Spitaler9, Roman Zantl10, Arne Seitz
1INL – International Iberian Nanotechnology Laboratory; 2CRFS – Light Microscope Facility, German Center for Neurodegenerative Diseases (DZNE); 3Prior Scientific Instruments Limited; Beatson Advanced Imaging Resource, The Beatson Institute for Cancer Research, Glasgow, UK; 5Life Imaging Center, University of Freiburg, Germany; 6Nikon Europe BV; 7Märzhäuser Wetzlar; 8ISO International Standards Organization TC172 SC5; 9Max Planck Institute of Biochemistry; 10ibidi GmbH; 11Ecole Polytechnique Fédérale de Lausanne (EPFL)
DOI: dx.doi.org/10.17504/protocols.io.kxygxz2rdv8j/v1
2023
8th of March
Getting started with Micro-Meta App Tutorial V.6
Authors:
Alessandro Rigano1, Mathias Hammer2, Joel Ryan3, Claire. Brown3, David Grunwald2, Caterina Strambio De Castillia1
1Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA; 2RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, USA; 3Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, Canada
DOI: dx.doi.org/10.17504/protocols.io.36wgq7ddxvk5/v6