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[Preprint]. 2023 Sep 14:arXiv:2302.07005v2.

Community-developed checklists for publishing images and image analyses

Christopher Schmied^{1

2}, Michael S Nelson³, Sergiy Avilov⁴, Gert-Jan Bakker⁵, Cristina Bertocchi^{6

7}, Johanna Bischof⁸, Ulrike Boehm⁹, Jan Brocher¹⁰, Mariana Carvalho¹¹, Catalin Chiritescu¹², Jana Christopher¹³, Beth A Cimini¹⁴, Eduardo Conde-Sousa¹⁵, Michael Ebner¹, Rupert Ecker^{16

17

18}, Kevin Eliceiri¹⁹, Julia Fernandez-Rodriguez²⁰, Nathalie Gaudreault²¹, Laurent Gelman²², David Grunwald²³, Tingting Gu²⁴, Nadia Halidi²⁵, Mathias Hammer²³, Matthew Hartley²⁶, Marie Held²⁷, Florian Jug¹, Varun Kapoor²⁸, Ayse Aslihan Koksoy²⁹, Judith Lacoste³⁰, Sylvia Le Dévédec³¹, Sylvie Le Guyader³², Penghuan Liu³³, Gabriel G Martins³⁴, Aastha Mathur⁸, Kota Miura³⁵, Paula Montero Llopis³⁶, Roland Nitschke³⁷, Alison North³⁸, Adam C Parslow³⁹, Alex Payne-Dwyer⁴⁰, Laure Plantard²², Rizwan Ali⁴¹, Britta Schroth-Diez⁴², Lucas Schütz⁴³, Ryan T Scott⁴⁴, Arne Seitz⁴⁵, Olaf Selchow⁴⁶, Ved P Sharma³⁸, Martin Spitaler⁴⁷, Sathya Srinivasan⁴⁸, Caterina Strambio-De-Castillia⁴⁹, Douglas Taatjes⁵⁰, Christian Tischer⁵¹, Helena Klara Jambor⁵²

Affiliations

¹ Fondazione Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milano, Italy.
² Present address: Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany.
³ Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA.
⁴ Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
⁵ Medical BioSciences department, Radboud University Medical Centre, Nijmegen, Netherlands.
⁶ Laboratory for Molecular mechanics of cell adhesions, Pontificia Universidad Católica de Chile Santiago.
⁷ Osaka University, Graduate School of Engineering Science, Japan.
⁸ Euro-BioImaging ERIC, Bio-Hub, Meyerhofstr. 1, 69117 Heidelberg, Germany.
⁹ Carl Zeiss AG, Carl-Zeiss-Straße 22, 73447 Oberkochen, Germany.
¹⁰ BioVoxxel, Scientific Image Processing and Analysis, Eugen-Roth-Strasse 8, 67071 Ludwigshafen, Germany.
¹¹ Nanophotonics and BioImaging Facility at INL, International Iberian Nanotechnology Laboratory, 4715-330, Portugal.
¹² Phi Optics, Inc., 1800 S. Oak St, Ste 106, Champaign, IL 61820, USA.
¹³ Biochemistry Center Heidelberg, Heidelberg University, Germany.
¹⁴ Imaging Platform, Broad Institute, Cambridge, MA 02142.
¹⁵ i3S, Instituto de Investigação e Inovação Em Saúde and INEB, Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal.
¹⁶ Translational Research Institute, Queensland University of Technology, 37 Kent Street, Woolloongabba, QLD 4102, Australia.
¹⁷ School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4059, Australia.
¹⁸ TissueGnostics GmbH, 1020 Vienna, Austria.
¹⁹ Department of Medical Physics and Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA.
²⁰ Centre for Cellular Imaging Core Facility, Sahlgrenska Academy, University of Gothenburg, Sweden.
²¹ Allen Institute for Cell Science, Seattle, WA, USA.
²² Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
²³ RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
²⁴ University of Oklahoma, Norman, OK, USA.
²⁵ Advanced Light Microscopy Unit, Centre for Genomic Regulation, Barcelona, Spain.
²⁶ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK.
²⁷ Centre for Cell Imaging, The University of Liverpool, UK.
²⁸ Department of AI research, Kapoor Labs, Paris, 75005, France.
²⁹ MD Anderson Cancer Center, Houston, TX, USA.
³⁰ MIA Cellavie Inc., Montreal, QC Canada.
³¹ Division of Drug Discovery and Safety, Cell Observatory, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands.
³² Karolinska Institutet, Hälsovägen 7C, 14157, Huddinge, Sweden.
³³ Key Laboratory for Modern Measurement Technology and Instruments of Zhejiang Province, College of Optical and Electronic Technology, China Jiliang University, Hangzhou, China.
³⁴ Advanced Imaging Facility, Instituto Gulbenkian de Ciência, Oeiras 2780-156 - Portugal.
³⁵ Bioimage Analysis & Research, 69127 Heidelberg/Germany.
³⁶ MicRoN Core, Harvard Medical School, Boston, MA, USA.
³⁷ Life Imaging Center, Signalling Research Centres CIBSS and BIOSS, University of Freiburg, Germany.
³⁸ Bio-Imaging Resource Center, The Rockefeller University, New York, NY USA.
³⁹ Baker Institute Microscopy Platform, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.
⁴⁰ School of Physics, Engineering and Technology, University of York, Heslington, YO10 5DD, UK.
⁴¹ King Abdullah International Medical Research Center (KAIMRC), Medical Research Core Facility and Platforms (MRCFP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11481, Saudi Arabia.
⁴² Light Microscopy Facility, Max Planck Institute of Molecular Cell Biology and Genetics Dresden, Pfotenhauerstrasse 108, 01307 Dresden, Germany.
⁴³ ariadne.ai (Germany) GmbH, 69115 Heidelberg, Germany.
⁴⁴ Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA.
⁴⁵ BioImaging & Optics Platform (BIOP), Ecole Polytechnique Fédérale de Lausanne (EPFL), Faculty of Life sciences (SV), CH-1015 Lausanne.
⁴⁶ Microscopy & BioImaging Consulting, Image Processing & Large Data Handling, Tobias-Hoppe-Strassse 3, 07548 Gera, Germany.
⁴⁷ Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
⁴⁸ Imaging and Morphology Support Core, Oregon National Primate Research Center - (ONPRC - OHSU West Campus), Beaverton, Oregon 97006, USA.
⁴⁹ Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
⁵⁰ Department of Pathology and Laboratory Medicine, Microscopy Imaging Center (RRID# SCR_018821), Center for Biomedical Shared Resources, University of Vermont, Burlington, VT 05405 USA.
⁵¹ Centre for Bioimage Analysis, EMBL Heidelberg, Meyerhofstr. 1, 69117 Heidelberg, Germany.
⁵² NCT-UCC, Medizinische Fakultät TU Dresden, Fetscherstrasse 105, 01307 Dresden/Germany.

PMID: 36824427
PMCID: PMC9949169

Community-developed checklists for publishing images and image analyses

Christopher Schmied et al. ArXiv. 2023.

[Preprint]. 2023 Sep 14:arXiv:2302.07005v2.

Authors

Affiliations

¹ Fondazione Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milano, Italy.
² Present address: Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany.
³ Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA.
⁴ Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
⁵ Medical BioSciences department, Radboud University Medical Centre, Nijmegen, Netherlands.
⁶ Laboratory for Molecular mechanics of cell adhesions, Pontificia Universidad Católica de Chile Santiago.
⁷ Osaka University, Graduate School of Engineering Science, Japan.
⁸ Euro-BioImaging ERIC, Bio-Hub, Meyerhofstr. 1, 69117 Heidelberg, Germany.
⁹ Carl Zeiss AG, Carl-Zeiss-Straße 22, 73447 Oberkochen, Germany.
¹⁰ BioVoxxel, Scientific Image Processing and Analysis, Eugen-Roth-Strasse 8, 67071 Ludwigshafen, Germany.
¹¹ Nanophotonics and BioImaging Facility at INL, International Iberian Nanotechnology Laboratory, 4715-330, Portugal.
¹² Phi Optics, Inc., 1800 S. Oak St, Ste 106, Champaign, IL 61820, USA.
¹³ Biochemistry Center Heidelberg, Heidelberg University, Germany.
¹⁴ Imaging Platform, Broad Institute, Cambridge, MA 02142.
¹⁵ i3S, Instituto de Investigação e Inovação Em Saúde and INEB, Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal.
¹⁶ Translational Research Institute, Queensland University of Technology, 37 Kent Street, Woolloongabba, QLD 4102, Australia.
¹⁷ School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4059, Australia.
¹⁸ TissueGnostics GmbH, 1020 Vienna, Austria.
¹⁹ Department of Medical Physics and Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA.
²⁰ Centre for Cellular Imaging Core Facility, Sahlgrenska Academy, University of Gothenburg, Sweden.
²¹ Allen Institute for Cell Science, Seattle, WA, USA.
²² Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
²³ RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
²⁴ University of Oklahoma, Norman, OK, USA.
²⁵ Advanced Light Microscopy Unit, Centre for Genomic Regulation, Barcelona, Spain.
²⁶ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK.
²⁷ Centre for Cell Imaging, The University of Liverpool, UK.
²⁸ Department of AI research, Kapoor Labs, Paris, 75005, France.
²⁹ MD Anderson Cancer Center, Houston, TX, USA.
³⁰ MIA Cellavie Inc., Montreal, QC Canada.
³¹ Division of Drug Discovery and Safety, Cell Observatory, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands.
³² Karolinska Institutet, Hälsovägen 7C, 14157, Huddinge, Sweden.
³³ Key Laboratory for Modern Measurement Technology and Instruments of Zhejiang Province, College of Optical and Electronic Technology, China Jiliang University, Hangzhou, China.
³⁴ Advanced Imaging Facility, Instituto Gulbenkian de Ciência, Oeiras 2780-156 - Portugal.
³⁵ Bioimage Analysis & Research, 69127 Heidelberg/Germany.
³⁶ MicRoN Core, Harvard Medical School, Boston, MA, USA.
³⁷ Life Imaging Center, Signalling Research Centres CIBSS and BIOSS, University of Freiburg, Germany.
³⁸ Bio-Imaging Resource Center, The Rockefeller University, New York, NY USA.
³⁹ Baker Institute Microscopy Platform, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.
⁴⁰ School of Physics, Engineering and Technology, University of York, Heslington, YO10 5DD, UK.
⁴¹ King Abdullah International Medical Research Center (KAIMRC), Medical Research Core Facility and Platforms (MRCFP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11481, Saudi Arabia.
⁴² Light Microscopy Facility, Max Planck Institute of Molecular Cell Biology and Genetics Dresden, Pfotenhauerstrasse 108, 01307 Dresden, Germany.
⁴³ ariadne.ai (Germany) GmbH, 69115 Heidelberg, Germany.
⁴⁴ Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA.
⁴⁵ BioImaging & Optics Platform (BIOP), Ecole Polytechnique Fédérale de Lausanne (EPFL), Faculty of Life sciences (SV), CH-1015 Lausanne.
⁴⁶ Microscopy & BioImaging Consulting, Image Processing & Large Data Handling, Tobias-Hoppe-Strassse 3, 07548 Gera, Germany.
⁴⁷ Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
⁴⁸ Imaging and Morphology Support Core, Oregon National Primate Research Center - (ONPRC - OHSU West Campus), Beaverton, Oregon 97006, USA.
⁴⁹ Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
⁵⁰ Department of Pathology and Laboratory Medicine, Microscopy Imaging Center (RRID# SCR_018821), Center for Biomedical Shared Resources, University of Vermont, Burlington, VT 05405 USA.
⁵¹ Centre for Bioimage Analysis, EMBL Heidelberg, Meyerhofstr. 1, 69117 Heidelberg, Germany.
⁵² NCT-UCC, Medizinische Fakultät TU Dresden, Fetscherstrasse 105, 01307 Dresden/Germany.

PMID: 36824427
PMCID: PMC9949169

Update in

Community-developed checklists for publishing images and image analyses.
Schmied C, Nelson MS, Avilov S, Bakker GJ, Bertocchi C, Bischof J, Boehm U, Brocher J, Carvalho MT, Chiritescu C, Christopher J, Cimini BA, Conde-Sousa E, Ebner M, Ecker R, Eliceiri K, Fernandez-Rodriguez J, Gaudreault N, Gelman L, Grunwald D, Gu T, Halidi N, Hammer M, Hartley M, Held M, Jug F, Kapoor V, Koksoy AA, Lacoste J, Le Dévédec S, Le Guyader S, Liu P, Martins GG, Mathur A, Miura K, Montero Llopis P, Nitschke R, North A, Parslow AC, Payne-Dwyer A, Plantard L, Ali R, Schroth-Diez B, Schütz L, Scott RT, Seitz A, Selchow O, Sharma VP, Spitaler M, Srinivasan S, Strambio-De-Castillia C, Taatjes D, Tischer C, Jambor HK. Schmied C, et al. Nat Methods. 2024 Feb;21(2):170-181. doi: 10.1038/s41592-023-01987-9. Epub 2023 Sep 14. Nat Methods. 2024. PMID: 37710020 Free PMC article. Review.

Abstract

Images document scientific discoveries and are prevalent in modern biomedical research. Microscopy imaging in particular is currently undergoing rapid technological advancements. However for scientists wishing to publish the obtained images and image analyses results, there are to date no unified guidelines. Consequently, microscopy images and image data in publications may be unclear or difficult to interpret. Here we present community-developed checklists for preparing light microscopy images and image analysis for publications. These checklists offer authors, readers, and publishers key recommendations for image formatting and annotation, color selection, data availability, and for reporting image analysis workflows. The goal of our guidelines is to increase the clarity and reproducibility of image figures and thereby heighten the quality and explanatory power of microscopy data is in publications.

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Figures

**Figure 1.**
Scope of the checklists of image figure and image analysis requirements. The checklists present easy-to-use guidelines for publishing microscopy image figures and image analysis workflows.

**Figure 2.**
Checklist for image publication including points to be addressed on image format, image colors and channels, image annotations, and image availability.

**Figure 3.**
Image formatting may include (A) image cropping, rotation, and resizing, (B) image spacing in the figure, and (C) presenting several magnifications (zoom, inset) of images.

**Figure 4.**
Image colors and channels. (A) Adjust brightness/contrast to achieve good visibility of the imaging signal. (B) Channel information should be annotated and visible to audiences (high contrast to background color, visible to color-blind audiences). (C) Image details are most unbiased in grayscale. (D) It is best practice to publish legends to color scales with images, and mandatory for pseudo-color scales.

**Figure 5.**
Image Annotation. (A) Possible ways to provide scale information. (B) Features in images can be annotated with symbols, letters, or region-of- interest. (C) For advanced image publication, information on z-stack or voxel size, anatomical view, or camera settings such as pixel-dwell time, exposure time, or frame-time may be required.

**Figure 6.**
Image Availability. (A) Currently, image data is often shared ‘upon request’. (B) More images along with the image metadata should be available for download in public databases, and in the future (C) also archived in dedicated, added-value databases, in which images are machine searchable or curated.

**Figure 7.**
Image analysis. (A) An established workflow template is applied on new image data to produce a result (plot). (B) A new sequence of existing image analysis components is assembled into a novel workflow for a specific analysis (image segmentation). (C) Machine learning workflows learn specific tasks from data, and the resulting model is applied to obtain results.

**Figure 8.**
Checklist for publication of image analysis workflows.

See this image and copyright information in PMC

References

1. Aaron J., Chew T.-L., 2021. A guide to accurate reporting in digital image processing - can anyone reproduce your quantitative analysis? J. Cell Sci. 134, jcs254151. 10.1242/jcs.254151 - DOI - PubMed
1. Arganda-Carreras I., Kaynig V., Rueden C., Eliceiri K.W., Schindelin J., Cardona A., Sebastian Seung H., 2017. Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification. Bioinforma. Oxf. Engl. 33, 2424–2426. 10.1093/bioinformatics/btx180 - DOI - PubMed
1. Arzt M., Deschamps J., Schmied C., Pietzsch T., Schmidt D., Tomancak P., Haase R., Jug F., 2022. LABKIT: Labeling and Segmentation Toolkit for Big Image Data. Front. Comput. Sci. 4.
1. Baker M., 2016. 1,500 scientists lift the lid on reproducibility. Nature 533, 452–454. 10.1038/533452a - DOI - PubMed
1. Berginski M.E., Gomez S.M., 2013. The Focal Adhesion Analysis Server: a web tool for analyzing focal adhesion dynamics. F1000Research 2, 68. 10.12688/f1000research.2-68.v1 - DOI - PMC - PubMed

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This is a preprint.

Community-developed checklists for publishing images and image analyses

Affiliations

Community-developed checklists for publishing images and image analyses

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Affiliations

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