Publications

Schmied, Christopher. “Image and Image Analysis Publication Checklists.” Imaging & Microscopy, May 1, 2024. https://analyticalscience.wiley.com/content/article-do/image-and-image-analysis-publication-checklists. Cite

Nitschke, Roland, and Hella Hartmann. “A Global Reproducibility Initiative in Light Microscopy.” Imaging & Microscopy, March 1, 2024. https://analyticalscience.wiley.com/content/magazine-do/imaging-microscopy-1-2024. Cite

Jambor, Helena Klara. “From Zero to Figure Hero. A Checklist for Designing Scientific Data Visualizations.” arXiv, August 14, 2024. https://doi.org/10.48550/arXiv.2408.16007. Cite

McFadden, David, Kees van der Oord, Luis-Francisco Acevedo-Hueso, Sergiy V. Avilov, Gert-Jan Bakker, Ivan Belyaev, Valeria Berno, et al. “5. Analysis - Characterization of the Photon Conversion Factor, Noise, and Dynamic Range,” January 13, 2025. https://www.protocols.io/view/5-analysis-characterization-of-the-photon-convers-dkuw4wxe. Cite

Berno, Valeria, Kees van der Oord, Luis-Francisco Acevedo-Hueso, Laszlo Barna, Sebastian Beer, Yann Cesbron, Orestis Faklaris, et al. “2. Sample Preparation - An Easy-to-Prepare Sample Slide,” January 13, 2025. https://www.protocols.io/view/2-sample-preparation-an-easy-to-prepare-sample-sli-dkus4wwe. Cite

Hammer, Mathias, Britta Schroth-Diez, Luis-Francisco Acevedo-Hueso, Gert-Jan Bakker, Laszlo Barna, Sebastian Beer, Valeria Berno, et al. “3. Data Generation - Systems with an Area Detector,” January 13, 2025. https://www.protocols.io/view/3-data-generation-systems-with-an-area-detector-dkuu4www. Cite

Bakker, Gert-Jan, Mathias Hammer, Luis-Francisco Acevedo-Hueso, Sergiy V. Avilov, Laszlo Barna, Sebastian Beer, Valeria Berno, et al. “1. Introduction - Background and Aims,” January 13, 2025. https://www.protocols.io/view/1-introduction-background-and-aims-dkut4wwn. Cite

Zeug, Andre, Valeria Berno, Luis-Francisco Acevedo-Hueso, Gert-Jan Bakker, Mariana T. Carvalho, Yann Cesbron, Orestis Faklaris, et al. “4. Data Generation - Systems with a Point Detector,” January 13, 2025. https://www.protocols.io/view/4-data-generation-systems-with-a-point-detector-dkuv4ww6. Cite

McFadden, David, Laszlo Barna, Luis-Francisco Acevedo-Hueso, Sergiy V. Avilov, Gert-Jan Bakker, Sebastian Beer, Ivan Belyaev, et al. “Characterization of the Photon Conversion Factor, Noise, and Dynamic Range of Light Microscope Detection Sy...,” January 13, 2025. https://www.protocols.io/view/characterization-of-the-photon-conversion-factor-n-dkux4wxn. Cite

Nelson, Glyn, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof, Claire M. Brown, Aurélien Dauphin, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” Journal of Microscopy 284, no. 1 (2021): 56–73. https://doi.org/10.1111/jmi.13041. Cite

Nelson, Glyn, Ioannis Alexopoulos, Maria Azevedo, Fabio Barachati, Yury Belyaev, Mariana T. Carvalho, Yann Cesbron, et al. “Monitoring the Point Spread Function for Quality Control of Confocal Microscopes Protocol Guidelines,” October 19, 2022. https://www.protocols.io/view/monitoring-the-point-spread-function-for-quality-ccsuswew/guidelines. Cite

Jambor, Helena Klara. “A Community-Driven Approach to Enhancing the Quality and Interpretability of Microscopy Images.” Journal of Cell Science 136, no. 24 (December 14, 2023): jcs261837. https://doi.org/10.1242/jcs.261837. Cite

Schmied, Christopher, Michael S. Nelson, Sergiy Avilov, Gert-Jan Bakker, Cristina Bertocchi, Johanna Bischof, Ulrike Boehm, et al. “Community-Developed Checklists for Publishing Images and Image Analyses.” Nature Methods, September 14, 2023, 1–12. https://doi.org/10.1038/s41592-023-01987-9. Cite

Marx, Vivien. “Imaging Standards to Ease Reproducibility and the Everyday.” Nature Methods 19, no. 7 (July 2022): 784–88. https://doi.org/10.1038/s41592-022-01544-w. Cite

Marx, Vivien. “The Making of Microscope Camera Standards.” Nature Methods 19, no. 7 (July 2022): 788–91. https://doi.org/10.1038/s41592-022-01545-9. Cite

Faklaris, Orestis, Leslie Bancel-Vallée, Aurélien Dauphin, Baptiste Monterroso, Perrine Frère, David Geny, Tudor Manoliu, et al. “Quality Assessment in Light Microscopy for Routine Use through Simple Tools and Robust Metrics.” Journal of Cell Biology 221, no. 11 (November 7, 2022): e202107093. https://doi.org/10.1083/jcb.202107093. Cite

Hammer, Mathias, Maximiliaan Huisman, Alessandro Rigano, Ulrike Boehm, James J. Chambers, Nathalie Gaudreault, Alison J. North, et al. “Towards Community-Driven Metadata Standards for Light Microscopy: Tiered Specifications Extending the OME Model.” Nature Methods, December 3, 2021, 1–14. https://doi.org/10.1038/s41592-021-01327-9. Cite

Swedlow, Jason R., Pasi Kankaanpää, Ugis Sarkans, Wojtek Goscinski, Graham Galloway, Leonel Malacrida, Ryan P. Sullivan, et al. “A Global View of Standards for Open Image Data Formats and Repositories.” Nature Methods, May 4, 2021, 1–7. https://doi.org/10.1038/s41592-021-01113-7. Cite

Moore, Josh, Chris Allan, Sébastien Besson, Jean-Marie Burel, Erin Diel, David Gault, Kevin Kozlowski, et al. “OME-NGFF: A next-Generation File Format for Expanding Bioimaging Data-Access Strategies.” Nature Methods, November 29, 2021, 1–3. https://doi.org/10.1038/s41592-021-01326-w. Cite

Montero Llopis, Paula, Rebecca A. Senft, Tim J. Ross-Elliott, Ryan Stephansky, Daniel P. Keeley, Preman Koshar, Guillermo Marqués, et al. “Best Practices and Tools for Reporting Reproducible Fluorescence Microscopy Methods.” Nature Methods, June 7, 2021, 1–14. https://doi.org/10.1038/s41592-021-01156-w. Cite

Sarkans, Ugis, Wah Chiu, Lucy Collinson, Michele C. Darrow, Jan Ellenberg, David Grunwald, Jean-Karim Hériché, et al. “REMBI: Recommended Metadata for Biological Images—Enabling Reuse of Microscopy Data in Biology.” Nature Methods, May 21, 2021, 1–5. https://doi.org/10.1038/s41592-021-01166-8. Cite

Kunis, Susanne, Sebastian Hänsch, Christian Schmidt, Frances Wong, Caterina Strambio-De-Castillia, and Stefanie Weidtkamp-Peters. “MDEmic: A Metadata Annotation Tool to Facilitate Management of FAIR Image Data in the Bioimaging Community.” Nature Methods, October 11, 2021, 1–2. https://doi.org/10.1038/s41592-021-01288-z. Cite

Ryan, Joel, Thomas Pengo, Alex Rigano, Paula Montero Llopis, Michelle S. Itano, Lisa A. Cameron, Guillermo Marqués, Caterina Strambio-De-Castillia, Mark A. Sanders, and Claire M. Brown. “MethodsJ2: A Software Tool to Capture Metadata and Generate Comprehensive Microscopy Methods Text.” Nature Methods, October 15, 2021, 1–3. https://doi.org/10.1038/s41592-021-01290-5. Cite

Rigano, Alessandro, Shannon Ehmsen, Serkan Utku Öztürk, Joel Ryan, Alexander Balashov, Mathias Hammer, Koray Kirli, et al. “Micro-Meta App: An Interactive Tool for Collecting Microscopy Metadata Based on Community Specifications.” Nature Methods, December 3, 2021, 1–7. https://doi.org/10.1038/s41592-021-01315-z. Cite

Boehm, Ulrike, Glyn Nelson, Claire M. Brown, Steve Bagley, Peter Bajcsy, Johanna Bischof, Aurelien Dauphin, et al. “QUAREP-LiMi: A Community Endeavor to Advance Quality Assessment and Reproducibility in Light Microscopy.” Nature Methods, May 21, 2021. https://doi.org/10.1038/s41592-021-01162-y. Cite