FMI The new protocol represents a worldwide standard to assess illumination quality in microscopy

March 22, 2022

Community-based initiative improves reproducibility in microscopy and imaging

Researchers from the FMI Facility for Advanced Imaging and Microscopy (FAIM) are drivers of a large-scale international initiative dedicated to improving quality assessment and quality control in light microscopy. Recently, the workgroup chaired by the Head of FAIM delivered the first protocol for this initiative. It will help researchers from around the world improve the reliability, accuracy, and eventually reproducibility of their imaging experiments.

Technology development is at the forefront of scientific advances. The technology platforms that support our research groups at the FMI are state-of-the-art. They are run by experts who not only stay at the forefront of their field but also actively contribute to pushing its boundaries, together with colleagues from around the world.

Our Facility for Advanced Imaging and Microscopy (FAIM) is a prime example. It is run by Laurent Gelman who is a member of the international initiative called QUAREP-LiMi (Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy). The initiative was founded in 2020 and has nearly 400 members from 34 countries worldwide by now. Participants come from academia, industry, national and international microscopy networks, and standardization institutions. They share a strong interest in improving quality assessment and quality control in light microscopy.

Gelman is the co-chair of a workgroup called “Illumination Power Stability and Linearity” (workgroup 1), together with Nathalie Gaudreault from the Allen Institute in Seattle. His workgroup recently delivered the first protocol collaboratively developed by QUAREP-LiMi members. The protocol describes how to measure the stability and linearity of the illumination in microscopes, using calibrated external power sensors. It is indeed critical to understand how the instrument used for an observation or a measure can affect data accuracy, reproducibility, and ultimately its interpretation. This protocol, which builds on the collective experience of 60 imaging scientists and is published on the platform, represents a worldwide standard operation procedure to assess illumination quality. The workgroup also created online videos for beginners, software repositories for automation of the procedure on diverse microscopes, and a reference database collecting measurements made on instruments from all around the world to offer the possibility for anyone using the QUAREP-LiMi protocol to benchmark their instrument and quality control results.

“It is essential that scientists understand how to assess the quality of the tools they use for their experimental research, this is the key to reproducibility.” says Gelman. “It is also important that funding agencies and publishers encourage scientists to assess the quality of their instruments in a way that is internationally acknowledged, and that scientists interpret their results by comparing them to those gathered by the community, as there are often no official specifications given by companies for instrument properties.”

Laurent Gelman, and his FMI FAIM colleague Laure Plantard, participate in the workgroup 5 as well, contributing to the development of tools and protocols to assess the resolution of light microscopes.

» More about the QUAREP-LiMi initiative
» The new protocol on
» Software repositories on Github
» Reference database (account required)
» More about the FMI FAIM technology platform

FMI The new protocol represents a worldwide standard to assess illumination quality in microscopy

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