Enhancing Microscopy Image Quality in Scientific Publications: Global Recommendations

In a concerted global effort, researchers have formulated a set of guidelines for the publication of microscopy images in scientific publications. These guidelines, presented in the form of concise checklists, serve as the cornerstone for ensuring the comprehensibility and reproducibility of bioimaging data in the fields of life sciences and medicine. Such measures are indispensable for unlocking the full research potential inherent in these data.

These significant findings, the collaborative work of 54 researchers hailing from over 48 institutions worldwide, were published in the esteemed journal Nature Methods. This groundbreaking work is poised to exert a substantial influence on the global practices governing the publication of microscopy images. These researchers constitute a vital working group within the broader global initiative known as Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy (QUAREP-LiMi).

EMBL, renowned globally for its data and microscopy services, has long championed open access principles. These newly established guidelines play a pivotal role in realizing this vision by standardizing the manner in which bioimaging data are shared.

Christian Tischer, a team leader at EMBL’s Data Science Center, represented EMBL and played an indispensable role in crafting the checklists at the core of this initiative. Tischer emphasized the importance of scientific accuracy, reproducibility, and accessibility in published research, particularly in the realm of microscopy-based investigations. This encompasses issues such as image data legibility in publication figures, provision of scale information, judicious contrast adjustments, as well as the sharing of image data in public archives and making analysis pipelines accessible on cloud computing platforms.

Each year, over a million scientific papers emerge in the fields of life sciences and medicine, with approximately one-third of them featuring images, including microscopy data of cells and tissues. Regrettably, many of these images remain cryptic to their target audience due to missing critical information, such as scale details. Furthermore, they often lack comprehensive descriptions of the methods used to generate the microscopy data, hindering the reproducibility of such research by fellow scientists.

Now, as part of the global QUAREP-LiMi initiative, this specialized working group has devised communication guidelines, particularly tailored to microscopy images and image analysis data.

Helena Jambor, the initiator of the working group responsible for these guidelines and an author of the scientific paper, emphasized the pressing need for publication standards for microscopy images, echoing the sentiments of scientists worldwide and leading scientific journals. She highlighted the importance of researchers themselves crafting these guidelines, as they possess the insight required to define the crucial quality criteria for their work. The group’s success in achieving a broad consensus involved researchers from numerous world-leading institutes in the life sciences.

The checklists provided by the group offer specific guidance, such as ensuring the selection of relevant image sections, the proper naming of color channels in fluorescence microscopy images, and the selection of colors discernible to color-blind readers. Recognizing that many publications involve image analysis results, the group mandates precise descriptions of data generation methods, including software tools and settings, alongside the availability of sample data for result verification. In general, the guidelines advocate the sharing of images in suitable databases to foster further research within the scientific community.

Christopher Schmied, the first author of the research paper and a scientist at the Human Technopole Foundation in Milan and the Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) in Berlin, underlined that these guidelines cater to researchers of all levels, from novices to experts. They empower researchers to publish images and image analysis results that meet rigorous quality standards, ensuring reproducibility and credibility while providing a solid foundation for future research endeavors.

Within the checklists, the criteria are categorized into three tiers, enabling users to select between minimal, recommended, and ideal requirements for effective bioimaging data communication. Helena Jambor expressed optimism that these criteria could become mandatory standards for publication in leading scientific journals, citing the proactive nature of the global initiative members, who continually update the checklists. The initiative also intends to develop training materials and tutorials for effective communication of microscopy images.

Christian Tischer expressed the hope that the continued adoption of these guidelines by scientists and scientific journals would foster a culture where life science research thrives with enhanced transparency, stemming from the clear and consistent sharing of bioimaging data. For educators like him, who train life scientists in managing and analyzing bioimaging data, this information can be disseminated more effectively in courses, thereby perpetuating these vital practices.

Source: European Molecular Biology Laboratory

Leave a Comment