Effective image visualization for publications - a workflow using open access tools and concepts

Community-developed checklists for publishing images and image analyses

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 obtained images and image-analysis results, there are currently no unified guidelines for best practices. 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 describing image analyses for publications. These checklists offer authors, readers and publishers key recommendations for image formatting and annotation, color selection, data availability and reporting image-analysis workflows. The goal of our guidelines is to increase the clarity and reproducibility of image figures and thereby to heighten the quality and explanatory power of microscopy data.

A community-driven approach to enhancing the quality and interpretability of microscopy images

Scientific publications in the life sciences regularly include image data to display and communicate revelations about cellular structure and function. In 2016, a set of guiding principles known as the 'FAIR Data Principles' were put forward to ensure that research data are findable, accessible, interoperable and reproducible. However, challenges still persist regarding the quality, accessibility and interpretability of image data, and how to effectively communicate microscopy data in figures. This Perspective article details a community-driven initiative that aims to promote the accurate and understandable depiction of light microscopy data in publications. The initiative underscores the crucial role of global and diverse scientific communities in advancing the standards in the field of biological images. Additionally, the perspective delves into the historical context of scientific images, in the hope that this look into our past can help ongoing community efforts move forward.

A timer gene network is spatially regulated by the terminal system in the Drosophila embryo

In insect embryos, anteroposterior patterning is coordinated by the sequential expression of the 'timer' genes caudal, Dichaete, and odd-paired, whose expression dynamics correlate with the mode of segmentation. In Drosophila, the timer genes are expressed broadly across much of the blastoderm, which segments simultaneously, but their expression is delayed in a small 'tail' region, just anterior to the hindgut, which segments during germband extension. Specification of the tail and the hindgut depends on the terminal gap gene tailless, but beyond this the regulation of the timer genes is poorly understood. We used a combination of multiplexed imaging, mutant analysis, and gene network modelling to resolve the regulation of the timer genes, identifying 11 new regulatory interactions and clarifying the mechanism of posterior terminal patterning. We propose that a dynamic Tailless expression gradient modulates the intrinsic dynamics of a timer gene cross-regulatory module, delineating the tail region and delaying its developmental maturation.

Glutamine-dependent signaling controls pluripotent stem cell fate

Human pluripotent stem cells (hPSCs) can self-renew indefinitely or can be induced to differentiate. We previously showed that exogenous glutamine (Gln) withdrawal biased hPSC differentiation toward ectoderm and away from mesoderm. We revealed that, although all three germ lineages are capable of de novo Gln synthesis, only ectoderm generates sufficient Gln to sustain cell viability and differentiation, and this finding clarifies lineage fate restrictions under Gln withdrawal. Furthermore, we found that Gln acts as a signaling molecule for ectoderm that supersedes lineage-specifying cytokine induction. In contrast, Gln in mesoderm and endoderm is the preferred precursor of α-ketoglutarate without a direct signaling role. Our work raises a question about whether the nutrient environment functions directly in cell differentiation during development. Interestingly, transcriptome analysis of a gastrulation-stage human embryo shows that unique Gln enzyme-encoding gene expression patterns may also distinguish germ lineages in vivo. Together, our study suggests that intracellular Gln may help coordinate differentiation of the three germ layers.

Reproducible image handling and analysis

Image data are universal in life sciences research. Their proper handling is not. A significant proportion of image data in research papers show signs of mishandling that undermine their interpretation. We propose that a precise description of the image processing and analysis applied is required to address this problem. A new norm for reporting reproducible image analyses will diminish mishandling, as it will alert co-authors, referees, and journals to aberrant image data processing or, if published nonetheless, it will document it to the reader. To promote this norm, we discuss the effectiveness of this approach and give some step-by-step instructions for publishing reproducible image data processing and analysis workflows.