Cellular & Molecular Imaging

Bacteria occupy heterogeneous environments, attaching and growing within pores in materials, living hosts, and matrices like soil. Systems that permit high-resolution visualization of dynamic bacterial processes within the physical confines of a realistic and tractable porous media environment are rare. Here we use microfluidics to replicate the grain shape and packing density of natural sands in a 2D platform to study the flow-induced spatial evolution of bacterial biofilms underground. We introduce a wildtype strain (Pantoea sp. YR343, n=3) or an EPS-defective strain (Pantoea sp. YR343 ΔUDP, n=3) to the porous media platform and then simulate a rainfall event using gravity-driven flow of bacterial growth media.

This dataset comprises electron microscopy images of the adipose organ and mammary gland from the laboratory of Saverio Cinti MD (Universita Politecnica delle Marche, univPM, Ancona, Italy). The 16 images are grouped by the resulting publication they contributed to (1-8 images per publication; the source publication of each image is given in the Publication column of the accompanying file list). Samples are mouse adipose organ / mammary gland, except the lipedema images (folder 2025_Obesity), which are human adipose tissue. Saverio Cinti MD univPM, Ancona, Italy, published in: (1) De Matteis R, Zingaretti MC, Murano I, Vitali A, Frontini A, Giannulis I, Barbatelli G, Marcucci F, Bordicchia M, Sarzani R, Raviola E, Cinti S. In Vivo Physiological Transdifferentiation of Adult Adipose Cells. Stem Cells, 2009; 27(11):2761-2768 (folder STEM CELLS 2009; 1 image). (2) Cinti S. Transdifferentiation properties of adipocytes in the adipose organ. American Journal of Physiology - Endocrinology and Metabolism, 2009; 297(5):E977-E986 (folder AM J PHYSIOL 2009; 2 images). (3) Smorlesi A, Frontini A, Giordano A, Cinti S. The adipose organ: white-brown adipocyte plasticity and metabolic inflammation. Obesity Reviews, 2012; 13(Suppl 2):83-96 (folder 2012_Obesity_Rev; 1 image, very early alveolar structure in pregnant mouse). (4) Colleluori G, Perugini J, Barbatelli G, Cinti S. Mammary gland adipocytes in lactation cycle, obesity and breast cancer. Reviews in Endocrine and Metabolic Disorders, 2021; 22(2):241-255 (folder 2021_REMD; 1 image). (5) Michelini S, Greco S, Vaia N, Puleo V, Pellegrino P, Di Vincenzo A, Michelini S, Herbst KL, Goteri G, Luca T, Castorina S, Giordano A, Ciarmela P, Cinti S. Endothelial cell alterations in capillaries of adipose tissue from patients affected by lipedema. Obesity, 2025; 33(4):695-708 (folder 2025_Obesity; 8 images; human). (6) Cinti S. The triangle of transdifferentiation in the adipose organ. Obesity and Endocrinology, 2025; 1(1):wjaf005 (folder OBENDO 2025; 3 images).

The large variety of inflorescence architectures evolved in grasses depends on shape, longevity and determinacy of meristems directing growth of the main and lateral axes. The CLAVATA pathway is known to regulate meristem size and inflorescence architecture in grasses. However, how individual meristem activities are determined and integrated to generate specific inflorescences is not yet understood. We found that activity of distinct meristems in the barley inflorescence is controlled by a signalling pathway comprising the receptor-like kinase Hordeum vulgare CLAVATA1 (HvCLV1) and the secreted CLAVATA3/EMBRYO-SURROUNDING REGION RELATED (CLE)-family peptide FON2-LIKE CLE PROTEIN1 (HvFCP1). HvFCP1 and HvCLV1 interact to promote spikelet formation, but restrict inflorescence meristem and rachilla proliferation. Hvfcp1 or Hvclv1 mutants generate additional rows of spikelets and supernumerary florets from extended rachilla activity. HvFCP1/HvCLV1 signalling coordinates meristem activity through regulation of trehalose-6-phosphate levels. Our discoveries outline a path to engineer inflorescence architecture via specific regulation of distinct meristem activities.

The analysis of behavioural mutants has led to the identification and characterisation of numerous genes affecting nervous system function. For example, in the nematode Caenorhabditis elegans hundreds of genes have been identified whose loss of function leads to abnormal locomotion. We previously published a dataset of high-content, quantitative phenotypes for over 300 locomotion-abnormal mutants. Here we present the raw data underlying this database, consisting of approximately 12,000 videos recordings of locomotion mutants and parallel wild-type controls. Each genotype is represented by at least 15 videos of approximately 15 minutes (27000 frames); accessory files containing records of stage movements and other tracking data are also included. These data represent a useful resource for investigating the behavioural repertoire of C. elegans and assessing the impact of specific genes on locomotion.

Vascular systems are intimately related to the shape and spatial arrangement of the plant organs they support. We investigate the largely unexplored association between spiral phyllotaxis and the vascular system in Asteraceae flowers heads. We imaged heads of eight species using synchrotron-based X-ray micro-computed tomography and applied original virtual reality and haptic software to explore head vasculature in three dimensions. We then constructed a computational model to infer a plausible patterning mechanism. The vascular system in the head of the model plant Gerbera hybrida is qualitatively different from those of Bellis perennis and Helianthus annuus, characterized previously. Cirsium vulgare, Craspedia globosa, Echinacea purpurea, Echinops bannaticus, and Tanacetum vulgare represent variants of the Bellis and Helianthus systems. In each species the layout of the main strands is stereotypical, but details vary. The observed vascular patterns can be generated by a common computational model with different parameter values. In spite of the observed differences of vascular systems in heads, they may be produced by a conserved mechanism. The diversity and irregularities of vasculature stand in contrast with the relative uniformity and regularity of phyllotactic patterns, confirming that phyllotaxis in heads is not driven by the vasculature.

figures and data from EMBOR-2023-58638V2 - Spermatocytes have the capacity to segregate chromosomes despite centriole duplication failure

Our calendar goes into a second round! After having a first edition of the NFDI4BIOIMAGE calendar in 2024, we were eager to assemble an improved version for 2025. This time, we invited also other consortia of the National Research Data Infrastructure (NFDI) to contribute with the aim to extend our calendar to a consortium spanning edition. In this year’s calendar we present very different types of images, taken by mobile phones, cameras, drones, and microscopes, representing the work of our colleagues from the various consortia of NFDI. As you may know, biological images often include additional information in the form of technical metadata, detailing the conditions under which the image was captured. Ideally, this technical data is paired with biological metadata, which explains the specimen depicted and how it was prepared. This year, we also requested that authors submit their images with complete accompanying metadata – a "full package". In bioimaging, the use of metadata standards, specifically the Recommended Metadata for Biological Images (REMBI) guideline (https://doi.org/10.1038/s41592-021-01166-8), has become increasingly common. Many of the submissions for this calendar adhere to REMBI guidelines with comprehensive metadata annotations alongside the bioimage data, as you can observe on the right accompanying our cover image. However, for images captured with other tools, such as mobile phones or drones – images not typically classified as biological – the required metadata differs to accurately convey what is shown and why the image was created. Through this calendar, we step outside the bioimaging sphere to explore how metadata for other types of images might be structured. We hope you will find it as exciting as we do to see all the different contributions and the plethora of information that will teach you more about the respective images. NFDI4BIOMAGE – who we are and what we are aiming for The NFDI4BIOIMAGE consortium started its work in March 2023 as one of the third round applicants within the NFDI, funded by the Federal Ministry for Education and Research (BMBF) and the Länder. Our consortium is working on solutions for bioimage data management along the bioimage life cycle. Bioimaging is an indispensable tool within life and medical sciences. But bioimaging data is also a very divers type of data that is present in numerous proprietary file types, is usually of large size and covers many different imaging modalities. Due to this heterogeneity, storage and interaction with bioimaging data is not trivial and is handled very differently within the research community. Our aim is to find solutions for appropriate bioimage storage, data handling, data analysis, data publication, and to provide overarching standards and support for bioimage data management for the scientific community. Our final goal is to enable researchers to make their bioimaging data Findable, Accessible, Interoperable, and Reusable (FAIR). If you need help or advise on how to handle your bioimaging data, NFDI4BIOIMAGE Data Stewards are here to provide support. Beginning of 2024 we have set up a Help Desk to get in contact with our Data Steward team. You can use the help request form (https://nfdi4bioimage.de/help-desk/) or write an e-mail to helpdesk@nfdi4bioimage.de. For further information you can also get in contact with our project office via e-mail (office@nfdi4bioimage.de) or visit our webpage https://nfdi4bioimage.de.

The Darwin Tree of Life project has the goal to sequence the genomes of 70,000 species of eukaryotic organisms in Britain and Ireland. This is a collection of photographs of the samples included in the study, provided by the National History Museum (NHM).

Time-lapse images of the seed germination procedure for 21 wheat genotypes, 12 barley genotypes, and 6 rice genotypes.

A sustainable approach to address climate change and increasing water demand in agriculture is breeding for plant functional traits that conserve water and enhance climate resilience. Stomata regulate plant-water relations and are promising targets for crop improvement. Here, we investigate the variation in stomatal density (SD) in a diverse apple population (Malus domestica Borkh.) consisting of 269 accessions. Genome-wide association studies identified robust associations with SD on chromosomes 2, 9, and 10 (classified as SNPs with p value higher than adjusted Bonferroni threshold of -log10(p) > 8.78 that were consistently identified across datasets). On chromosome 9, a candidate gene that negatively regulates stomatal development, EPIDERMAL PATTERNING FACTOR 1 (EPF1), was identified inside a genomic region of 241 kb determined by six robust associations. On chromosome 10, a positive regulator candidate gene, EPIDERMAL PATTERNING FACTOR LIKE 9 (STOMAGEN), was identified 1680 kb from the robust association. Identification of positive (STOMAGEN) and negative (EPF1) regulators of SD suggest potential antagonistic roles at the population scale in determining SD. On chromosome 2, a gene co-expression analysis identified a gene cluster containing both EPF1 and STOMAGEN together with a novel candidate gene, CYTOCHROME P450 (CYP77A4), that was located 544 kb from the robust association. The percentage of SD phenotypic variance explained by each robust association was between 7% and 10%. These findings provide a foundation for understanding SD variation at the population scale and opportunities to modulate SD by genomics-assisted breeding strategies.