Reference bioimaging to assess the phenotypic trait diversity of bryophytes within the family Scapaniaceae

Abstract

Macro- and microscopic images of organisms are pivotal in biodiversity research. Despite that bioimages have manifold applications such as assessing the diversity of form and function, FAIR bioimaging data in the context of biodiversity are still very scarce, especially for difficult taxonomic groups such as bryophytes. Here, we present a high-quality reference dataset containing macroscopic and bright-field microscopic images documenting various phenotypic characters of the species belonging to the liverwort family of Scapaniaceae occurring in Europe. To encourage data reuse in biodiversity and adjacent research areas, we annotated the imaging data with machine-actionable metadata using community-accepted semantics. Furthermore, raw imaging data are retained and any contextual image processing like multi-focus image fusion and stitching were documented to foster good scientific practices through source tracking and provenance. The information contained in the raw images are also of particular interest for machine learning and image segmentation used in bioinformatics and computational ecology. We expect that this richly annotated reference dataset will encourage future studies to follow our principles.

Untargeted Metabolomics for Integrative Taxonomy: Metabolomics, DNA Marker-Based Sequencing, and Phenotype Bioimaging

“…Acquisition of images was based on the methods described in [ 78 ] and was only slightly modified for thallose liverwort species. In short, a Zeiss Axio Scope.A1 microscope was used for brightfield microscopy.…”

“…Images were manually segmented and interfering background removed using the flood select, brush selection, and freehand selection tools in the software Affinity Photo. Microscopic scales were then placed onto the segmented images using the approach described in [ 78 ].…”

Estimating essential phenotypic and molecular traits from integrative biodiversity data

“…Validations of metadata, image properties and technical quality of fused composite images were conducted with the approach described in 40 . Species identities were kindly validated by Tomas Hallingbäck and Galin Gospodinov.…”