Segmenting the nuclei of cells in microscopy images is often the first step in the quantitative analysis of imaging data for biological and biomedical applications. Many bioimage analysis tools can segment nuclei in images but need to be selected and configured for every experiment. The 2018 Data Science Bowl attracted 3,891 teams worldwide to make the first attempt to build a segmentation method that could be applied to any two-dimensional light microscopy image of stained nuclei across experiments, with no human interaction. Top participants in the challenge succeeded in this task, developing deep-learning-based models that identified cell nuclei across many image types and experimental conditions without the need to manually adjust segmentation parameters. This represents an important step toward configuration-free bioimage analysis software tools.

Image-based profiling has emerged as a powerful technology for various steps in basic biological and pharmaceutical discovery, but the community has lacked a large, public reference set of data from chemical and genetic perturbations. Here we present data generated by the Joint Undertaking for Morphological Profiling (JUMP)-Cell Painting Consortium, a collaboration between 10 pharmaceutical companies, six supporting technology companies, and two non-profit partners. When completed, the dataset will contain images and profiles from the Cell Painting assay for over 116,750 unique compounds, over-expression of 12,602 genes, and knockout of 7,975 genes using CRISPR-Cas9, all in human osteosarcoma cells (U2OS). The dataset is estimated to be 115 TB in size and capturing 1.6 billion cells and their single-cell profiles. File quality control and upload is underway and will be completed over the coming months at the Cell Painting Gallery: https://registry.opendata.aws/cellpainting-gallery. A portal to visualize a subset of the data is available at https://phenaid.ardigen.com/jumpcpexplorer/.

Forums and email lists play a major role in assisting scientists in using software. Previously, each open-source bioimaging software package had its own distinct forum or email list. Although each provided access to experts from various software teams, this fragmentation resulted in many scientists not knowing where to begin with their projects. Thus, the scientific imaging community lacked a central platform where solutions could be discussed in an open, software-independent manner. In response, we introduce the Scientific Community Image Forum, where users can pose software-related questions about digital image analysis, acquisition, and data management.

The skin of aquatic vertebrates surrounds all the mechanical lineages of the body and must, therefore, play an important role in locomotion. A cross-woven collagenous dermal design has converged across several clades of vertebrates. Despite this intriguing pattern, the biomechanical role of skin in swimming fishes remains largely unknown. A direct force transmission role for fish skin has been proposed, a hypothesis that is supported by the arrangement of the connective tissues linking the skin to the axial musculature. To evaluate this direct force-transmission hypothesis, we undertook hundreds of uniaxial tensile tests on skin samples from coho salmon (Oncorhynchus kisutch), Florida pompano (Trachinotus carolinus), and red snapper (Lutjanus campechanus). To do this, we developed highly precise, low-cost, custom-built material testing units. To augment our data, we also assembled a data set of skin stiffness of four additional species of actinopterygians fishes from previously published studies. We found that stiffness varies significantly between species and that the skin of our study species was increasingly stiff along a rostrocaudal gradient. Placing our results in the context of the limited body of previous work, we found that species with lower skin stiffness exhibit shorter propulsive wavelengths and low thrust production at the caudal fin and species with higher skin stiffness possess longer propulsive wavelengths and high thrust production at the caudal fin. In addition, we found that mean collagen fiber angle was close to 50° and that fiber angle was lower in posterior samples than in anterior and midlateral samples. Taken as a whole, our mechanical and morphological results support the hypothesis that the skin functions as an important direct force-transmission device in actinopterygians whereby muscular force generated in anterior myotomes is transmitted to the posterior of the body through the increasingly stiff skin.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.