Superpixel quality in microscopy images: the impact of noise & denoising

Microscopy is a valuable imaging tool in various biomedical research areas. Recent developments have made high resolution acquisition possible within a relatively short time. State-of-the-art imaging equipment such as serial block-face electron microscopes acquire gigabytes of data in a matter of hours. In order to make these amounts of data manageable, a more data-efficient representation is required. A popular approach for such data efficiency are superpixels which are designed to cluster homogeneous regions without crossing object boundaries. The use of superpixels as a pre-processing step has shown significant improvements in making computationally intensive computer vision analysis algorithms more tractable on large amounts of data. However, microscopy datasets in particular can be degraded by noise and most superpixel algorithms do not take this artifact into account. In this paper, we give a quantitative and qualitative comparison of superpixels generated on original and denoised images. We show that several advanced superpixel techniques are hampered by noise artifacts and require denoising and parameter tuning as a pre-processing step. The evaluation is performed on the Berkeley segmentation dataset as well as on fluorescence and scanning electron microscopy data

PAPER Early sex differences in weighting geometric cues

Abstract When geometric and non-geometric information are both available for specifying location, men have been shown to rely more heavily on geometry compared to women. To shed insight on the nature and developmental origins of this sex difference, we examined how 18-to 24-month-olds represented the geometry of a surrounding (rectangular) space when direct non-geometric information (i.e. a beacon) was also available for localizing a hidden object. Children were tested on a disorientation task with multiple phases. Across experiments, boys relied more heavily than girls on geometry to guide localization, as indicated by their errors during the initial phase of the task, and by their search choices following transformations that left only geometry available, or that, under limited conditions, created a conflict between beacon and geometry. Analyses of search times suggested that girls, like boys, had encoded geometry, and testing in a square space ruled out explanations concerned with motivational and methodological variables. Taken together, the findings provide evidence for an early sex difference in the weighting of geometry. This sex difference, we suggest, reflects subtle variation in how boys and girls approach the problem of combining multiple sources of location information

Rational design of a ligand-controlled protein conformational switch

Design of a regulatable multistate protein is a challenge for protein engineering. Here we design a protein with a unique topology, called uniRapR, whose conformation is controlled by the binding of a small molecule. We confirm switching and control ability of uniRapR in silico, in vitro, and in vivo. As a proof of concept, uniRapR is used as an artificial regulatory domain to control activity of kinases. By activating Src kinase using uniRapR in single cells and whole organism, we observe two unique phenotypes consistent with its role in metastasis. Activation of Src kinase leads to rapid induction of protrusion with polarized spreading in HeLa cells, and morphological changes with loss of cell–cell contacts in the epidermal tissue of zebrafish. The rational creation of uniRapR exemplifies the strength of computational protein design, and offers a powerful means for targeted activation of many pathways to study signaling in living organisms