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U-Net is a generic deep-learning solution for frequently occurring quantification tasks such as cell detection and shape measurements in biomedical image data. We present an ImageJ plugin that enables non-machine-learning experts to analyze their data with U-Net on either a local computer or a remote server/cloud service. The plugin comes with pretrained models for single-cell segmentation and allows for U-Net to be adapted to new tasks on the basis of a few annotated samples.

The Tertiary Lausitz Volcanic Field covers a broad area encompassing parts of Eastern Saxony (Germany), Lower Silesia (Poland) and North Bohemia (Czech Republic). Volcanism was predominantly controlled by the volcano-tectonic evolution of the Ohře Rift and culminated in the Lower Oligocene. This paper deals with the highest volcano of this area, the Lausche Hill (792.6 m a.s.l.) situated in the Lausitz Mountains. We offer a reconstruction of the volcanic edifice and its eruptive history. Its complex genesis is reflected by six different eruption styles and an associated petrographic variety. Furthermore, the Lausche Volcano provides valuable information concerning the morphological evolution of its broader environs. The remnant of an alluvial fan marking a Middle Paleocene–Lower Eocene (62–50 Ma) palaeo-surface is preserved at the base of the volcano. The deposition of this fan can be attributed to a period of erosion of its nearby source area, the Lausitz Block that has undergone intermittent uplift at the Lausitz Overthrust since the Upper Cretaceous. The Lausche Hill is one of at least six volcanoes in the Lausitz Mountains which show an eminent low level of erosion despite their Oligocene age and position on elevated terrain. These volcanoes are exposed in their superficial level which clearly contradicts their former interpretation as subvolcanoes. Among further indications, this implies that the final morphotectonic uplift of the Lausitz Mountains started in the upper Lower Pleistocene (~ 1.3 Ma) due to revived subsidence of the nearby Zittau Basin. It is likely that this neotectonic activity culminated between the Elsterian and Saalian Glaciation (~ 320 ka). The formation of the low mountain range was substantially controlled by the intersection of the Lausitz Overthrust and the Ohře Rift.

On the 24th January 2019 the former director of the Senckenberg Museum of Natural History Görlitz (formerly the Staatliches Museum für Naturkunde Görlitz) Prof. Dr. Wolfram Dunger passed away at the age of 89. The employees of the Museum, his colleagues and friends will always remember him as an international authority on soil zoology and as the ‘leader of the Museum’.

U-Net is a generic deep-learning solution for frequently occurring quantification tasks such as cell detection and shape measurements in biomedical image data. We present an ImageJ plugin that enables non-machine-learning experts to analyze their data with U-Net on either a local computer or a remote server/cloud service. The plugin comes with pretrained models for single-cell segmentation and allows for U-Net to be adapted to new tasks on the basis of a few annotated samples.

Climate change is known to affect the stability of agricultural production all over the world. One of the most important problems associated with agriculture is uptake of water and nutrients by plants. Plant roots are vital organs, which are involved in water and nutrient acquisition and gravitropic responses. This review describes the pivotal role of auxin in root growth, gravitropic and abiotic stress responses, focusing on the regulatory role of CDPK superfamily members in stress tolerance.

The gravitropic bending in plant roots is caused by asymmetric cell elongation. This requires an asymmetric increase in cell surface and therefore plasma membrane components such as lipids, sterols, and membrane proteins. We have identified an early gravity-regulated protein in Arabidopsis thaliana root apices that binds stigmasterol and phosphoethanolamines. This root-specific protein interacts with the membrane transport protein synaptotagmin-1 and was therefore named InteractoR Of SYnaptotagmin1 (ROSY1). While interactions between ML-domain proteins with membrane transport proteins and their impact have been reported from animal cell systems, this is the first report of such an interaction in a plant system. Homozygous mutants of ROSY1 exhibit decreased basipetal auxin transport, a faster root gravitropic response, and an increase in salt stress tolerance. Our results suggest that ROSY1 plays a role in root gravitropism, possibly by facilitating membrane trafficking and asymmetric cell elongation via its interaction with synaptotagmin-1.

Ground-based simulators of microgravity such as fast rotating 2-D clinostats are valuable tools to study gravity related processes. We describe here a versatile g-value-adjustable 2-D clinostat that is suitable for plant analysis. To avoid seedling adaptation to 1 g after clinorotation, we designed chambers that allow rapid fixation. A detailed protocol for fixation, RNA isolation and the analysis of selected genes is described. Using this clinostat we show that mRNA levels of LONG HYPOCOTYL 5 (HY5), MIZU-KUSSEI 1 (MIZ1) and microRNA MIR163 are down-regulated in 5-day-old Arabidopsis thaliana roots after 3 min and 6 min of clinorotation using a maximal reduced g-force of 0.02 g, hence demonstrating that this 2-D clinostat enables the characterization of early transcriptomic events during root response to microgravity. We further show that this 2-D clinostat is able to compensate the action of gravitational force as both gravitropic-dependent statolith sedimentation and subsequent auxin redistribution (monitoring D R5 r e v ::G F P reporter) are abolished when plants are clinorotated. Our results demonstrate that 2-D clinostats equipped with interchangeable growth chambers and tunable rotation velocity are suitable for studying how plants perceive and respond to simulated microgravity.

Three out of seven institutes belonging to the Senckenberg Gesellschaft fur Naturforschung (SGN) house considerable palaeontological collections: The Senckenberg Research Institute and Natural History Museum in Frankfurt on the Main including the Research Station on Quaternary Palaeontology in Weimar, the Senckenberg Naturhistorische Sammlungen Dresden and the Senckenberg Museum fur Naturkunde in Gorlitz. The palaeontological collections of the SGN comprise a total of more than two million specimens and series. Traditionally the different institutes have different stratigraphic and regional focal points, due to the long history of most collections. Frankfurt has a focus on the Palaeozoic (especially Devonian) of the Rhenish slate mountains and the Eocene of the Messel fossil pit (an UNESCO world-heritage site since 1995), Dresden has a focus on the Cretaceous of Saxony and the Tertiary of Central Germany, whereas the smaller collections in Gorlitz have a focus on Eastern Saxony and the Lausitz.

In the version of this paper originally published, one of the affiliations for Dominic Mai was incorrect: "Center for Biological Systems Analysis (ZBSA), Albert-Ludwigs-University, Freiburg, Germany" should have been "Life Imaging Center, Center for Biological Systems Analysis, Albert-Ludwigs-University, Freiburg, Germany." This change required some renumbering of subsequent author affiliations. These corrections have been made in the PDF and HTML versions of the article, as well as in any cover sheets for associated Supplementary Information.

Image quality in light-sheet fluorescence microscopy is strongly affected by the shape of the illuminating laser beam inside embryos, plants or tissue. While the phase of Gaussian or Bessel beams propagating through thousands of cells can be partly controlled holographically, the propagation of fluorescence light to the detector is difficult to control. With each scatter process a fluorescence photon loses information necessary for the image generation. Using Arabidopsis root tips we demonstrate that ballistic and diffusive fluorescence photons can be separated by analyzing the image spectra in each plane without a priori knowledge. We introduce a theoretical model allowing to extract typical scattering parameters of the biological material. This allows to attenuate image contributions from diffusive photons and to amplify the relevant image contributions from ballistic photons through a depth dependent deconvolution. In consequence, image contrast and resolution are significantly increased and scattering artefacts are minimized especially for Bessel beams with confocal line detection.

6 School of Biological Science and Technology, University of Jinan, 336, West Road of Nan Xinzhuang, Jinan 250022, China Wang et al.: 2-D Clinostat for Simulated Microgravity Experiments with Arabidopsis Seedlings Microgravity Sci. Technol. 28, 59–66 (2016). doi:10.1007/s12217-015-94781 was published in an earlier issue instead of being included in this “Topical issue on Ground-Based Facilities”.