We present Biomedisa, a free and easy-to-use open-source online platform developed for semi-automatic segmentation of large volumetric images. The segmentation is based on a smart interpolation of sparsely pre-segmented slices taking into account the complete underlying image data. Biomedisa is particularly valuable when little a priori knowledge is available, e.g. for the dense annotation of the training data for a deep neural network. The platform is accessible through a web browser and requires no complex and tedious configuration of software and model parameters, thus addressing the needs of scientists without substantial computational expertise. We demonstrate that Biomedisa can drastically reduce both the time and human effort required to segment large images. It achieves a significant improvement over the conventional approach of densely pre-segmented slices with subsequent morphological interpolation as well as compared to segmentation tools that also consider the underlying image data. Biomedisa can be used for different 3D imaging modalities and various biomedical applications.

Reliable sample delivery is essential to biological imaging using X-ray Free Electron Lasers (XFELs). Continuous injection using the Gas Dynamic Virtual Nozzle (GDVN) has proven valuable, particularly for time-resolved studies. However, many important aspects of GDVN functionality have yet to be thoroughly understood and/or refined due to fabrication limitations. We report the application of 2-photon polymerization as a form of high-resolution 3D printing to fabricate high-fidelity GDVNs with submicron resolution. This technique allows rapid prototyping of a wide range of different types of nozzles from standard CAD drawings and optimization of crucial dimensions for optimal performance. Three nozzles were tested with pure water to determine general nozzle performance and reproducibility, with nearly reproducible off-axis jetting being the result. X-ray tomography and index matching were successfully used to evaluate the interior nozzle structures and identify the cause of off-axis jetting. Subsequent refinements to fabrication resulted in straight jetting. A performance test of printed nozzles at an XFEL provided high quality femtosecond diffraction patterns.

Climate change increases the occurrence of prolonged drought periods with large implications for forest functioning. Scots pine (Pinus sylvestris L.) is one of the most abundant conifers worldwide and evidence is rising that its resilience to severe drought is limited. However, we know little about its ability to recover from drought-induced embolism. To analyze post-drought hydraulic recovery, we investigated stress and recovery dynamics of leaf gas exchange, nonstructural carbohydrates (NSC), and hydraulic properties in 2.5-year-old Scots pine seedlings. We quantified the degree of xylem embolism by combining in vivo X-ray microtomography (micro-CT) with intrusive techniques including measurements of hydraulic conductivity and dye staining during drought progression, shortterm (2 days), and long-term (4 weeks) recovery. Seedlings were grown under controlled conditions and irrigation was withheld until stomata closed and xylem water potential (Ψ Xylem) declined to-3.2 MPa on average, causing a 46% loss of stem hydraulic conductivity (K s). Following drought release, we found a gradual recovery of leaf gas exchange to 50-60% of control values. This partial recovery indicates hydraulic limitations due to drought-induced damage. Whereas Ψ Xylem recovered close to control values within 2 days, both micro-CT and intrusive measurements revealed no recovery of K s. Moreover, we did not find indications for NSC reserves limiting hydraulic recovery. Our findings demonstrate that Scots pine is able to survive severe drought and to partially recover, although we assume that xylem development during the next growing season might compensate some of the hydraulic impairment. Such drought-induced legacy effects are important when considering vegetation responses to extreme events.

Real-time processing of X-ray image data acquired at synchrotron radiation facilities allows for smart high-speed experiments. This includes workflows covering parameterized and image-based feedback-driven control up to the final storage of raw and processed data. Nevertheless, there is presently no system that supports an efficient construction of such experiment workflows in a scalable way. Thus, here an architecture based on a high-level control system that manages low-level data acquisition, data processing and device changes is described. This system is suitable for routine as well as prototypical experiments, and provides specialized building blocks to conduct four-dimensional in situ, in vivo and operando tomography and laminography.

Background Suction organs provide powerful yet dynamic attachments for many aquatic animals, including octopus, squid, remora, and clingfish. While the functional morphology of suction organs from some cephalopods and fishes has been investigated in detail, there are only few studies on such attachment devices in insects. Here we characterise the morphology and ultrastructure of the suction attachment organs of net-winged midge larvae (genus Liponeura; Diptera: Blephariceridae) – aquatic insects that live on rocks in rapid alpine waterways where flow speeds can reach 3 m s− 1 – using scanning electron microscopy, confocal laser scanning microscopy, and X-ray computed micro-tomography (micro-CT). Furthermore, we study the function of these organs in vivo using interference reflection microscopy. Results We identified structural adaptations important for the function of the suction attachment organs in L. cinerascens and L. cordata. First, a dense array of spine-like microtrichia covering each suction disc comes into contact with the substrate upon attachment, analogous to hairy structures on suction organs from octopus, clingfish, and remora fish. These spine-like microtrichia may contribute to the seal and provide increased shear force resistance in high-drag environments. Second, specialised rim microtrichia at the suction disc periphery were found to form a continuous ring in close contact and may serve as a seal on a variety of surfaces. Third, a V-shaped cut on the suction disc (“V-notch“) is actively opened via two cuticular apodemes inserting on its flanks. The apodemes are attached to dedicated V-notch opening muscles, thereby providing a unique detachment mechanism. The complex cuticular design of the suction organs, along with specialised muscles that attach to them, allows blepharicerid larvae to generate powerful attachments which can withstand strong hydrodynamic forces and quickly detach for locomotion. Conclusion The suction organs from Liponeura are underwater attachment devices specialised for resisting extremely fast flows. Structural adaptations from these suction organs could translate into future bioinspired attachment systems that perform well on a wide range of surfaces.