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.

Characterization results of the JUNGFRAU full scale readout ASIC A. Mozzanica, A. Bergamaschi, M.

Tofu is a toolkit for processing large amounts of images and for tomographic reconstruction. Complex image processing tasks are organized as workflows of individual processing steps. The toolkit is able to reconstruct parallel and cone beam as well as tomographic and laminographic geometries. Many pre- and post-processing algorithms needed for high-quality 3D reconstruction are available, e.g. phase retrieval, ring removal and de-noising. Tofu is optimized for stand-alone GPU workstations on which it achieves reconstruction speed comparable with costly CPU clusters. It automatically utilizes all GPUs in the system and generates 3D reconstruction code with minimal number of instructions given the input geometry (parallel/cone beam, tomography/laminography), hence yielding optimal run-time performance. In order to improve accessibility for researchers with no previous knowledge of programming, tofu contains graphical user interfaces for both optimization of 3D reconstruction parameters and batch processing of data with pre-configured workflows for typical computed tomography reconstruction. The toolkit is open source and extensive documentation is available for both end-users and developers. Thanks to the mentioned features, tofu is suitable for both expert users with specialized image processing needs (e.g. when dealing with data from custom-built computed tomography scanners) and for application-specific end-users who just need to reconstruct their data on off-the-shelf hardware.

Severe drought causes persistent damage to the water transport system of Scots pine seedlings and reduces carbon dioxide uptake of needles for at least 1 month

The spectroscopic performance of photon counting detectors is limited by the effects of charge sharing between neighboring pixels and the emission of characteristic X-rays. For these reasons, an event can be either missed or counted more than once. These effects become more and more of a concern when pixel pitches are reduced, and for the technology available so far, this meant that there would always be a trade-off between a high spatial and a high spectral resolution. In this work, we present first measurements obtained with the new Medipix3RX ASIC, which features a network of charge summing circuits establishing a communication between pixels which helps to mitigate these effects. Combined with cadmium telluride sensors, we show that this new technology is successful at improving a detector's spectroscopic capabilities even at pixel pitches as small as 55 μm. At this pitch, we measure an energy response function similar to that observed for a pixel pitch of 165 μm in the absence of a charge summing circuitry. This amounts to an effective reduction of the pixel area by at least one order of magnitude at a comparable energy response. Additionally, we present synchrotron measurements at high X-ray fluxes, where significant pulse pile-up occurs, and provide first experimental evidence for a net benefit when balancing spectroscopic performance and high flux tolerance in charge summing mode.