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The endothelial blood-brain barrier (BBB) strictly controls immune cell trafficking into the central nervous system (CNS). In neuroinflammatory diseases such as multiple sclerosis, this tight control is however disturbed leading to immune cell infiltration into the CNS. The development ofin vitromodels of the BBB combined with microfluidic devices has advanced our understanding of the cellular and molecular mechanisms mediating the multi-step T-cell extravasation across the BBB. A major bottleneck of thesein vitrostudies is the absence of a robust and automated pipeline suitable for analyzing and quantifying the sequential interaction steps of different immune cell subsets with the BBB under physiological flowin vitro.Here we present the Under-Flow Migration Tracker (UFMTrack) framework and a pipeline built with it to study the entire multi-step extravasation cascade of immune cells across brain microvascular endothelial cells under physiological flowin vitro. UFMTrack achieves 90% track reconstruction efficiency and allows for scaling due to the reduction of the analysis cost and by eliminating experimenter bias. This allowed for performing an in-depth analysis of all behavioral regimes involved in the multi-step immune cell extravasation cascade. The study summarizes how UFMTrack can be employed to delineate the interactions of CD4+and CD8+T cells with the BBB under physiological flow.Author summaryImmune cells continuously travel through our body to perform immune surveillance. They travel within blood vessels at a very high speed, and slow down upon reaching their target organ by the sequential interaction with different adhesion and signaling molecules on the vascular endothelial cells.The study of molecular mechanisms mediating this multi-step extravasation of immune cells has been significantly advanced byin vitrocultures of microvascular endothelial cell monolayers. The dynamic interaction of the immune cells with endothelial monolayers can be imaged over timein vitroin microfluidic devices under physiological flow. The manual analysis of the acquired imaging data is time-consuming and prone to experimenter error. Analysis automation is however hampered by the similar appearance of the unlabeled immune and endothelial cells, and by the flow causing rapid immune cell displacement.Here we introduce UFMTrack, the under-flow migration tracker framework allowing for automated analysis of immune cell interactions with microvascular endothelial cells under flowin vitro. UFMTrack performs comparably to manual analysis of an experienced researcher, eliminates experimenter’s bias, and improves the accuracy of the immune cell tracking. Taken together, UFMTrack sets the stage for scalability ofin vitrolive cell imaging studies of immune cell extravasation.

Knowledge about muon tomography has spread in recent years in the geoscientific community and several collaborations between geologists and physicists have been founded. As the data analysis is still mostly done by particle physicists, we address the need of the geoscientific community to participate in the data analysis, while not having to worry too much about the particle physics equations in the background. The result hereof is SMAUG, a toolbox consisting of several modules that cover the various aspects of data analysis in a muon tomographic experiment. In this study we show how a comprehensive geophysical model can be built from basic physics equations. The emerging uncertainties are dealt with by a probabilistic formulation of the inverse problem, which is finally solved by a Monte Carlo Markov Chain algorithm. Finally, we benchmark the SMAUG results against those of a recent study, which however, have been established with an approach that is not easily accessible to the geoscientific community. We show that they reach identical results with the same level of accuracy and precision.

Arteriogenesis strongly depends on leukocyte and platelet recruitment to the perivascular space of growing collateral vessels. The standard approach for analyzing collateral arteries and leukocytes in arteriogenesis is ex vivo (immuno-) histological methodology. However, this technique does not allow the measurement of dynamic processes such as blood flow, shear stress, cell-cell interactions, and particle velocity. This paper presents a protocol to monitor in vivo processes in growing collateral arteries during arteriogenesis utilizing intravital imaging. The method described here is a reliable tool for dynamics measurement and offers a high-contrast analysis with minimal photo-cytotoxicity, provided by multiphoton excitation microscopy. Prior to analyzing growing collateral arteries, arteriogenesis was induced in the adductor muscle of mice by unilateral ligation of the femoral artery. After the ligation, the preexisting collateral arteries started to grow due to increased shear stress. Twenty-four hours after surgery, the skin and subcutaneous fat above the collateral arteries were removed, constructing a pocket for further analyses. To visualize blood flow and immune cells during in vivo imaging, CD41-fluorescein isothiocyanate (FITC) (platelets) and CD45-phycoerythrin (PE) (leukocytes) antibodies were injected intravenously (i.v.) via a catheter placed in the tail vein of a mouse. This article introduces intravital multiphoton imaging as an alternative or in vivo complementation to the commonly used static ex vivo (immuno-) histological analyses to study processes relevant for arteriogenesis. In summary, this paper describes a novel and dynamic in vivo method to investigate immune cell trafficking, blood flow, and shear stress in a hindlimb model of arteriogenesis, which enhances evaluation possibilities notably.

Poster:Training Applied Data Science

In the DsTau experiment at the CERN SPS (NA65), an independent and direct way to measure tau neutrino production following high energy proton interactions was proposed. As the main source of tau neutrinos is a decay of D$_{s}$ mesons, produced in proton-nucleus interactions, the project aims at measuring a differential cross section of this reaction. The experimental method is based on a use of high resolution emulsion detectors for effective registration of events with short lived particle decays. Here we present the motivation of the study, details of the experimental technique, and the first results of the analysis of the data collected during test runs, which prove feasibility of the full scale study of the process in future. In the DsTau experiment at the CERN SPS, an independent and direct way to measure tau neutrino production following high energy proton interactions was proposed. As the main source of tau neutrinos is a decay of Ds mesons, produced in proton-nucleus interactions, the project aims at measuring a differential cross section of this reaction. The experimental method is based on a use of high resolution emulsion detectors for effective registration of events with short lived particle decays. Here we present the motivation of the study, details of the experimental technique, and the first results of the analysis of the data collected during test runs, which prove feasibility of the full scale study of the process in future.

The use of muon tomography in geoscience projects has been continuously increasing over the past few years. This led to a variety of applications that often use custom-tailored solutions for data acquisition and processing. The respective know-how is splintered and mainly available in a semi-published state in various physics departments that developed these methods. This complicates the design of new studies and the decision whether muon tomography is a suitable tool and feasible for a specific geoscientific question. In this study we review the current state of how muon tomography has been applied in the field of geosciences with the goal of equipping interested geoscientists with the basic knowledge on the physical basics that constitute muon tomography. After an explanation of how muons are produced, how they traverse matter and how they are recorded, a showcase is made of recent applications. These studies show the variety of how muon tomography can be applied in experiments, such that interested readers may implement this technology for their own research. Finally, we provide a guide to best practice to help interested geoscientists decide if and how muon tomography could be implemented in their own research. We believe that through a better mutual understanding, new interdisciplinary collaborations can be initiated that advance the whole field of muon tomography.

Efficient tracking algorithms are a crucial part of particle tracking detectors. While a lot of work has been done in designing a plethora of algorithms, these usually require tedious tuning for each use case. (Weakly) supervised Machine Learning-based approaches can leverage the actual raw data for maximal performance. Yet in realistic scenarios, sufficient high-quality labeled data is not available. While training might be performed on simulated data, the reproduction of realistic signal and noise in the detector requires substantial effort, compromising this approach. Here we propose a novel, fully unsupervised, approach to track reconstruction. The introduced model for learning to disentangle the factors of variation in a geometrically meaningful way employs geometrical space invariances. We train it through constraints on the equivariance between the image space and the latent representation in a Deep Convolutional Autoencoder. Using experimental results on synthetic data we show that a combination of different space transformations is required for meaningful disentanglement of factors of variation. We also demonstrate the performance of our model on real data from tracking detectors., Accepted for publication in JINST

Moalli et al. combine in vitro CD8+ T cell motility analysis with intravital imaging of mouse tissues to identify the actomyosin regulator Myo9b as a central player for nonlymphoid tissue infiltration during adaptive immune responses by facilitating crossing of tissue barriers., T cells are actively scanning pMHC-presenting cells in lymphoid organs and nonlymphoid tissues (NLTs) with divergent topologies and confinement. How the T cell actomyosin cytoskeleton facilitates this task in distinct environments is incompletely understood. Here, we show that lack of Myosin IXb (Myo9b), a negative regulator of the small GTPase Rho, led to increased Rho-GTP levels and cell surface stiffness in primary T cells. Nonetheless, intravital imaging revealed robust motility of Myo9b−/− CD8+ T cells in lymphoid tissue and similar expansion and differentiation during immune responses. In contrast, accumulation of Myo9b−/− CD8+ T cells in NLTs was strongly impaired. Specifically, Myo9b was required for T cell crossing of basement membranes, such as those which are present between dermis and epidermis. As consequence, Myo9b−/− CD8+ T cells showed impaired control of skin infections. In sum, we show that Myo9b is critical for the CD8+ T cell adaptation from lymphoid to NLT surveillance and the establishment of protective tissue–resident T cell populations.

Cosmic ray muons can be used to image the interior of geological sites provided that one employs detectors able to operate in the specific harsh conditions of the mountain environment. We designed and developed a detector exploiting the nuclear emulsion technique to assess the bedrock profile underneath an alpine glacier. Nuclear emulsions do not need any electric power supply or maintenance and allow for the measurement of the muon flux and direction behind a large target volume. The 3D density distribution of the material traversed by muons can then be assessed, bringing relevant information on the shape of the boundary between the glacial ice and the underlying bedrock. This new methodology in the geological field was recently tested in a campaign of measurements in the Jungfrau region of the central Swiss Alps. It was shown that the bedrock surface position can be measured with a resolution of about 5 % when the traversed target is about 100 m thick. Characteristics and performance of the method are reported here and demonstrate that muon radiography based on emulsion detectors represents a powerful tool for the geological study of glaciers.

The development of multi-photon intravital microscopy, in particular two-photon microscopy (2PM), has been a breakthrough technique for deep-tissue imaging of dynamic cell behavior inside live organisms and has substantially advanced the field of immunology. However, intravital time-lapse imaging over prolonged time periods is complicated by slow tissue drifts caused by vital activity, leading to shifting fields of views and making the acquired image sequence partially or completely unanalyzable. To solve this issue, we have established a system that performs continuous drift offset correction in real time using fine pattern matching during 2PM acquisition. We incorporated an extensive use of graphical processing unit (GPU) for high-speed computing required for real time correction during data acquisition. This allowed us to perform prolonged acquisitions and increase the proportion of analyzable datasets to nearly 100% in lymphoid and non-lymphoid tissues. Considering the straightforward implementation of our newly developed system, we anticipate that it will be applicable for other users interested in improving the quality of live imaging data acquisition.

Nuclear emulsions are capable of very high position resolution in the detection of ionizing particles. This feature can be exploited to directly resolve the micrometric-scale fringe pattern produced by a matter-wave interferometer for low energy positrons (in the 10-20 keV range). We have tested the performance of emulsion films in this specific scenario. Exploiting silicon nitride diffraction gratings as absorption masks, we produced periodic patterns with features comparable to the expected interferometer signal. Test samples with periodicities of 6, 7 and 20 {\mu}m were exposed to the positron beam, and the patterns clearly reconstructed. Our results support the feasibility of matter-wave interferometry experiments with positrons., Comment: 15 pages, 10 figures

The OPERA experiment was designed to search for $\nu_{\mu} \rightarrow \nu_{\tau}$ oscillations in appearance mode, i.e. by detecting the $\tau$-leptons produced in charged current $\nu_{\tau}$ interactions. The experiment took data from 2008 to 2012 in the CERN Neutrinos to Gran Sasso beam. The observation of $\nu_{\mu} \rightarrow \nu_{\tau}$ appearance, achieved with four candidate events in a sub-sample of the data, was previously reported. In this paper, a fifth $\nu_{\tau}$ candidate event, found in an enlarged data sample, is described. Together with a further reduction of the expected background, the candidate events detected so far allow assessing the discovery of $\nu_{\mu}\rightarrow \nu_{\tau}$ oscillations in appearance mode with a significance larger than 5 $\sigma$., Comment: 7 pages, 3 figures

Nowadays there is compelling evidence for the existence of dark matter in the Universe. A general consensus has been expressed on the need for a directional sensitive detector to confirm, with a complementary approach, the candidates found in conventional searches and to finally extend their sensitivity beyond the limit of neutrino-induced background. We propose here the use of a detector based on nuclear emulsions to measure the direction of WIMP-induced nuclear recoils. The production of nuclear emulsion films with nanometric grains is established. Several measurement campaigns have demonstrated the capability of detecting sub-micrometric tracks left by low energy ions in such emulsion films. Innovative analysis technologies with fully automated optical microscopes have made it possible to achieve the track reconstruction for path lengths down to one hundred nanometers and there are good prospects to further exceed this limit. The detector concept we propose foresees the use of a bulk of nuclear emulsion films surrounded by a shield from environmental radioactivity, to be placed on an equatorial telescope in order to cancel out the effect of the Earth rotation, thus keeping the detector at a fixed orientation toward the expected direction of galactic WIMPs. We report the schedule and cost estimate for a one-kilogram mass pilot experiment, aiming at delivering the first results on the time scale of six years.