Scalable in situ single-cell profiling by electrophoretic capture of mRNA

Methods to spatially profile the transcriptome are dominated by a trade-off between resolution and throughput. Here, we developed a method named EEL FISH that can rapidly process large tissue samples without compromising spatial resolution. By electrophoretically transferring RNA from a tissue section onto a capture surface, EEL speeds up data acquisition by reducing the amount of imaging needed, while ensuring that RNA molecules move straight down towards the surface, preserving single-cell resolution. We applied EEL on eight entire sagittal sections of the mouse brain and measured the expression patterns of up to 440 genes to reveal complex tissue organisation. Moreover, EEL enabled the study of challenging human samples by removing autofluorescent lipofuscin, so that we could study the spatial transcriptome of the human visual cortex. We provide full hardware specification, all protocols and complete software for instrument control, image processing, data analysis and visualization.

SpinSPJ: a novel NMR scripting system to implement artificial intelligence and advanced applications

Background Software for nuclear magnetic resonance (NMR) spectrometers offer general functionality of instrument control and data processing; these applications are often developed with non-scripting languages. NMR users need to flexibly integrate rapidly developing NMR applications with emerging technologies. Scripting systems offer open environments for NMR users to write custom programs. However, existing scripting systems have limited capabilities for both extending the functionality of NMR software’s non-script main program and using advanced native script libraries to support specialized application domains (e.g., biomacromolecules and metabolomics). Therefore, it is essential to design a novel scripting system to address both of these needs. Result Here, a novel NMR scripting system named SpinSPJ is proposed. It works as a plug-in in the Java based NMR spectrometer software SpinStudioJ. In the scripting system, both Java based NMR methods and original CPython based libraries are supported. A module has been developed as a bridge to integrate the runtime environments of Java and CPython. The module works as an extension in the CPython environment and interacts with Java via the Java Native Interface. Leveraging this bridge, Java based instrument control and data processing methods of SpinStudioJ can be called with the CPython style. Compared with traditional scripting systems, SpinSPJ better supports both extending the non-script main program and implementing advanced NMR applications with a rich variety of script libraries. NMR researchers can easily call functions of instrument control and data processing as well as developing complex functionality (such as multivariate statistical analysis, deep learning, etc.) with CPython native libraries. Conclusion SpinSPJ offers a user-friendly environment to implement custom functionality leveraging its powerful basic NMR and rich CPython libraries. NMR applications with emerging technologies can be easily integrated. The scripting system is free of charge and can be downloaded by visiting http://www.spinstudioj.net/spinspj.

Lumos: A Python Instrument Control Library for Photonics

We present a simulation library in Python 3 called Lumos. Different optimization routines areimplemented using multiple instruments. Automated measurements are implemented in this librarywhich lead to faster measurements as compared to manual sweeps. We elaborate on the experimentalmethods and also example usage is mentioned.

ARINC653 Channel Robustness Verification Using LeonViP-MC, a LEON4 Multicore Virtual Platform

Multicore hardware platforms are being incorporated into spacecraft on-board systems to achieve faster and more efficient data processing. However, such systems lead to increased complexity in software development and represent a considerable challenge, especially concerning the runtime verification of fault-tolerance requirements. To address the ever-challenging verification of this kind of requirement, we introduce a LEON4 multicore virtual platform called LeonViP-MC. LeonViP-MC is an evolution of a previous development called Leon2ViP, carried out by the Space Research Group of the University of Alcalá (SRG-UAH), which has been successfully used in the development and testing of the flight software of the instrument control unit (ICU) of the energetic particle detector (EPD) on board the Solar Orbiter. This paper describes the LeonViP-MC architectural design decisions oriented towards fault-injection campaigns to verify software fault-tolerance mechanisms. To validate the simulator, we developed an ARINC653 communications channel that incorporates fault-tolerance mechanisms and is currently being used to develop a hypervisor level for the GR740 platform.

SYSTEM OF STANDARDIZATION AND METROLOGICAL SUPPORT OF SPEED DEFECTIVE MEANS OF RAILS IN THEIR PRODUCTION AND OPERATION

The importance of standardization and metrological support for high-speed rail flaw detection is noted. JSC “Firm TVEMA” has created a service for quality, factory testing and metrological support. The data on the development and development of the production of JSC “Firma TVEMA” of a complex of removable and mobile technical means of NDT with maximum automation of instrument control and processing of control data, creation of a quality service, factory testing and metrological support are given. It is shown that the service includes structural subdivisions: the department of metrology and quality, a metrological laboratory, a testing laboratory, a technical control bureau that provide scientific and methodological support for the development of measuring instruments, testing, verification and calibration of flaw detection instruments during their production and operation. JSC “Firma TVEMA” organized the production and delivery of models of rail defects to railways with primary certification by the metrological laboratory for dynamic testing of mobile NDT vehicles. A test section was put into operation at the Experimental Ring of JSC VNIIZhT with certified defect models, which made it possible to accumulate research material for the further development of high-speed flaw detectors.