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Abstract: Tickit is an event-based multi-device simulation framework providing configuration and orchestration of complex simulations. It was developed at Diamond Light Source in order to overcome limitations presented to us by some of our existing hardware simulations. With the Tickit framework, simulations can be addressed with a compositional approach. It allows devices to be simulated individually while still maintaining the interconnected behaviour exhibited by their hardware counterparts. This is achieved by modelling the interactions between devices, such as electronic signals. Devices can be collated into larger simulated systems providing a layer of simulated hardware against which to test the full stack of Data Acquisition and Controls tools. We aim to use this framework to extend the scope and improve the interoperability of our simulations; enabling us to further improve the testing of current systems and providing a preferential platform to assist in development of the new Acquisition and Controls tools.

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Abstract: Diamond Light Source has chosen the MicroTCA platform for high performance data acquisition and controls as part of the Diamond-II 4th generation light source upgrade. One requirement is the ability to create custom advanced mezzanine cards (AMCs) for signal conditioning and interlock support. To facilitate this, a module management controller (MMC) is required to negotiate payload power and communications between the AMC and MicroTCA shelf. A popular open-source firmware for controlling such a device is OpenMMC, a project from the Brazillian Light Source (LNLS), which employs a modular approach using FreeRTOS on ARM microcontrollers. Initially, OpenMMC supported the NXP LPC series of devices. However, to make use of Diamond’s existing ST Microelectronics (STM32) infrastructure, we have integrated a CERN fork of the project supporting STM32 microcontrollers into OpenMMC. In this paper, we outline our workflow and experiences introducing a new ARM device into the project.

Open Access

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Abstract: We report about multiscale tomography with high throughput at the Diamond beamline I13L. The beamline has the purpose of multi-scale and operando imaging and consists of two independent branchlines operating in real and reciprocal space. The imaging branch -called Diamond-Manchester branchline- hosts micro-tomography, grating interferometry and a full-field microscope. For rapid recording a broad spectrum of the undulator radiation is used either with band-passing the light with a combination of a filter and a deflecting mirror or using a multilayer monochromator. For all the methods similar recording times can be achieved, with typical scanning times of some minutes and covering the resolution range from microns to the 100nm range. Most recently a robot arm has been installed to increase the throughput to 300 samples per day. The system is now implemented for user operation in remote operation mode for the micro-tomography setup and can be expanded to the two other experiments. The instrumental capabilities are applied on various topics such as the study of biodiversity of insects or the structural variations of electrode materials in batteries. Fast recording with dedicated sample environments (not using the sample changing robot) enables operando studies in many areas, the charging/discharging cycles on batteries, the degradation of teeth enamel under various conditions or loading brine sandstone mixtures with CO2, to name some examples. For imaging with highest spatial resolution we managed to improve significantly the recording speed of ptycho-tomography, which is now in the order of hours and will be reduced further. We demonstrated in the past 2-D recording with 10kHz and expand the instrumental capability with specific hardware dependent triggering and scanning schemes. We expand the research program for multi-scale imaging across both branchlines (imaging and coherence branchlines) with first studies such as batteries, brain research, concrete.

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Abstract: With the wider accessibility of fast direct-electron detectors, collecting electron diffraction patterns in the scanning mode of the transmission electron microscope is becoming common place. These datasets – also known as 4D-STEM, with two dimensions on the scan array and two on the detector plane containing the diffraction corresponding to a given probe position – can be used to reconstruct both the complex object and the probe using ptychographic algorithms. Solving for the object via ptychography, in principle, can relax the requirements on the optical hardware to achieve atomic resolution imaging and has also been shown to be beneficial in reducing the total dose received by the sample. Given the large number of parameters that the experimentalist operating a modern electron microscope can vary, carrying out an electron ptychography experiment, while ensuring that the collected data is conducive to a satisfactory reconstruction, can at times be a daunting task. Here we present a workflow to simulate a matrix of optical and sampling conditions to provide feedback on the optimal conditions to be used for the electron ptychography experiment. As there are various ptychographic reconstruction algorithms with different sampling criteria, our focus here is the extended ptychographical iterative engine (ePIE) implemented by one of the present authors in the ptyREX python library.

Open Access

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Abstract: The Diamond Light Source data analysis infrastructure, Zocalo, is built on a messaging framework. Analysis tasks are processed by a scalable pool of workers running on cluster nodes. Results can be written to a common file system, sent to another worker for further downstream processing and/or streamed to a LIMS. Zocalo allows increased parallelization of computationally expensive tasks and makes the use of computational resources more efficient. The infrastructure is low-latency, fault-tolerant, and allows for highly dynamic data processing. Moving away from static workflows expressed in shell scripts we can easily re-trigger processing tasks in the event that an issue is found. It allows users to re-run tasks with additional input and ensures that automatically and manually triggered processing results are treated equally. Zocalo was originally conceived to cope with the additional demand on infrastructure by the introduction of Eiger detectors with up to 18 Mpixels and running at up to 560 Hz framerate on single crystal diffraction beamlines. We are now adapting Zocalo to manage processing tasks for ptychography, tomography, cryo-EM, and serial crystallography workloads.