Mattia Donato

Image scanning microscopy (ISM) is emerging as the natural evolution of confocal laser-scanning microscopy, combining optical sectioning and a two-fold improvement in lateral resolution with high signal-to-noise ratio. Single-photon avalanche diode (SPAD) array detectors enable an effective implementation of ISM by recording a micro-image at each scan position with single-photon sensitivity, negligible read-out noise, and without the fixed frame-readout constraints of conventional cameras. Nevertheless, SPAD array-based ISM remains largely confined to laboratories with expertise in microscope development. Here, we present BrightEyes-Scope, a reference implementation of a SPAD array-based ISM system. We provide step-by-step guidelines for optical design, system construction, alignment, calibration, data acquisition, and image reconstruction. Presented as a complete ISM microscope, BrightEyes-Scope also serves as a reference for upgrading existing laser-scanning microscopes. We anticipate that it will accelerate the adoption of ISM for quantitative super-resolution imaging.

Fast detector arrays enable an effective implementation of image scanning microscopy, which overcomes the trade-off between spatial resolution and signal-to-noise ratio of confocal microscopy. However, current image scanning microscopy approaches do not provide optical sectioning and fail with thick samples unless the detector size is limited, thereby introducing a new trade-off between optical sectioning and signal-to-noise ratio. Here we propose a method that overcomes such a limitation. From single-plane acquisition, we reconstruct an image with digital and optical super-resolution, high signal-to-noise ratio and enhanced optical sectioning. On the basis of the observation that imaging with a detector array inherently embeds axial information, we designed a straightforward reconstruction algorithm that inverts the physical model of image scanning microscopy image formation. We present a comprehensive theoretical framework and validate our method with images of biological samples captured using a custom setup equipped with a single-photon avalanche diode array detector. We demonstrate the feasibility of our approach by exciting fluorescence emission in both linear and nonlinear regimes. Moreover, we generalize the algorithm for fluorescence lifetime imaging, fully exploiting the single-photon timing ability of the single-photon avalanche diode array detector. Our method outperforms conventional reconstruction techniques and can be extended to any laser scanning microscopy technique.

Fluorescence confocal laser-scanning microscopy (LSM) is one of the most popular tools for life science research. This popularity is expected to grow thanks to single-photon array detectors tailored for LSM. These detectors offer unique single-photon spatiotemporal information, opening new perspectives for gentle and quantitative super-resolution imaging. However, a flawless recording of this information poses significant challenges for the microscope data-acquisition system. Here, we present a data-acquisition module based on the digital frequency domain principle, able to record photons’ essential spatial and temporal features. We use this module to extend the capabilities of established imaging techniques based on single-photon avalanche diode (SPAD) array detectors, such as fluorescence lifetime image scanning microscopy. Furthermore, we use the module to introduce a robust multi-species approach encoding the fluorophore’s excitation spectra in the time domain. Lastly, we combine time-resolved stimulated emission depletion microscopy with image scanning microscopy, boosting spatial resolution. Our results demonstrate how a conventional fluorescence laser scanning microscope can transform into a simple, information-rich, super-resolved imaging system with the simple addition of a SPAD array detector with a tailored data acquisition system. We expected a blooming of advanced single-photon imaging techniques which effectively harness all the sample information encoded in each photon.

Fluorescence laser-scanning microscopy (LSM) is experiencing a revolution thanks to new single-photon (SP) array detectors, which give access to an entirely new set of single-photon information. Together with the blooming of new SP LSM techniques and the development of tailored SP array detectors, there is a growing need for (i) DAQ systems capable of handling the high-throughput and high-resolution photon information generated by these detectors, and (ii) incorporating these DAQ protocols in existing fluorescence LSMs. We developed an open-source, low-cost, multi-channel time-tagging module (TTM) based on a field-programmable gate array that can tag in parallel multiple single-photon events, with 30 ps precision, and multiple synchronisation events, with 4 ns precision. We use the TTM to demonstrate live-cell super-resolved fluorescence lifetime image scanning microscopy and fluorescence lifetime fluctuation spectroscopy. We expect that our BrightEyes-TTM will support the microscopy community in spreading SP-LSM in many life science laboratories.

Fluorescence laser-scanning microscopy (LSM) is experiencing a revolution thanks to the introduction of new asynchronous read-out single-photon (SP) array detectors. These detectors give access to an entirely new set of single-photon information typically lost in conventional fluorescence LSM, thus triggering a new imaging/spectroscopy paradigm – the so-called singlephoton LSM (SP-LSM). The revolution’s outcomes are, from one side, the blooming of new SP-LSM techniques and tailored SP array detectors; from the other side, the need for data-acquisition (DAQ) systems effectively supporting such innovations. In particular, there is a growing need for DAQ systems capable of handling the high throughput and high temporal resolution information generated by the single-photon detectors. To fill this gap, we developed an open-source multi-channel timetagging module (TTM) based on a field-programmable-gatearray (FPGA), that can temporally tag single-photon events – with 30 ps precision – and synchronisation events – with 4 ns precision. Furthermore, being an open-access project, the TTM can be upgraded, modified, and customized by the microscopy-makers. We connected the TTM to a fluorescence LSM equipped with a single-photon avalanche diode (SPAD) bi-dimensional array detector, and we implemented fluorescence lifetime image scanning microscopy (FLISM) and, for the first time, fluorescence lifetime fluctuation spectroscopy (FLFS). We expect that our BrigthEyes-TTM will support the microscopy community to spread SP-LSM in many life science labs.

The first DSSC 1-Mpixel camera became available at the European XFEL (EuXFEL) in the Hamburg area in February 2019. It was successfully tested, installed, and commissioned at the Spectroscopy and Coherent Scattering Instrument. DSSC is a high-speed, large-area, 2-D imaging detector system optimized for photon science applications in the energy range between 0.25 and 6 keV. The camera is based on direct conversion Si sensors and is composed of 1024 ×1024 pixels of hexagonal shape with a side length of 136 μm. The 256 application-specific integrated circuits (ASICs) provide full parallel readout, comprising analog filtering, digitization, and in-pixel data storage. In order to cope with the demanding X-ray pulse time structure of the EuXFEL, the DSSC provides a peak frame rate of 4.5 MHz. The first Mpixel camera is equipped with miniaturized silicon drift detector (MiniSDD) pixel arrays. The intrinsic response of the pixels and the linear readout limit the dynamic range but allow one to achieve noise values of about 60 electrons r.m.s. at the highest frame rate. The challenge of providing high-dynamic range (~10 ⁴ photons/pixel/pulse) and single-photon detection simultaneously requires a nonlinear system front end, which will be obtained with the DEPFET active pixel technology foreseen for the advanced version of the camera. This technology will provide lower noise and a nonlinear response at the sensor level. This article describes the architecture of the whole detector system together with the main experimental results achieved up to now.

The DSSC (DEPFET Sensor with Signal Compression) is a new instrument with non-linear response and with parallel signal processing (filtering, linear amplification, and 8bit digitization) for all pixels. The DSSC will serve as ultra-fast megapixel imaging detector at the European XFEL (X-ray Free Electron Laser) in Schenefeld, Germany, which began science operation in September this year. In December 2016, at the Variable Polarization XUV Beamline (P04) ofPETRA III, the Synchrotron Radiation Source at DESY in Hamburg, Germany, a prototype ladder system with 128×512 pixels was operated and studied for the first time.The prototype system could be operated and read-out continuously throughout the beamtime. First studies of the performance of the prototype ladder system were performed using the collecteddata. For example, we measured for the first time the system gain for different coarse ASIC gain settings, and studied the dispersion of the gain in a 17×57pixel sensor sub-matrix after using fine ASIC gain settings for gain trimming.

The European X-ray Free Electron Laser is a high-intensity X-ray light source currently being constructed in the Hamburg region that will provide spatially coherent X-rays in the energy range between 0.25 keV-25 keV. The machine will deliver 10 trains/s, consisting of up to 2700 pulses, with a 4.5 MHz repetition rate. The LPD, DSSC and AGIPD detectors are being developed to provide high dynamic range Mpixel imaging capabilities at the mentioned repetition rates. A consequence of these detectors' characteristics is that they generate raw data volumes of up to 12.8 Gbyte/s. In addition, the detectors' on-sensor memory-cell and multi-/non-linear gain architectures pose unique challenges in data correction and calibration, especially given the in the order of one billion calibration parameters. We present how these challenges are addressed for the AGIPD and LPD prototypes within XFEL's control and analysis framework Karabo, which integrates access to hardware conditions, acquisition settings and distributed computing. Implementation is mainly in Python, using self-optimizing (py)CUDA code, numpy and iPython. parallel to achieve near-real time performance for calibration application.