Kilohertz droplet-on-demand serial femtosecond crystallography at the European XFEL station FXE.

X-ray Free Electron Lasers (XFELs) allow the collection of high-quality serial femtosecond crystallography data. The next generation of megahertz superconducting FELs promises to drastically reduce data collection times, enabling the capture of more structures with higher signal-to-noise ratios and facilitating more complex experiments. Currently, gas dynamic virtual nozzles (GDVNs) stand as the sole delivery method capable of best utilizing the repetition rate of megahertz sources for crystallography. However, their substantial sample consumption renders their use impractical for many protein targets in serial crystallography experiments. Here, we present a novel application of a droplet-on-demand injection method, which allowed operation at 47 kHz at the European XFEL (EuXFEL) by tailoring a multi-droplet injection scheme for each macro-pulse. We demonstrate a collection rate of 150 000 indexed patterns per hour. We show that the performance and effective data collection rate are comparable to GDVN, with a sample consumption reduction of two orders of magnitude. We present lysozyme crystallographic data using the Large Pixel Detector at the femtosecond x-ray experiment endstation. Significant improvement of the crystallographic statistics was made by correcting for a systematic drift of the photon energy in the EuXFEL macro-pulse train, which was characterized from indexing the individual frames in the pulse train. This is the highest resolution protein structure collected and reported at the EuXFEL at 1.38 Å resolution.

FIRST radio galaxy data set containing curated labels of classes FRI, FRII, compact and bent.

Automated classification of astronomical sources is often challenging due to the scarcity of labelled training data. We present a data set with a total number of 2158 data items that contains radio galaxy images with their corresponding morphological labels taken from various catalogues [1,2]. The data set is curated by removing duplicates, ambiguous morphological labels and by different meta data formats. The image data was acquired by the VLA FIRST (Faint Images of the Radio Sky at Twenty-Centimeters) survey [3]. The morphological labels are collected and the catalogue specific classification definition is converted into a 4-class classification scheme: FRI, FRII, Compact and Bent sources. FRI and FRII correspond to the two classes of the widely used Faranoff-Riley classification [4]. We consider two more classes: compact sources and bent-tail galaxies. For duplicates with different morphological labels, the galaxy is regarded as ambiguously labeled and both coordinates are removed. For the remaining list of coordinates, the radio galaxy images are collected from the virtual observatory skyview (https://skyview.gsfc.nasa.gov/current/cgi/query.pl). The gray value images are provided in the size of 300 × 300 pixel and all pixels with a value below three times the local RMS of the noise are set to this threshold value. The data set is useful for the development of robust machine learning models that automate the classification of radio galaxy images.

In-Vitro MPI-guided IVOCT catheter tracking in real time for motion artifact compensation.

PURPOSE: Using 4D magnetic particle imaging (MPI), intravascular optical coherence tomography (IVOCT) catheters are tracked in real time in order to compensate for image artifacts related to relative motion. Our approach demonstrates the feasibility for bimodal IVOCT and MPI in-vitro experiments. MATERIAL AND METHODS: During IVOCT imaging of a stenosis phantom the catheter is tracked using MPI. A 4D trajectory of the catheter tip is determined from the MPI data using center of mass sub-voxel strategies. A custom built IVOCT imaging adapter is used to perform different catheter motion profiles: no motion artifacts, motion artifacts due to catheter bending, and heart beat motion artifacts. Two IVOCT volume reconstruction methods are compared qualitatively and quantitatively using the DICE metric and the known stenosis length. RESULTS: The MPI-tracked trajectory of the IVOCT catheter is validated in multiple repeated measurements calculating the absolute mean error and standard deviation. Both volume reconstruction methods are compared and analyzed whether they are capable of compensating the motion artifacts. The novel approach of MPI-guided catheter tracking corrects motion artifacts leading to a DICE coefficient with a minimum of 86% in comparison to 58% for a standard reconstruction approach. CONCLUSIONS: IVOCT catheter tracking with MPI in real time is an auspicious method for radiation free MPI-guided IVOCT interventions. The combination of MPI and IVOCT can help to reduce motion artifacts due to catheter bending and heart beat for optimized IVOCT volume reconstructions.

OpenMPIData: An initiative for freely accessible magnetic particle imaging data.

Magnetic particle imaging is a tomographic imaging technique capable of measuring the local concentration of magnetic nanoparticles that can be used as tracers in biomedical applications. Since MPI is still at a very early stage of development, there are only a few MPI systems worldwide that are primarily operated by technical research groups that develop the systems themselves. It is therefore difficult for researchers without direct access to an MPI system to obtain experimental MPI data. The purpose of the OpenMPIData initiative is to make experimental MPI data freely accessible via a web platform. Measurements are performed with multiple phantoms and different image sequences from 1D to 3D. The datasets are stored in the magnetic particle image data format (MDF), an open document standard for storing MPI data. The open data is mainly intended for mathematicians and algorithm developers working on new reconstruction algorithms. Each dataset is designed to pose a specific challenge to image reconstruction. In addition to the measurement data, computer aided design (CAD) drawings of the phantoms are also provided so that the exact dimensions of the particle concentrations are known. Thus, the phantoms can be reproduced by other research groups using additive manufacturing. These reproduced phantoms can be used to compare different MPI systems.

Bimodal intravascular volumetric imaging combining OCT and MPI.

PURPOSE: Intravascular optical coherence tomography (IVOCT) is a catheter-based image modality allowing for high-resolution imaging of vessels. It is based on a fast sequential acquisition of A-scans with an axial spatial resolution in the range of 5-10 µm, that is, one order of magnitude higher than in conventional methods like intravascular ultrasound or computed tomography angiography. However, position and orientation of the catheter in patient coordinates cannot be obtained from the IVOCT measurements alone. Hence, the pose of the catheter needs to be established to correctly reconstruct the three-dimensional vessel shape. Magnetic particle imaging (MPI) is a three-dimensional tomographic, tracer-based, and radiation-free image modality providing high temporal resolution with unlimited penetration depth. Volumetric MPI images are angiographic and hence suitable to complement IVOCT as a comodality. We study simultaneous bimodal IVOCT MPI imaging with the goal of estimating the IVOCT pullback path based on the 3D MPI data. METHODS: We present a setup to study and evaluate simultaneous IVOCT and MPI image acquisition of differently shaped vessel phantoms. First, the influence of the MPI tracer concentration on the optical properties required for IVOCT is analyzed. Second, using a concentration allowing for simultaneous imaging, IVOCT and MPI image data are acquired sequentially and simultaneously. Third, the luminal centerline is established from the MPI image volumes and used to estimate the catheter pullback trajectory for IVOCT image reconstruction. The image volumes are compared to the known shape of the phantoms. RESULTS: We were able to identify a suitable MPI tracer concentration of 2.5 mmol/L with negligible influence on the IVOCT signal. The pullback trajectory estimated from MPI agrees well with the centerline of the phantoms. Its mean absolute error ranges from 0.27 to 0.28 mm and from 0.25 mm to 0.28 mm for sequential and simultaneous measurements, respectively. Likewise, reconstructing the shape of the vessel phantoms works well with mean absolute errors for the diameter ranging from 0.11 to 0.21 mm and from 0.06 to 0.14 mm for sequential and simultaneous measurements, respectively. CONCLUSIONS: Magnetic particle imaging can be used in combination with IVOCT to estimate the catheter trajectory and the vessel shape with high precision and without ionizing radiation.

Moving table magnetic particle imaging: a stepwise approach preserving high spatio-temporal resolution.

Magnetic particle imaging (MPI) is a highly sensitive imaging method that enables the visualization of magnetic tracer materials with a temporal resolution of more than 46 volumes per second. In MPI, the size of the field of view (FoV) scales with the strengths of the applied magnetic fields. In clinical applications, those strengths are limited by peripheral nerve stimulation, specific absorption rates, and the requirement to acquire images of high spatial resolution. Therefore, the size of the FoV is usually a few cubic centimeters. To bypass this limitation, additional focus fields and/or external object movements can be applied. The latter approach is investigated. An object is moved through the scanner bore one step at a time, whereas the MPI scanner continuously acquires data from its static FoV. Using a 3-D phantom and dynamic 3-D in vivo data, it is shown that the data from such a moving table experiment can be jointly reconstructed after reordering the data with respect to the stepwise object shifts and heart beat phases.