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Bioimaging refers to a collection of methods to visualize the internal structures and mechanisms of living organisms. The fundamental tool, the microscope, has enabled seminal discoveries like that of the cell as the smallest unit of life, and continues to expand our understanding of biological processes. Today, we can follow the interaction of single molecules within nanoseconds in a living cell, and the development of complete small organisms like fish and flies over several days starting from the fertilized egg. Each image pixel encodes multiple spatiotemporal and spectral dimensions, compounding the massive volume and complexity of bioimage data. Proper handling of this data is indispensable for analysis and its lack has become a growing hindrance for the many disciplines of the life and biomedical sciences relying on bioimaging. No single domain has the expertise to tackle this bottleneck alone. As a method-specific consortium, NFDI4BIOMAGE seeks to address these issues, enabling bioimaging data to be shared and re-used like they are acquired, i.e., independently of disciplinary boundaries. We will provide solutions for exploiting the full information content of bioimage data and enable new discoveries through sharing and re-analysis. Our RDM strategy is based on a robust needs analysis that derives not only from a community survey but also from over a decade of experience in German BioImaging, the German Society for Microscopy and Image Analysis. It considers the entire lifecycle of bioimaging data, from acquisition to archiving, including analysis and enabling re-use. A foundational element of this strategy is the definition of a common, cloud-compatible, and interoperable digital object that bundles binary images with their descriptive and provenance metadata. With members from plant biology to neuroscience, NFDI4BIOIMAGE will champion the standardization of bioimage data to create a framework that answers discipline-specific needs while ensuring communicati

We present a scalable GPU-based software framework for simulating photon scattering processes of X-ray beams in matter using Monte-Carlo methods. These simulations enable us to predict SAXS signals for experiments at upcoming superlative research facilities like the European XFEL. Often the expected outcome of SAXS experiments is produced by a Fourier Transform of a static 2D electron density distribution. Our new framework provides the opportunity to simulate the probing of femtosecond timescale 3D3V electron dynamics with single and multiple scattering and is extendable by more complex physics processes like laser absorption, atomic excitation and de-excitation to further enhance its predictive capability. As a foundation we use libPMacc, a powerful particle-mesh accelerator library that is also used by PIConGPU, the reportedly fastest fully-relativistic 3D3V particle-in-cell code in the world.

SIMEX progress report June 2017

We present our scientific roadmap towards in-situ modeling of non-LTE interactions of XFEL type X-rays with solid density plasmas using a symbiosis of our performance portable, open source, 3D3V particle-in-cell (PIC) code PIConGPU and its X-ray tracing prototype ParaTAXIS. Treating radiation transport via various atomic processes will enable us to synthesize detector signals and gain predictive capabilities for upcoming pump-probe experiments at the European XFEL. With the world’s fastest particle-in-cell code PIConGPU and the raw computational power of the largest high performance computers we open up the possibility for large-scale case studies of unprecedented repeatability.

This talk shows the progress of PIConGPU on modeling transient high-energy density plasmas for the EUCALL annual workshop. We report on new features in PIConGPU, challenges in HPC-scale I/O for PIC simulations and how we interact with simex_platform and our approach for collisional-radiative non-LTE modeling within the scope of particle-in-cell.

Laser-driven solid density plasmas can be used to generate highly energetic electrons and ions. Diagnosing properties within those plasmas at nm length scales and down to fs timescales is crucial in understanding the involved processes. This has recently become feasible through the advent of X-Ray Free Electron Lasers (XFELs). For instance, XFELs allow imaging the electron density distribution within plasmas via Small Angle X-Ray Scattering (SAXS). We present a scalable GPU-based software framework for simulating photon scattering processes of X-ray beams in matter using Monte-Carlo methods. These simulations enable us to produce synthetic SAXS signals from the interaction of a modeled X-ray pulse with an arbitrarily complex, 3D electron density distribution obtained e.g. from detailed particle-in-cell simulations. Additionally, we present radiation transport methods in our 3D3V fully-relativistic PIC code PIConGPU. These methods enhance modeling of self-imaging of solid-density plasmas and lay the foundation for in-situ simulations of pump-probe experiments. Our new framework allows for single and multiple scattering and is extendable to include complex physics processes like ionization, atomic excitation and de-excitation along the photon path to further enhance its predictive capability.

EUCALL annual meeting poster

Simulations of experiments at modern light sources, such as optical laser laboratories, synchrotrons, and free electron lasers, become increasingly important for the successful preparation, execution, and analysis of these experiments investigating ever more complex physical systems, e.g. biomolecules, complex materials, and ultra-short lived states of matter at extreme conditions. We have implemented a platform for complete start-to-end simulations of various types of photon science experiments, tracking the radiation from the source through the beam transport optics to the sample or target under investigation, its interaction with and scattering from the sample, and registration in a photon detector. This tool allows researchers and facility operators to simulate their experiments and instruments under real life conditions, identify promising and unattainable regions of the parameter space and ultimately make better use of valuable beamtime. In this paper, we present an overview about status and future development of the simulation platform and discuss three applications: 1.) Single-particle imaging of biomolecules using x-ray free electron lasers and optimization of x-ray pulse properties, 2.) x-ray scattering diagnostics of hot dense plasmas in high power laser-matter interaction and identification of plasma instabilities, and 3.) x-ray absorption spectroscopy in warm dense matter created by high energy laser-matter interaction and pulse shape optimization for low-isentrope dynamic compression.

This talk shows the progress of PIConGPU on modeling transient high-energy density plasmas for the EUCALL annual workshop. We report on new features in PIConGPU, challenges in HPC-scale I/O for PIC simulations and how we interact with simex_platform and our approach for collisional-radiative non-LTE modeling within the scope of particle-in-cell.

Simulations of experiments at modern light sources, such as optical laser laboratories, synchrotrons, and free electron lasers, become increasingly important for the successful preparation, execution, and analysis of these experiments investigating ever more complex physical systems, e.g. biomolecules, complex materials, and ultra-short lived states of matter at extreme conditions. We have implemented a platform for complete start-to-end simulations of various types of photon science experiments, tracking the radiation from the source through the beam transport optics to the sample or target under investigation, its interaction with and scattering from the sample, and registration in a photon detector. This tool allows researchers and facility operators to simulate their experiments and instruments under real life conditions, identify promising and unattainable regions of the parameter space and ultimately make better use of valuable beamtime. In this paper, we present an overview about status and future development of the simulation platform and discuss three applications: 1.) Single-particle imaging of biomolecules using x-ray free electron lasers and optimization of x-ray pulse properties, 2.) x-ray scattering diagnostics of hot dense plasmas in high power laser-matter interaction and identification of plasma instabilities, and 3.) x-ray absorption spectroscopy in warm dense matter created by high energy laser-matter interaction and pulse shape optimization for low-isentrope dynamic compression.

We present our scientific roadmap towards in-situ modeling of non-LTE interactions of XFEL type X-rays with solid density plasmas using a symbiosis of our performance portable, open source, 3D3V particle-in-cell (PIC) code PIConGPU and its X-ray tracing prototype ParaTAXIS. Treating radiation transport via various atomic processes will enable us to synthesize detector signals and gain predictive capabilities for upcoming pump-probe experiments at the European XFEL. With the world’s fastest particle-in-cell code PIConGPU and the raw computational power of the largest high performance computers we open up the possibility for large-scale case studies of unprecedented repeatability.

SIMEX progress report June 2017

We present a scalable GPU-based software framework for simulating photon scattering processes of X-ray beams in matter using Monte-Carlo methods. These simulations enable us to predict SAXS signals for experiments at upcoming superlative research facilities like the European XFEL. Often the expected outcome of SAXS experiments is produced by a Fourier Transform of a static 2D electron density distribution. Our new framework provides the opportunity to simulate the probing of femtosecond timescale 3D3V electron dynamics with single and multiple scattering and is extendable by more complex physics processes like laser absorption, atomic excitation and de-excitation to further enhance its predictive capability. As a foundation we use libPMacc, a powerful particle-mesh accelerator library that is also used by PIConGPU, the reportedly fastest fully-relativistic 3D3V particle-in-cell code in the world.

Laser-driven solid density plasmas can be used to generate highly energetic electrons and ions. Diagnosing properties within those plasmas at nm length scales and down to fs timescales is crucial in understanding the involved processes. This has recently become feasible through the advent of X-Ray Free Electron Lasers (XFELs). For instance, XFELs allow imaging the electron density distribution within plasmas via Small Angle X-Ray Scattering (SAXS). We present a scalable GPU-based software framework for simulating photon scattering processes of X-ray beams in matter using Monte-Carlo methods. These simulations enable us to produce synthetic SAXS signals from the interaction of a modeled X-ray pulse with an arbitrarily complex, 3D electron density distribution obtained e.g. from detailed particle-in-cell simulations. Additionally, we present radiation transport methods in our 3D3V fully-relativistic PIC code PIConGPU. These methods enhance modeling of self-imaging of solid-density plasmas and lay the foundation for in-situ simulations of pump-probe experiments. Our new framework allows for single and multiple scattering and is extendable to include complex physics processes like ionization, atomic excitation and de-excitation along the photon path to further enhance its predictive capability.

We present the scientific workflow using our performance portable, open source, 3D3V particle-in-cell (PIC) code PIConGPU and its X-Ray tracing prototype ParaTAXIS to model the interaction of XFEL type X-Rays with solid density plasmas. With an open and modern software environment, our infrastructure is already suited for the largest available supercomputers today and key numerical and methodical challenges have been solved towards first simulations of upcoming pump-probe experiments at the European XFEL.

Realistic simulations of experiments at large scale photon facilities, such as optical laser laboratories, synchrotrons, and free electron lasers, are of vital importance for the successful preparation, execution, and analysis of these experiments investigating ever more complex physical systems, e.g. biomolecules, complex materials, and ultra--short lived states of highly excited matter. Traditional photon science modelling takes into account only isolated aspects of an experiment, such as the beam propagation, the photon-matter interaction, or the scattering process, making idealized assumptions about the remaining parts, e.g. the source spectrum, temporal structure and coherence properties of the photon beam, or the detector response. In SIMEX, we have implemented a platform for complete start-to-end simulations, following the radiation from the source, through the beam transport optics to the sample or target under investigation, its interaction with and scattering from the sample, and its registration in a photon detector, including a realistic model of the detector response to the radiation. Data analysis tools can be hooked up to the modelling pipeline easily. This allows researchers and facility operators to simulate their experiments and instruments in real life scenarios, identify promising and unattainable regions of the parameter space and ultimately make better use of valuable beamtime.

Technische Aspekte des Datenaustauschs SIMEX XFEL Wavefronts -> XRT/PIConGPU via openPMD, die wir zusammen erstellt haben und aktueller Stand der Photon-Plasma Streuung der dann anschließenden HPC Simulation auf unserer Seite. Topics: - SIMEX Platform: Short intro functional parts, PIConGPU = interaction - SIMEX Platform: Wavefronts to Photon Picture - openPMD: why, what, how - status XRT (PIConGPU photon scattering code prototype) - typical HPC size of a PIConGPU simulation for dense targets - continuous integration (simex platform & PIConGPU) - maybe some future ideas such as successful docker-ization of PIConGPU for our "relatively fixed" beamline

Realistic simulations of experiments at large scale photon facilities, such as optical laser laboratories, synchrotrons, and free electron lasers, are of vital importance for the successful preparation, execution, and analysis of these experiments investigating ever more complex physical systems, e.g. biomolecules, complex materials, and ultra--short lived states of highly excited matter. Traditional photon science modelling takes into account only isolated aspects of an experiment, such as the beam propagation, the photon-matter interaction, or the scattering process, making idealized assumptions about the remaining parts, e.g. the source spectrum, temporal structure and coherence properties of the photon beam, or the detector response. In SIMEX, we have implemented a platform for complete start-to-end simulations, following the radiation from the source, through the beam transport optics to the sample or target under investigation, its interaction with and scattering from the sample, and its registration in a photon detector, including a realistic model of the detector response to the radiation. Data analysis tools can be hooked up to the modelling pipeline easily. This allows researchers and facility operators to simulate their experiments and instruments in real life scenarios, identify promising and unattainable regions of the parameter space and ultimately make better use of valuable beamtime.

We present the scientific workflow using our performance portable, open source, 3D3V particle-in-cell (PIC) code PIConGPU and its X-Ray tracing prototype ParaTAXIS to model the interaction of XFEL type X-Rays with solid density plasmas. With an open and modern software environment, our infrastructure is already suited for the largest available supercomputers today and key numerical and methodical challenges have been solved towards first simulations of upcoming pump-probe experiments at the European XFEL.

Technische Aspekte des Datenaustauschs SIMEX XFEL Wavefronts -> XRT/PIConGPU via openPMD, die wir zusammen erstellt haben und aktueller Stand der Photon-Plasma Streuung der dann anschließenden HPC Simulation auf unserer Seite. Topics: - SIMEX Platform: Short intro functional parts, PIConGPU = interaction - SIMEX Platform: Wavefronts to Photon Picture - openPMD: why, what, how - status XRT (PIConGPU photon scattering code prototype) - typical HPC size of a PIConGPU simulation for dense targets - continuous integration (simex platform & PIConGPU) - maybe some future ideas such as successful docker-ization of PIConGPU for our "relatively fixed" beamline