ImageJ2: ImageJ for the next generation of scientific image data

ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software's ability to handle the requirements of modern science. Due to these new and emerging challenges in scientific imaging, ImageJ is at a critical development crossroads. We present ImageJ2, a total redesign of ImageJ offering a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace. ImageJ2 provides a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs

Photonic Phase Gate via an Exchange of Fermionic Spin Waves in a Spin Chain

We propose a new protocol for implementing the two-qubit photonic phase gate. In our approach, the pi phase is acquired by mapping two single photons into atomic excitations with fermionic character and exchanging their positions. The fermionic excitations are realized as spin waves in a spin chain, while photon storage techniques provide the interface between the photons and the spin waves. Possible imperfections and experimental systems suitable for implementing the gate are discussed.Comment: 4 pages, 1 figure. V2: extended the discussion of the main idea, removed supplementary information and inessential extensions, added references. V3: slightly modified references and text - final version as published in Phys. Rev. Let

A joint time-dependent density-functional theory for excited states of electronic systems in solution

We present a novel joint time-dependent density-functional theory for the description of solute-solvent systems in time-dependent external potentials. Starting with the exact quantum-mechanical action functional for both electrons and nuclei, we systematically eliminate solvent degrees of freedom and thus arrive at coarse-grained action functionals which retain the highly accurate \emph{ab initio} description for the solute and are, in principle, exact. This procedure allows us to examine approximations underlying popular embedding theories for excited states. Finally, we introduce a novel approximate action functional for the solute-water system and compute the solvato-chromic shift of the lowest singlet excited state of formaldehyde in aqueous solution, which is in good agreement with experimental findings.Comment: 11 page

The radical character of the acenes: A density matrix renormalization group study

We present a detailed investigation of the acene series using high-level wavefunction theory. Our ab-initio Density Matrix Renormalization Group algorithm has enabled us to carry out Complete Active Space calculations on the acenes from napthalene to dodecacene correlating the full pi-valence space. While we find that the ground-state is a singlet for all chain-lengths, examination of several measures of radical character, including the natural orbitals, effective number of unpaired electrons, and various correlation functions, suggests that the longer acene ground-states are polyradical in nature.Comment: 10 pages, 8 figures, supplementary material, to be published in J. Chem. Phys. 127, 200

A critical assessment of the pairing symmetry in NaxCoO2.yH2O

We examine each of the symmetry-allowed pairing states of NaxCoO2.yH2O and compare their properties to what is experimentally and theoretically established about the compound. In this way, we can eliminate the vast majority of states that are technically allowed and narrow the field to two, both of f-wave type states. We discuss the expected features of these states and suggest experiments that can distinguish between them. We also discuss odd-frequency gap pairing and how it relates to available experimental evidence

Willmore minimizers with prescribed isoperimetric ratio

Motivated by a simple model for elastic cell membranes, we minimize the Willmore functional among two-dimensional spheres embedded in R^3 with prescribed isoperimetric ratio

Existing fluid responsiveness studies using the mini-fluid challenge may be misleading:Methodological considerations and simulations

BACKGROUND: The mini-fluid challenge (MFC) is a clinical concept of predicting fluid responsiveness by rapidly infusing a small amount of intravenous fluids, typically 100 ml, and systematically assessing its haemodynamic effect. The MFC method is meant to predict if a patient will respond to a subsequent, larger fluid challenge, typically another 400 ml, with a significant increase in stroke volume. METHODS: We critically evaluated the general methodology of MFC studies, with statistical considerations, secondary analysis of an existing study, and simulations. RESULTS: Secondary analysis of an existing study showed that the MFC could predict the total fluid response (MFC + 400 ml) with an area under the receiver operator characteristics curve (AUROC) of 0.92, but that the prediction was worse than random for the response to the remaining 400 ml (AUROC = 0.33). In a null simulation with no response to both the MFC and the subsequent fluid challenge, the commonly used analysis could predict fluid responsiveness with an AUROC of 0.73. CONCLUSION: Many existing MFC studies are likely overestimating the classification accuracy of the MFC. This should be considered before adopting the MFC into clinical practice. A better study design includes a second, independent measurement of stroke volume after the MFC. This measurement serves as reference for the response to the subsequent fluid challenge

Fire and Smoke Remote Sensing and Modeling Uncertainties: Case Studies in Northern Sub‐Saharan Africa

Significant uncertainties are incurred in deriving various quantities related to biomass burning from satellite measurements at different scales, and, in general, the coarser the resolution of observation the larger the uncertainty. WRF‐Chem model simulations of smoke over the northern sub‐Saharan African (NSSA) region for January–February 2010, using fire energetics and emissions research version 1.0 (FEERv1) aerosol emissions derived from MODIS measurements of fire radiative power (FRP) and aerosol optical depth (AOD), resulted in a severe model underestimation of AOD compared with satellite retrievals. Such uncertainties are attributable to three major factors: limitations in the spatial and temporal resolutions of the satellite observations used to quantify emissions, modeling parameters and assumptions, and the unique geographic characteristics of NSSA. It is recommended that field campaigns involving synergistic coordination of ground‐based, airborne, and satellite measurements with modeling be conducted in major and complex biomass burning regions such as the NSSA, and that significant improvements in the spatial and temporal resolutions of observation systems needed to reduce uncertainties in biomass burning characterization be seriously considered in future satellite missions