Abstract. We describe the physical model, numerical algorithms, and software structure of a model consisting of the Weather Research and Forecasting (WRF) model, coupled with the fire-spread model (SFIRE) module. In every time step, the fire model inputs the surface wind, which drives the fire, and outputs the heat flux from the fire into the atmosphere, which in turn influences the atmosphere. SFIRE is implemented by the level set method, which allows a submesh representation of the burning region and a flexible implementation of various kinds of ignition. The coupled model is capable of running on a cluster faster than real time even with fine resolution in dekameters. It is available as a part of the Open Wildland Fire Modeling (OpenWFM) environment at http://openwfm.org, which contains also utilities for visualization, diagnostics, and data processing, including an extended version of the WRF Preprocessing System (WPS). The SFIRE code with a subset of the features is distributed with WRF 3.3 as WRF-Fire.

Convergence of the ensemble Kalman filter in the limit for large ensembles to the Kalman filter is proved. In each step of the filter, convergence of the ensemble sample covariance follows from a weak law of large numbers for exchangeable random variables, the continuous mapping theorem gives convergence in probability of the ensemble members, and Lp bounds on the ensemble then give Lp convergence.

Motivation While deep-learning algorithms have demonstrated outstanding performance in semantic image segmentation tasks, large annotation datasets are needed to create accurate models. Annotation of histology images is challenging due to the effort and experience required to carefully delineate tissue structures, and difficulties related to sharing and markup of whole-slide images. Results We recruited 25 participants, ranging in experience from senior pathologists to medical students, to delineate tissue regions in 151 breast cancer slides using the Digital Slide Archive. Inter-participant discordance was systematically evaluated, revealing low discordance for tumor and stroma, and higher discordance for more subjectively defined or rare tissue classes. Feedback provided by senior participants enabled the generation and curation of 20 000+ annotated tissue regions. Fully convolutional networks trained using these annotations were highly accurate (mean AUC=0.945), and the scale of annotation data provided notable improvements in image classification accuracy. Availability and Implementation Dataset is freely available at: https://goo.gl/cNM4EL. Supplementary information Supplementary data are available at Bioinformatics online.

A wildfire model is formulated based on balance equations for energy and fuel, where the fuel loss due to combustion corresponds to the fuel reaction rate. The resulting coupled partial differential equations have coefficients that can be approximated from prior measurements of wildfires. An ensemble Kalman filter technique with regularization is then used to assimilate temperatures measured at selected points into running wildfire simulations. The assimilation technique is able to modify the simulations to track the measurements correctly even if the simulations were started with an erroneous ignition location that is quite far away from the correct one.

Tissue based cancer studies can generate large amounts of histology data in the form of glass slides. These slides contain important diagnostic, prognostic, and biological information, and can be digitized into expansive and high-resolution whole-slide images (WSI) using slide-scanning devices. Effectively utilizing digital pathology data in cancer research requires the ability to manage, visualize, share and perform quantitative analysis on these large amounts of image data, tasks that are often complex and difficult for investigators with the current state of commercial digital pathology software. In this paper we describe the Digital Slide Archive (DSA), an open source web-based platform for digital pathology. DSA allows investigators to manage large collections of histologic images and integrate them with clinical and genomic metadata. The open-source model enables DSA to be extended to provide additional capabilities.

A B S T R A C TA new type of ensemble filter is proposed, which combines an ensemble Kalman filter (EnKF) with the ideas of morphing and registration from image processing. This results in filters suitable for non-linear problems whose solutions exhibit moving coherent features, such as thin interfaces in wildfire modelling. The ensemble members are represented as the composition of one common state with a spatial transformation, called registration mapping, plus a residual. A fully automatic registration method is used that requires only gridded data, so the features in the model state do not need to be identified by the user. The morphing EnKF operates on a transformed state consisting of the registration mapping and the residual. Essentially, the morphing EnKF uses intermediate states obtained by morphing instead of linear combinations of the states.

Abstract. Coupled atmosphere-fire models can now generate forecasts in real time, owing to recent advances in computational capabilities. WRF-SFIRE consists of the Weather Research and Forecasting (WRF) model coupled with the fire-spread model SFIRE. This paper presents new developments, which were introduced as a response to the needs of the community interested in operational testing of WRF-SFIRE. These developments include a fuel-moisture model and a fuel-moisture-data-assimilation system based on the Remote Automated Weather Stations (RAWS) observations, allowing for fire simulations across landscapes and time scales of varying fuel-moisture conditions. The paper also describes the implementation of a coupling with the atmospheric chemistry and aerosol schemes in WRF-Chem, which allows for a simulation of smoke dispersion and effects of fires on air quality. There is also a data-assimilation method, which provides the capability of starting the fire simulations from an observed fire perimeter, instead of an ignition point. Finally, an example of operational deployment in Israel, utilizing some of the new visualization and datamanagement tools, is presented.

In this study, we describe how WRF-Sfire is coupled with WRF-Chem to construct WRFSC, an integrated forecast system for wildfire and smoke prediction. The integrated forecast system has the advantage of not requiring a simple plume-rise model and assumptions about the size and heat release from the fire in order to determine fire emissions into the atmosphere. With WRF-Sfire, wildfire spread, plume and plume-top heights are predicted directly, at every WRF time-step, providing comprehensive meteorology and fire emissions to the chemical transport model WRF-Chem.Evaluation of WRFSC was based on comparisons between available observations to the results of two WRFSC simulations.The study found overall good agreement between forecasted and observed fire spread and smoke transport for the Witch-Guejito fire. Also the simulated PM2.5 (fine particulate matter) peak concentrations matched the observations. However, the NO and ozone levels were underestimated in the simulations and the peak concentrations were mistimed. Determining the terminal or plume-top height is one of the most important aspects of simulating wildfire plume transport, and the study found overall good agreement between simulated and observed plume-top heights, with some (10% or less) underestimation by the simulations. One of the most promising results of the study was the agreement between passive-tracer modeled plumetop heights for the Barker Canyon fire simulation and observations. This simulation took only 13h, with the first 24h forecast ready in almost 3h, making it a possible operational tool for providing emission profiles for external chemical transport models.