Charles N. Christensen

Niál Perry, Peter P. Pedersen, Charles N. Christensen et al.

Low-cost mobile sensors can be used to collect PM$_{2.5}$ concentration data throughout an entire city. However, identifying air pollution hotspots from the data is challenging due to the uneven spatial sampling, temporal variations in the background air quality, and the dynamism of urban air pollution sources. This study proposes a method to identify urban PM$_{2.5}$ hotspots that addresses these challenges, involving four steps: (1) equip citizen scientists with mobile PM$_{2.5}$ sensors while they travel; (2) normalise the raw data to remove the influence of background ambient pollution levels; (3) fit a Gaussian process regression model to the normalised data and (4) calculate a grid of spatially explicit 'hotspot scores' using the probabilistic framework of Gaussian processes, which conveniently summarise the relative pollution levels throughout the city. We apply our method to create the first ever map of PM$_{2.5}$ pollution in Kigali, Rwanda, at a 200m resolution. Our results suggest that the level of ambient PM$_{2.5}$ pollution in Kigali is dangerously high, and we identify the hotspots in Kigali where pollution consistently exceeds the city-wide average. We also evaluate our method using simulated mobile sensing data for Beijing, China, where we find that the hotspot scores are probabilistically well calibrated and accurately reflect the 'ground truth' spatial profile of PM$_{2.5}$ pollution. Thanks to the use of open-source software, our method can be re-applied in cities throughout the world with a handful of low-cost sensors. The method can help fill the gap in urban air quality information and empower public health officials.

Charles N. Christensen, Meng Lu, Edward N. Ward et al.

Structured illumination microscopy (SIM) is an optical super-resolution technique that enables live-cell imaging beyond the diffraction limit. Reconstruction of SIM data is prone to artefacts, which becomes problematic when imaging highly dynamic samples because previous methods rely on the assumption that samples are static. We propose a new transformer-based reconstruction method, VSR-SIM, that uses shifted 3-dimensional window multi-head attention in addition to channel attention mechanism to tackle the problem of video super-resolution (VSR) in SIM. The attention mechanisms are found to capture motion in sequences without the need for common motion estimation techniques such as optical flow. We take an approach to training the network that relies solely on simulated data using videos of natural scenery with a model for SIM image formation. We demonstrate a use case enabled by VSR-SIM referred to as rolling SIM imaging, which increases temporal resolution in SIM by a factor of 9. Our method can be applied to any SIM setup enabling precise recordings of dynamic processes in biomedical research with high temporal resolution.

Charles N. Christensen, Edward N. Ward, Pietro Lio et al.

Structured illumination microscopy (SIM) has become an important technique for optical super-resolution imaging because it allows a doubling of image resolution at speeds compatible for live-cell imaging. However, the reconstruction of SIM images is often slow and prone to artefacts. Here we propose a versatile reconstruction method, ML-SIM, which makes use of machine learning. The model is an end-to-end deep residual neural network that is trained on a simulated data set to be free of common SIM artefacts. ML-SIM is thus robust to noise and irregularities in the illumination patterns of the raw SIM input frames. The reconstruction method is widely applicable and does not require the acquisition of experimental training data. Since the training data are generated from simulations of the SIM process on images from generic libraries the method can be efficiently adapted to specific experimental SIM implementations. The reconstruction quality enabled by our method is compared with traditional SIM reconstruction methods, and we demonstrate advantages in terms of noise, reconstruction fidelity and contrast for both simulated and experimental inputs. In addition, reconstruction of one SIM frame typically only takes ~100ms to perform on PCs with modern Nvidia graphics cards, making the technique compatible with real-time imaging. The full implementation and the trained networks are available at http://ML-SIM.com.