Political scientists rely on complex software to conduct research, and much of the software they use is written and distributed for free by other researchers. This article contends that creating and maintaining these public goods is costly for individual software developers but that it is not adequately incentivized by the academic community. We demonstrate that statistical software is used widely but rarely cited in political science, and we highlight a partial solution to this problem: software bibliographies. To facilitate their creation, we introduce softbib, an R package that scans analysis scripts, detects the software used in those scripts, and automatically creates bibliographies. We hope that recognizing the contribution of software developers to science will encourage more scholars to create public goods, which could yield important downstream benefits.

Spatially resolved in situ transmission electron microscopy (TEM), equipped with direct electron detection systems, is a suitable technique to record information about the atom-scale dynamics with millisecond temporal resolution from materials. However, characterizing dynamics or fluxional behavior requires processing short time exposure images which usually have severely degraded signal-to-noise ratios. The poor signal-to-noise associated with high temporal resolution makes it challenging to determine the position and intensity of atomic columns in materials undergoing structural dynamics. To address this challenge, we propose a noise-robust, processing approach based on blob detection, which has been previously established for identifying objects in images in the community of computer vision. In particular, a blob detection algorithm has been tailored to deal with noisy TEM image series from nanoparticle systems. In the presence of high noise content, our blob detection approach is demonstrated to outperform the results of other algorithms, enabling the determination of atomic column position and its intensity with a higher degree of precision.

A deep convolutional neural network has been developed to denoise atomic-resolution transmission electron microscope image datasets of nanoparticles acquired using direct electron counting detectors, for applications where the image signal is severely limited by shot noise. The network was applied to a model system of CeO2-supported Pt nanoparticles. We leverage multislice image simulations to generate a large and flexible dataset for training the network. The proposed network outperforms state-of-the-art denoising methods on both simulated and experimental test data. Factors contributing to the performance are identified, including (a) the geometry of the images used during training and (b) the size of the network's receptive field. Through a gradient-based analysis, we investigate the mechanisms learned by the network to denoise experimental images. This shows that the network exploits both extended and local information in the noisy measurements, for example, by adapting its filtering approach when it encounters atomic-level defects at the nanoparticle surface. Extensive analysis has been done to characterize the network's ability to correctly predict the exact atomic structure at the nanoparticle surface. Finally, we develop an approach based on the log-likelihood ratio test that provides a quantitative measure of the agreement between the noisy observation and the atomic-level structure in the network-denoised image.

There is often a need to locate the same cellular structure of interest in light and electron microscopy, which can be a difficult task. Here we present a method that uses only commercially available reagents and standard epi-fluorescence and transmission electron microscopy (TEM) technology to make correlative light and electron microscopy (CLEM) available to a large group of researchers without specialized CLEM hardware. This was achieved by seeding cells on photo-etched gridded cover slips and staining the protein to be localized with a secondary antibody coupled to both a fluorophore and 10 nm gold. The presence of the grid allowed for the alignment of light microscopy images with TEM images and the double-labeled antibody revealed co-localization of the fluorophore with gold particles.