Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a full two-dimensional (2D) image of the diffracted electron beam at each probe position, typically a 2D grid of probe positions. These 4D-STEM datasets are rich in information, including signatures of the local structure, orientation, deformation, electromagnetic fields, and other sample-dependent properties. However, extracting this information requires complex analysis pipelines that include data wrangling, calibration, analysis, and visualization, all while maintaining robustness against imaging distortions and artifacts. In this paper, we present py4DSTEM, an analysis toolkit for measuring material properties from 4D-STEM datasets, written in the Python language and released with an open-source license. We describe the algorithmic steps for dataset calibration and various 4D-STEM property measurements in detail and present results from several experimental datasets. We also implement a simple and universal file format appropriate for electron microscopy data in py4DSTEM, which uses the open-source HDF5 standard. We hope this tool will benefit the research community and help improve the standards for data and computational methods in electron microscopy, and we invite the community to contribute to this ongoing project.

The finite-amplitude space–time mean flows that are precessionally forced in rotating finite circular cylinders are examined. The findings show that, in addition to conventional Reynolds-stress-type source terms for streaming in oscillatory forced flows, a set of Coriolis-type source terms due the background rotation also contribute. These terms result from the interaction between the equatorial component of the total rotation vector and the overturning flow that is forced by the precession, both of which have azimuthal wavenumbers $m={\pm }1$. The interaction is particular to precessing flows and does not exist in rotating flows driven by libration ($m=0$ forcing) or tides ($m={\pm }2$ forcing). By examining typical example flows in the quasi-linear weakly forced streaming regime, we are able to consider the contributions from the Reynolds-stress terms and the equatorial-Coriolis terms separately, and find that they are of similar magnitude. In the cases examined, the azimuthal component of streaming flow driven by the equatorial-Coriolis terms is everywhere retrograde, whereas that driven by Reynolds stresses may have both retrograde and prograde regions, but the total streaming flows are everywhere retrograde. Even when the forcing frequency is larger than twice the background rotation rate, we find that there is a streaming flow driven by both the Reynolds-stress and the equatorial-Coriolis terms. For cases forced at precession frequencies in near resonance with the eigenfrequencies of the intrinsic inertial modes of the linear inviscid unforced rotating cylinder flow, we quantify theoretically how the amplitude of streaming flow scales with respect to variations in Reynolds number, cylinder tilt angle and aspect ratio, and compare these with numerical simulations.

Contained rotating flows subject to precessional forcing are well known to exhibit rapid and energetic transitions to disorder. Triadic resonance of inertial modes has been previously proposed as an instability mechanism in such flows, and that idea was developed into a successful model for predicting instability in a cylindrical container when departures from solid-body rotation are sufficiently small. Using direct numerical simulation and dynamic mode decomposition, we analyse instabilities of precessing cylinder flows whose three-dimensional basic states, steady in the gimbal frame of reference, may depart substantially from solid-body rotation. In the gimbal frame, the instability can be interpreted as resulting from a supercritical Hopf bifurcation that results in a limit-cycle flow. In the cylinder frame of reference, the basic state is a rotating wave with azimuthal wavenumber $m=1$, and the instability satisfies triadic-resonance conditions with the instability mode maintaining a fixed orientation with respect to the basic state. Thus, we are able to demonstrate the existence of two alternative but congruent explanations for the instability. Additionally, we show that basic states may depart substantially from solid-body rotation even with modest cylinder tilt angles, and growth rates for instabilities may be sufficiently large that nonlinear saturation to disordered states can occur within approximately ten cylinder revolutions, in agreement with experimental observations.

Weed resistance monitoring has been routinely conducted in the Northern Great Plains of Canada (Prairies) since the mid-1990s. Most recently, random surveys were conducted in Alberta in 2001, Manitoba in 2002, and Saskatchewan in 2003 totaling nearly 800 fields. In addition, nearly 1,300 weed seed samples were submitted by growers across the Prairies between 1996 and 2006 for resistance testing. Collected or submitted samples were screened for group 1 [acetyl-CoA carboxylase (ACCase) inhibitor] and/or group 2 [acetolactate synthase (ALS) inhibitor] resistance. Twenty percent of 565 sampled fields had an herbicide-resistant (HR) wild oat biotype. Most populations exhibited broad cross-resistance across various classes of group 1 or group 2 herbicides. In Manitoba, 22% of 59 fields had group 1–HR green foxtail. Group 2–HR biotypes of kochia were documented in Saskatchewan, common chickweed and spiny sowthistle in Alberta, and green foxtail and redroot pigweed in Manitoba. Across the Prairies, HR weeds are estimated to occur in fields covering an area of nearly 5 million ha. Of 1,067 wild oat seed samples submitted by growers and industry for testing between 1996 and 2006, 725 were group 1 HR, 34 group 2 HR, and 55 groups 1 and 2 HR. Of 80 submitted green foxtail samples, 26 were confirmed group 1 HR; most populations originated from southern Manitoba where the weed is most abundant. Similar to the field surveys, various group 2–HR biotypes were confirmed among submitted samples: kochia, wild mustard, field pennycress, Galium spp., common chickweed, and common hempnettle. Information from grower questionnaires indicates patterns of herbicide usage are related to location, changing with cropping system. Two herbicide modes of action most prone to select resistance, groups 1 and 2, continue to be widely and repeatedly used. There is little evidence that growers are aware of the level of resistance within their fields, but a majority have adopted herbicide rotations to proactively or reactively manage HR weeds.

Agricultural practices, other than herbicide use, can affect the rate of evolution of herbicide resistance in weeds. This study examined associations of farm management practices with the occurrence of herbicide (acetyl-CoA carboxylase or acetolactate synthase inhibitor)-resistant weeds, based upon a multi-year (2001 to 2003) random survey of 370 fields/growers from the Canadian Prairies. Herbicide-resistant weeds occurred in one-quarter of the surveyed fields. The primary herbicide-resistant weed species was wild oat, with lesser occurrence of green foxtail, kochia, common chickweed, spiny sowthistle, and redroot pigweed. The risk of weed resistance was greatest in fields with cereal-based rotations and least in fields with forage crops, fallow, or where three or more crop types were grown. Weed resistance risk also was greatest in conservation-tillage systems and particularly low soil disturbance no-tillage, possibly due to greater herbicide use or weed seed bank turnover. Large farms (> 400 ha) had a greater risk of weed resistance than smaller farms, although the reason for this association was unclear. The results of this study identify cropping system diversity as the foundation of proactive weed resistance management.

We have mapped cold atomic gas in 21cm line H i self-absorption (HISA) at arcminute resolution over more than 90% of the Milky Way's disk. To probe the formation of H2 clouds, we have compared our HISA distribution with CO J = 1-0 line emission. Few HISA features in the outer Galaxy have CO at the same position and velocity, while most inner-Galaxy HISA has overlapping CO. But many apparent inner-Galaxy HISA-CO associations can be explained as chance superpositions, so most inner-Galaxy HISA may also be CO-free. Since standard equilibrium cloud models cannot explain the very cold H i in many HISA features without molecules being present, these clouds may instead have significant CO-dark H2.

We investigate the physical properties of the interstellar gas in the nearby edge-on spiral galaxy NGC 891, using Herschel PACS/SPIRE observations of the most important far-infrared (FIR) cooling lines – [Cii] 158 μm, [Nii] 122, 205 μm, [Oi] 63, 145 μm, and [Oiii] 88 μm – obtained as part of the Very Nearby Galaxy Survey (P. I.: C. D. Wilson). We compare our observations to the predictions of a photo dissociation region (PDR) model to determine the gas density, n, and the strength of the incident FUV radiation field, G0, on a pixel-by-pixel basis. The majority of PDRs in NGC 891's disc exhibit properties similar to the physical conditions found in the spiral arm and inter-arm regions of the face-on M51 galaxy. We estimate a stronger FUV field in the far north-eastern side than compared to the rest of the disc.

We introduce a pilot project to measure metallicitiy gradients for a sample of twenty nearby galaxies drawn from the Herschel Reference Survey (HRS), representative of normal, star-forming spiral galaxies. We have obtained optical spectroscopic observations using the Very Large Telescope with the FORS2 instrument in multi-object mode, targeting individual Hii and star-forming regions across the galaxy discs (P. I.: L. Cortese). From the ratios of the strong emission lines, we estimate the local gas-phase oxygen abundance and construct metallicity gradients. Combining these new data with Herschel PACS/SPIRE far-infrared photometric observations and Hi 21 cm line maps, to trace the cold dust and gas respectively, will allow the study of the relationships between stars, gas, dust and metals on sub-kiloparsec scales.

We investigate the relationship between stellar mass, metallicity and gas content for a magnitude- and volume-limited sample of 260 nearby late-type galaxies in different environments. Combining new oxygen abundance measurements with ultraviolet to near-infrared photometry and Hi 21 cm line observations, we observe the relationship between stellar mass and metallicity. We also find that, at fixed stellar mass, galaxies with lower gas fractions typically possess higher oxygen abundances. Gas-poor galaxies are typically more metal-rich. Our results indicate that internal evolutionary processes, rather than environmental effects, play a key role in shaping the stellar mass-metallicity relation.