The best of two worlds: reprojecting 2D image annotations onto 3D models.

Imagery has become one of the main data sources for investigating seascape spatial patterns. This is particularly true in deep-sea environments, which are only accessible with underwater vehicles. On the one hand, using collaborative web-based tools and machine learning algorithms, biological and geological features can now be massively annotated on 2D images with the support of experts. On the other hand, geomorphometrics such as slope or rugosity derived from 3D models built with structure from motion (sfm) methodology can then be used to answer spatial distribution questions. However, precise georeferencing of 2D annotations on 3D models has proven challenging for deep-sea images, due to a large mismatch between navigation obtained from underwater vehicles and the reprojected navigation computed in the process of building 3D models. In addition, although 3D models can be directly annotated, the process becomes challenging due to the low resolution of textures and the large size of the models. In this article, we propose a streamlined, open-access processing pipeline to reproject 2D image annotations onto 3D models using ray tracing. Using four underwater image datasets, we assessed the accuracy of annotation reprojection on 3D models and achieved successful georeferencing to centimetric accuracy. The combination of photogrammetric 3D models and accurate 2D annotations would allow the construction of a 3D representation of the landscape and could provide new insights into understanding species microdistribution and biotic interactions.

Mental health is positively associated with biodiversity in Canadian cities.

Cities concentrate problems that affect human well-being and biodiversity. Exploring the link between mental health and biodiversity can inform more holistic public health and urban planning. Here we examined associations between bird and tree species diversity estimates from eBird community science datasets and national forest inventories with self-rated mental health metrics from the Canadian Community Health Survey. We linked data across 36 Canadian Metropolitan Areas from 2007-2022 at a postal code level. After controlling for covariates, we found that bird and tree species diversity were significantly positively related to good self-reported mental health. Living in a postal code with bird diversity one standard deviation higher than the mean increased reporting of good mental health by 6.64%. Postal codes with tree species richness one standard deviation more than the mean increased reporting of good mental health by 5.36%. Our results suggest that supporting healthy urban ecosystems may also benefit human well-being.

Protocol for detecting micro(nano)plastics released from intravenous infusion products.

Approaches for detecting micro(nano)plastics (MNPs) released from intravenous infusion products (IVIPs) are vital for evaluating the safety of both IVIPs and their derived MNPs on human health, yet current understanding is limited. Here, we present a protocol for detecting polyvinyl chloride (PVC) MNPs by combining Raman spectroscopy, scanning electron microscopy equipped with energy-dispersive X-ray spectroscopy (SEM-EDS), and pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS). We describe steps for collecting, pretreating, and measuring PVC MNPs released from IVIPs. For complete details on the use and execution of this protocol, please refer to Li et al.1.

Protocol to establish a disease model in Lepidocephalichthys guntea using Aeromonas hydrophila.

The fish disease model facilitates our understanding of disease dynamics, risk assessment for disease outbreaks, the response of the gut immune system, and the maintenance of ecosystem health. Here, we present a protocol for studying gut immunity modulation by infecting Lepidocephalichthys guntea, a loach fish, with Aeromonas hydrophila. We describe steps for performing intra-peritoneal injection on fish and a bath challenge. We detail procedures for conducting periodic population calculations during the infection phase to corroborate Aeromonas hydrophila invasion in the gut. For complete details on the use and execution of this protocol, please refer to Basak and Chakraborty.1.

Protocol to study the photosynthetic response of maize to the CO2-temperature coupling effect at ear stage using a specialized designed gradient.

Global warming will change the photosynthesis and transpiration of plants greatly and ultimately affect water use efficiency (WUE). Here, we present a protocol to investigate the response of maize WUE to the coupling effect of CO2 and temperature at ear stage using a specialized designed gradient. We describe steps for plant culture, parameter measurements, model fitting, and statistical analysis. This protocol holds potential for studying the response of WUE and CO2 adaptation across various plant species. For complete details on the use and execution of this protocol, please refer to Sun et al.1.

Protocol to discover machine-readable entities of the ecosystem management actions taxonomy.

The ecosystem management actions taxonomy (EMAT) consists of actions taken by humans and wildlife that affect an ecosystem. Here, I present a protocol for discovering machine-readable entities of the EMAT. I describe steps for acquiring stories from online locations, collecting them into a story file, and processing them through a software package to extract those actions that match EMAT taxa. I then detail procedures for using the story file to learn new EMAT taxa.

Protocol to sequence markers from pollen grains carried by long-range migratory butterflies using metabarcoding.

Molecular identification of pollen carried by insects informs about their history of visited plants. For migratory butterflies, it can be used to trace long-range movements enduring days of flight over thousands of kilometers. Here, we present a protocol to (1) isolate pollen grains from butterfly bodies and (2) prepare metabarcoding libraries for their identification using the internal transcribed spacer 2 fragment, a common barcode used to identify plants. This protocol would be applicable to other insect groups and metabarcoding markers. For complete details on the use and execution of this protocol, please refer to Suchan et al.1 and Gorki et al.2.

Protocol to operate a large-scale CO2 hydrogenation process for formic acid production.

Formic acid is a viable product of CO2 utilization. Here, we present a protocol for designing and operating a pilot-scale formic acid production plant with a 10 kg/day capacity produced via CO2 hydrogenation. We describe the essential process specifications required for successful operation, including prevention of corrosion and formic acid decomposition. We then detail procedures for steady-state operation of the individual units. This protocol provides the necessary information for further scale-up and commercialization of the CO2 hydrogenation process. For complete details on the use and execution of this protocol, please refer to Kim et al.1.