Automated morphometrics on microscopy images of Atlantic cod larvae using Mask R-CNN and classical machine vision techniques

Flow-through imaging and automated analysis of oil-exposed early stage Atlantic cod (Gadus morhua)

Toxicology studies in early fish life stages serve an important function in measuring the impact of potentially harmful substances, such as crude oil, on marine life. Morphometric analysis of larvae can reveal the effects of such substances in retarding growth and development. These studies are labor intensive and time consuming, typically resulting in only a small number of samples being considered. An automated system for imaging and measurement of experimental animals, using flow-through imaging and an artificial neural network to allow faster sampling of more individuals, has been described previously and used in toxicity experiments. This study compares the performance of the automated imaging and analysis system with traditional microscopy techniques in measuring biologically relevant endpoints using two oil treatments as positive controls. We demonstrate that while the automated system typically underestimates morphometric measurements relative to analysis of manual microscopy images, it shows similar statistical results to the manual method when comparing treatments across most endpoints. It allows for many more individual specimens to be sampled in a shorter time period, reducing labor requirements and improving statistical power in such studies, and is noninvasive allowing for repeated sampling of the same population.

Effects of gadolinium (Gd) and a Gd-based contrast agent (GBCA) on early life stages of zebrafish (Danio rerio)

Gadolinium (Gd) is one of the rare earth elements (REY) and is widely used in magnetic resonance imaging (MRI) contrast agents. Anthropogenic Gd enrichment has frequently been found in wastewater treatment plant effluents in industrialised countries, rising concerns regarding effects on aquatic biota. This study investigates the acute toxicity and sublethal effects of Gd in two forms, as inorganic salt (GdCl3) and as Gd-based contrast agent (GBCA), on early life stages of zebrafish (Danio rerio). Nominal exposure concentrations ranged from 3 to 3000 μg L-1, with an exposure duration of 96 h. None of the two tested compounds were acutely toxic to embryos and larvae. Similarly, we did not observe any effects on larval development and locomotive behaviour. However, we found significant changes in the brain activity of larvae exposed to the highest concentrations of GdCl3 and the GBCA. Our findings show that Gd can have sublethal effects on developing fish at lower concentrations than reported previously, highlighting the necessity of investigating the long-term fate and effects of GBCAs released into the aquatic environment.

Automated software for counting and measuring Hyalella genus using artificial intelligence

Amphipods belonging to the Hyalella genus are macroinvertebrates that inhabit aquatic environments. They are of particular interest in areas such as limnology and ecotoxicology, where data on the number of Hyalella individuals and their allometric measurements are used to assess the environmental dynamics of aquatic ecosystems. In this study, we introduce HyACS, a software tool that uses a model developed with the YOLOv3's architecture to detect individuals, and digital image processing techniques to extract morphological metrics of the Hyalella genus. The software detects body metrics of length, arc length, maximum width, eccentricity, perimeter, and area of Hyalella individuals, using basic imaging capture equipment. The performance metrics indicate that the model developed can achieve high prediction levels, with an accuracy above 90% for the correct identification of individuals. It can perform up to four times faster than traditional visual counting methods and provide precise morphological measurements of Hyalella individuals, which may improve further studies of the species populations and enhance their use as bioindicators of water quality.

Co-exposure to UV radiation and crude oil increases acute embryotoxicity and sublethal malformations in the early life stages of Atlantic haddock (Melanogrammus aeglefinus)

Crude oil causes severe abnormalities in developing fish. Photomodification of constituents in crude oil increases its toxicity several fold. We report on the effect of crude oil, in combination with ultraviolet (UV) radiation, on Atlantic haddock (Melanogrammus aeglefinus) embryos. Accumulation of crude oil on the eggshell makes haddock embryos particularly susceptible to exposure. At high latitudes, they can be exposed to UV radiation many hours a day. Haddock embryos were exposed to crude oil (5-300 μg oil/L nominal loading concentrations) for three days in the presence and absence of UV radiation (290-400 nm). UV radiation partly degraded the eggs' outer membrane resulting in less accumulation of oil droplets in the treatment with highest oil concentration (300 μg oil/L). The co-exposure treatments resulted in acute toxicity, manifested by massive tissue necrosis and subsequent mortality, reducing LC50 at hatching stage by 60 % to 0.24 μg totPAH/L compared to 0.62 μg totPAH/L in crude oil only. In the treatment with nominal low oil concentrations (5-30 μg oil/L), only co-exposure to UV led to sublethal morphological heart defects. Including phototoxicity as a parameter in risk assessments of accidental oil spills is recommended.

Monitoring ocean water quality by deployment of lumpfish (Cyclopterus lumpus) eggs: In situ bioaccumulation and toxicity in embryos

Fish embryos can bioaccumulate and are particularly sensitive to a wide range of contaminants, which makes them suitable sentinels for environmental biomonitoring. However, fish embryos are very rarely utilized in environmental monitoring surveys, possibly due to their fragility and seasonality. In the present work, we assessed the applicability of caged lumpfish (Cyclopterus lumpus) eggs for in situ biomonitoring of exposure and effects of organic contaminants focusing on polyaromatic hydrocarbons and phenolic compounds. Fertilized eggs (1 dpf) were transplanted for 17-19 days at different locations that differed in terms of contaminant load, depths and weather conditions, namely at three stations close to the city of Trondheim (two harbour areas and a one in the Fjord) and three stations at a coastal aquaculture facility. High survival upon retrieval after deployment showed that lumpfish eggs are relatively robust and survive encaging in different environments. Bioaccumulation of organic contaminants (PAHs and phenolic compounds) was measured and potential effects on hatching, development, survival and larvae morphometry were determined. Chemical analyses showed that especially PAHs were effectively accumulated in eggs in contaminated sites, with concentrations of ƩPAHs being 15 - 25 times higher in harbour areas compared to those at the aquaculture facility. A higher incidence of embryonic deformations was observed in the most polluted deployment location, but larvae morphometry revealed no evidence of toxicity related to pollutant body burden. In conclusion, the in-situ exposure method was proven to work well, making it attractive for implementations in environmental monitoring programs.

Application of chemical herders do not increase acute crude oil toxicity to cold-water marine species

Chemical herders may be used to sequester and thicken surface oil slicks to increase the time window for performing in situ burning of spilled oil on the sea surface. For herder use to be an environmentally safe oil spill response option, information regarding their potential ecotoxicity both alone and in combination with oil is needed. This study aimed at assessing if using herders can cause toxicity to cold-water marine organisms. Our objective was to test the two chemical herders Siltech OP-40 (OP-40) and ThickSlick-6535 (TS-6535) with and without oil for toxicity using sensitive life stages of cold-water marine copepod (Calanus finmarchicus) and fish (Gadus morhua). For herders alone, OP-40 was consistently more toxic than TS-6535. To test herders in combination with oil, low-energy water accommodated fractions (LE-WAFs, without vortex) with Alaskan North Slope crude oils were prepared with and without herders. Dissolution of oil components from surface oil was somewhat delayed following herder application, due to herder-induced reduction in contact area between water and oil. The LE-WAFs were also used for toxicity testing, and we observed no significant differences in toxicity thresholds between treatments to LE-WAFs generated with oil alone and oil treated with herders. The operational herder-to-oil ratio is very low (1:500), and the herders tested in the present work displayed acute toxicity at concentrations well above what would be expected following in situ application. Application of chemical herders to oil slicks is not expected to add significant effects to that of the oil for cold-water marine species exposed to herder-treated oil slicks.

FishSizer: Software solution for efficiently measuring larval fish size

Length and depth of fish larvae are part of the fundamental measurements in many marine ecology studies involving early fish life history. Until now, obtaining these measurements has required intensive manual labor and the risk of inter- and intra-observer variability.We developed an open-source software solution to semi-automate the measurement process and thereby reduce both time consumption and technical variability. Using contrast-based edge detection, the software segments images of a fish larva into "larva" and "background." Length and depth are extracted from the "larva" segmentation while taking curvature of the larva into consideration. The graphical user interface optimizes workflow and ease of usage, thereby reducing time consumption for both training and analysis. The software allows for visual verification of all measurements.A comparison of measurement methods on a set of larva images showed that this software reduces measurement time by 66%-78% relative to commonly used software.Using this software instead of the commonly used manual approach has the potential to save researchers from many hours of monotonous work. No adjustment was necessary for 89% of the images regarding length (70% for depth). Hence, the only workload on most images was the visual inspection. As the visual inspection and manual dimension extraction works in the same way as currently used software, we expect no loss in accuracy.

A flow-through imaging system for automated measurement of ichthyoplankton

Microscopic imaging and morphometric measurement of fish embryos and larvae is essential in environmental monitoring of fish populations and to evaluate larvae development in aquaculture. Traditional microscopy methods require time-consuming, repetitive work by human experts.

We present a method for fast imaging and analysis of millimetre-scale ichthyoplankton suspended in seawater. Our system can be easily built from common and off-the-shelf components and uses open-source software for image capture and analysis. Our system obtains images of similar quality to traditional microscopy, and biological measurements comparable to those by human experts, with minimal human interaction. This saves time and effort, while increasing the size of data sets obtained.

We demonstrate our approach with cod eggs and larvae, and present results showing biologically relevant endpoints including egg diameter, larval standard length, yolk volume and eye diameter, with comparison to similar measurements reported in the literature.

• High throughput, microscope-scale imaging of fish eggs and larvae

• Automated measurement of biologically relevant endpoints

• Easily built from off-the-shelf components and open-source software