Photo Identification of Individual Salmo trutta Based on Deep Learning

Individual fish identification and recognition is an important step in the conservation and management of fisheries. One of most frequently used methods involves capturing and tagging fish. However, these processes have been reported to cause tissue damage, premature tag loss, and decreased swimming capacity. More recently, marine video recordings have been extensively used for monitoring fish populations. However, these require visual inspection to identify individual fish. In this work, we proposed an automatic method for the identification of individual brown trouts, Salmo trutta. We developed a deep convolutional architecture for this purpose. Specifically, given two fish images, multi-scale convolutional features were extracted to capture low-level features and high-level semantic components for embedding space representation. The extracted features were compared at each scale for capturing representation for individual fish identification. The method was evaluated on a dataset called NINA204 based on 204 videos of brown trout and on a dataset TROUT39 containing 39 brown trouts in 288 frames. The identification method distinguished individual fish with 94.6% precision and 74.3% recall on a NINA204 video sequence with significant appearance and shape variation. The identification method takes individual fish and is able to distinguish them with precision and recall percentages of 94.6% and 74.3% on NINA204 for a video sequence with significant appearance and shape variation.

Computer vision based individual fish identification using skin dot pattern

Precision fish farming is an emerging concept in aquaculture research and industry, which combines new technologies and data processing methods to enable data-based decision making in fish farming. The concept is based on the automated monitoring of fish, infrastructure, and the environment ideally by contactless methods. The identification of individual fish of the same species within the cultivated group is critical for individualized treatment, biomass estimation and fish state determination. A few studies have shown that fish body patterns can be used for individual identification, but no system for the automation of this exists. We introduced a methodology for fully automatic Atlantic salmon (Salmo salar) individual identification according to the dot patterns on the skin. The method was tested for 328 individuals, with identification accuracy of 100%. We also studied the long-term stability of the patterns (aging) for individual identification over a period of 6 months. The identification accuracy was 100% for 30 fish (out of water images). The methodology can be adapted to any fish species with dot skin patterns. We proved that the methodology can be used as a non-invasive substitute for invasive fish tagging. The non-invasive fish identification opens new posiblities to maintain the fish individually and not as a fish school which is impossible with current invasive fish tagging.

Stomach Content of Tillapia zilli and Oreochromis nilocticus from Wanzun River, Lavun Local Government, Niger State Nigeria

This study was conducted to investigate the stomach contents of two commercially important fish species (Tilapia zilli and Oreochromis nilocticus) from Wanzun River, Northcentral Nigeria using frequency of occurrence and volumetric methods between January to April 2019. Fish samples were collected monthly with help of Fishermen using various fishing nets and traps. One hundred (100) individual fish of each species were collected and their stomach contents were examined. The results obtained expressed in mean percentage indicated that out of the one hundred (100) individual fish of each species examined,Twelve (12%) fish had an empty stomach contents in Tilapia zilli, and out of the 100 samples examined, Seventeen (17%) fish had an empty stomach content in Oreochromis nilocticus. The stomach contents of both Tilapia zilli and Oreochromis nilocticus consist of detritus, insects, fish remains. Algae/protozoans plant materials and molluscs. Both fish species are omnivorous feeders and occupy the same ecological niche.The study reveals the importance of algae, fish, insects and plant materials as food for fishes and they form important part in the diet of the species examined.

Hypoxia Performance Curve: Assess a Whole-Organism Metabolic Shift from a Maximum Aerobic Capacity towards a Glycolytic Capacity in Fish

The utility of measuring whole-animal performance to frame the metabolic response to environmental hypoxia is well established. Progressively reducing ambient oxygen (O2) will initially limit maximum metabolic rate as a result of a hypoxemic state and ultimately lead to a time-limited, tolerance state supported by substrate-level phosphorylation when the O2 supply can no longer meet basic needs (standard metabolic rate, SMR). The metabolic consequences of declining ambient O2 were conceptually framed for fishes initially by Fry’s hypoxic performance curve, which characterizes the hypoxemic state and its consequences to absolute aerobic scope (AAS), and Hochachka’s concept of scope for hypoxic survival, which characterizes time-limited life when SMR cannot be supported by O2 supply. Yet, despite these two conceptual frameworks, the toolbox to assess whole-animal metabolic performance remains rather limited. Here, we briefly review the ongoing debate concerning the need to standardize the most commonly used assessments of respiratory performance in hypoxic fishes, namely critical O2 (the ambient O2 level below which maintenance metabolism cannot be sustained) and the incipient lethal O2 (the ambient O2 level at which a fish loses the ability to maintain upright equilibrium), and then we advance the idea that the most useful addition to the toolbox will be the limiting-O2 concentration (LOC) performance curve. Using Fry & Hart’s (1948) hypoxia performance curve concept, an LOC curve was subsequently developed as an eco-physiological framework by Neil et al. and derived for a group of fish during a progressive hypoxia trial by Claireaux and Lagardère (1999). In the present review, we show how only minor modifications to available respirometry tools and techniques are needed to generate an LOC curve for individual fish. This individual approach to the LOC curve determination then increases its statistical robustness and importantly opens up the possibility of examining individual variability. Moreover, if peak aerobic performance at a given ambient O2 level of each individual is expressed as a percentage of its AAS, the water dissolved O2 that supports 50% of the individual’s AAS (DOAAS-50) can be interpolated much like the P50 for an O2 hemoglobin dissociation curve (when hemoglobin is 50% saturated with O2). Thus, critical O2, incipient lethal O2, DOAAS-50 and P50 and can be directly compared within and across species. While an LOC curve for individual fish represents a start to an ongoing need to seamlessly integrate aerobic to anaerobic capacity assessments in a single, multiplexed respirometry trial, we close with a comparative exploration of some of the known whole-organism anaerobic and aerobic capacity traits to examine for correlations among them and guide the next steps.

Coordinated gas release among the physostomous fish sprat (Sprattus sprattus)

Previous experimental studies suggest that the production of sound associated with expelling gas from an open swimbladder may play a role in communication. This would suggest non-random gas release. We used deployed echosounders to study patterns of gas release among a fjord population of sprat (Sprattus sprattus). The echosounder records concurrently revealed individual fish and their release of gas. The gas release primarily occurred at night, partly following recurrent temporal patterns, but also varying between nights. In testing for non-randomness, we formulated a data-driven simulation approach. Non-random gas release scaled with the length of the analyzed time intervals from 1 min to 6 h, and above 30 min the release events in more than 50% of the intervals were significantly connected.

Non-Lethal Sequential Individual Monitoring of Viremia in Relation to DNA Vaccination in Fish–Example Using a Salmon Alphavirus DNA Vaccine in Atlantic Salmon Salmo salar

Traditionally, commercial testing for vaccine efficacy has relied on the mass infection of vaccinated and unvaccinated animals and the comparison of mortality prevalence and incidence. For some infection models where disease does not cause mortality this approach to testing vaccine efficacy is not useful. Additionally, in fish experimental studies on vaccine efficacy and immune response the norm is that several individuals are lethally sampled at sequential timepoints, and results are extrapolated to represent the kinetics of immune and disease parameters of an individual fish over the entire experimental infection period. In the present study we developed a new approach to vaccine testing for viremic viruses in fish by following the same individuals over the course of a DNA vaccination and experimental infection through repeated blood collection and analyses. Injectable DNA vaccines are particularly efficient against viral disease in fish. To date, two DNA vaccines have been authorised for use in fish farming, one in Canada against Infectious Haemorrhagic Necrotic virus and more recently one in Europe against Salmon Pancreatic Disease virus (SPDv) subtype 3. In the current study we engineered and used an experimental DNA vaccine against SPDv subtype 1. We measured viremia using a reporter cell line system and demonstrated that the viremia phase was completely extinguished following DNA vaccination. Differences in viremia infection kinetics between fish in the placebo group could be related to subsequent antibody levels in the individual fish, with higher antibody levels at terminal sampling in fish showing earlier viremia peaks. The results indicate that sequential non-lethal sampling can highlight associations between infection traits and immune responses measured at asynchronous timepoints and, can provide biological explanations for variation in data. Similar to results observed for the SPDv subtype 3 DNA vaccine, the SPDv subtype 1 DNA vaccine also induced an interferon type 1 response after vaccination and provided high protection against SPDv under laboratory conditions when fish were challenged at 7 weeks post-vaccination.

PI3K inhibition reverses migratory direction of single cells but not cell groups in electric field

ABSTRACTMotile cells migrate directionally in the electric field in a process known as galvanotaxis. Galvanotaxis is important in wound healing, development, cell division, and nerve growth. Different cell types migrate in opposite directions in electric fields, to either cathode, or anode, and the same cell can switch the directionality depending on chemical conditions. We previously reported that individual fish keratocyte cells sense electric fields and migrate to the cathode, while inhibition of PI3K reverses single cells to the anode. Many physiological processes rely on collective, not individual, cell migration, so here we report on directional migration of cohesive cell groups in electric fields. Uninhibited cell groups of any size move to the cathode, with speed decreasing and directionality increasing with the group size. Surprisingly, large groups of PI3K-inhibited cells move to the cathode, in the direction opposite to that of individual cells, which move to the anode, while such small groups are not persistently directional. In the large groups, cells’ velocities are distributed unevenly: the fastest cells are at the front of the uninhibited groups, but at the middle and rear of the PI3K-inhibited groups. Our results are most consistent with the hypothesis, supported by the computational model, that cells inside and at the edge of the groups interpret directional signals differently. Namely, cells in the group interior are directed to the cathode independently of their chemical state. Meanwhile, edge cells behave like the individual cells: they are directed to the cathode/anode in uninhibited/PI3K-inhibited groups, respectively. As a result, all cells drive uninhibited groups to the cathode, but a mechanical tug-of-war between the inner and edge cells directs large PI3K-inhibited groups with cell majority in the interior to the cathode, while rendering small groups non-directional.Significance statementMotile cells migrate directionally in electric fields. This behavior – galvanotaxis – is important in many physiological phenomena. Individual fish keratocytes migrate to the cathode, while inhibition of PI3K reverses single cells to the anode. Uninhibited cell groups move to the cathode. Surprisingly, large groups of PI3K-inhibited cells also move to the cathode, in the direction opposite to that of individual cells. The fastest cells are at the front of the uninhibited groups, but at the middle and rear of the PI3K-inhibited groups. We posit that inner and edge cells interpret directional signals differently, and that a tug-of-war between the edge and inner cells directs the cell groups. These results shed light on general principles of collective cell migration.