Trout Identification

Context

Trouts are freshwater fish belonging to the family Salmonidae, which also includes salmon and char. They are found in various habitats, including rivers, lakes, and streams, and are known for their vibrant colors and distinctive markings.

Gallery / Westslope Cutthroat Trout

The Westslope Cutthroat Trout (Oncorhynchus clarkii lewisi) is a unique subspecies of cutthroat trout native to the freshwater systems of British Columbia, Canada, and parts of the northwestern United States. It is one of only two cutthroat trout subspecies found naturally in Canada, with distinct populations located in Alberta and the Pacific region of British Columbia.

Renowned for its striking appearance, the Westslope Cutthroat Trout boasts a vibrant golden-yellow body adorned with numerous small black spots, complemented by a characteristic red or orange slash beneath its jaw. This trout thrives in cold, clear streams, rivers, and lakes, where it plays a crucial role in the aquatic ecosystem. Due to its specific habitat requirements, the Westslope Cutthroat Trout is often regarded as an important indicator of ecosystem health.

Gallery / Map of the Elk River where the trout population is monitored

One fascinating aspect of trouts is their stable and unique spot patterns. Just like human fingerprints, these patterns can be used to identify individual fish. Each trout has a distinct arrangement of spots, which remain consistent throughout its life. Researchers and biologists utilize these unique markings to study trout populations, monitor their health, and track their movements in the wild. This method of identification not only aids in conservation efforts but also enhances our understanding of trout behavior and ecology, highlighting the importance of these remarkable fish in freshwater ecosystems.

Gallery / Unique spot patterns are like fingerprints

A vital role for the ecosystems

The Westslope Cutthroat Trout plays a crucial role in its ecosystem for several reasons:

• Biodiversity Support: As a native species, the Westslope Cutthroat Trout contributes to the overall biodiversity of freshwater ecosystems. Its presence helps maintain a balanced food web.
• Prey and Predator Dynamics: This trout serves as both a predator and prey within its habitat. It feeds on insects, crustaceans, and smaller fish, helping to control these populations. In turn, it is a food source for larger predators, such as birds of prey, bears, and other fish species.
• Nutrient Cycling: The Westslope Cutthroat Trout contributes to nutrient cycling in aquatic ecosystems. As it feeds and excretes waste, it helps to recycle nutrients that support the growth of aquatic plants and microorganisms.
• Indicator Species: The health of Westslope Cutthroat Trout populations can indicate the overall health of freshwater ecosystems. Their sensitivity to changes in water quality and habitat conditions makes them valuable indicators for environmental monitoring.
• Cultural and Economic Importance: This trout is significant for local communities, particularly for recreational fishing and tourism. Healthy populations can support local economies and promote conservation efforts.
• Habitat Formation: The activities of Westslope Cutthroat Trout, such as spawning, can influence the physical characteristics of their habitats. Their nesting behaviors can help create and maintain suitable environments for other aquatic organisms.

Overall, the Westslope Cutthroat Trout is vital for maintaining the ecological balance and health of freshwater ecosystems in British Columbia and beyond.

Conservation concerns

In some regions, the Westslope Cutthroat Trout is considered a species of concern or is listed as threatened or endangered.

Many populations of Westslope Cutthroat Trout have experienced significant declines, leading to concerns about their long-term viability. The species faces several conservation threats that impact its populations and habitats:

• Habitat Loss and Degradation: Urban development, agriculture, and logging can lead to the destruction and alteration of natural habitats. This includes the loss of riparian zones, which are crucial for maintaining water quality and providing shelter.
• Habitat Fragmentation: Habitat fragmentation caused by dams, roads, and other barriers can isolate populations, making it difficult for them to migrate, breed, and maintain genetic diversity.
• Pollution: Runoff from agricultural practices, industrial activities, and urban areas can introduce pollutants into waterways, negatively affecting water quality and the health of trout populations.
• Invasive Species: The introduction of non-native fish species, such as brook trout and rainbow trout, can lead to competition for resources, hybridization, and predation, which threaten the survival of Westslope Cutthroat Trout.
• Climate Change: Changes in temperature and precipitation patterns can alter stream flows and water temperatures, impacting the habitats that Westslope Cutthroat Trout rely on for spawning and growth.
• Overfishing: Unsustainable fishing practices can deplete local populations, particularly in areas where fishing pressure is high. This can lead to reduced genetic diversity and population declines.

Overall, addressing these threats and concerns is essential for the conservation of the Westslope Cutthroat Trout and the health of the ecosystems they inhabit.

Developed Tools

Pipeline Overview

Throughout this project, a variety of tools were developed to effectively utilize the unique biomarkers of trouts for enhanced identification and monitoring.

Gallery / Overview of the ML pipeline developed to identify trouts

Preprocessing Stage

The preprocessing stage is meticulously designed to transform a raw image of a trout into a normalized, segmented representation of the fish. This critical step ensures high accuracy during the subsequent identification phase of the pipeline.

The table below illustrates how the preprocessing stage transforms the original image into a normalized representation of the trout, allowing for the extraction of its unique markings.

Original Picture	Normalized Trout	Extracted Keypoints

Identification Stage

Once the trout image is normalized, the algorithm extracts key biomarkers, specifically the unique spot patterns of the trout, and compares them against a comprehensive database of known trout. If the comparison yields a sufficiently high score, the system identifies the fish as a match and retrieves its associated PIT tag and name. Conversely, if the comparison score is low, it indicates that the trout does not correspond to any entries in the database, and the system classifies it as a new individual.

The table below demonstrates the functionality of the matching algorithm using the extracted keypoints. On the left, you will find examples of matching pairs, while the right side displays examples of non-matching pairs.

✅ Keypoints match	❌ Keypoints do not match

Conclusion

In conclusion, a non-invasive trout identification system represents a transformative approach to monitoring trout populations effectively and sustainably. By utilizing unique spot patterns and other distinguishing features, researchers can gather critical data without disturbing the fish or their habitats. The advancement of these techniques not only enhances our understanding of trout ecology but also supports targeted conservation efforts. As we strive to protect and preserve aquatic ecosystems worldwide, such innovative methods will play a vital role in ensuring the long-term survival of trout species and the health of the environments they inhabit.

One can try out the model from the ML Space or directly from the snippet below: