Fish Scale Image Analysis of the Atlantic Salmon Ecosystems Research Team

Using Atlantic salmon scales to assess smolt and adult populations.

New England/Mid-Atlantic

Three Atlantic salmon swimming close to rocks — Atlantic salmon. Credit: NOAA Fisheries

Since 1992, we have conducted research on Atlantic salmon scales collected during annual field activities for assessing smolt and adult populations. Results from scale studies contribute to and inform stock assessments and support population dynamics research.

Project Goal

The Atlantic Salmon Ecosystems Research Team’s image analysis labs process numerous Atlantic salmon scales—imaging, aging, measuring, and analyzing—to support research into Atlantic salmon population dynamics and ecology.

Project Description

The salmon image analysis labs at the Northeast Fisheries Science Center are located in our Orono and Woods Hole Laboratories. These labs process over 1,000 salmon scales annually to assist population dynamics research. With the Maine Department of Natural Resources we monitor salmon smolts as they make their way from their natal river to the ocean each year.

Analyzing scales helps us determine age, rearing origin, and growth rates and patterns throughout Atlantic salmon life history. Ages from the different life stages help scientists understand many aspects of the fish’s life history, such as:

Survival and mortality
Age at maturity and spawning
Freshwater and marine residence

Study Methods

1. Collecting Scale Samples

Whether we’re collecting scales from juvenile salmon or adults, we usually use the same method. The sampler uses a small knife to wipe the slime coat from a small area of the fish, then carefully lifts scales off the fish, and places them in a small envelope for storage.

A small salmon approximately 22cm long who has been briefly put to sleep on a wooden measuring board. A small section of scales near the dorsal fin are in a box showing where scales are removed from the fish for analysis. — The young salmon (smolt) pictured above is alive but has been put to sleep for approximately one minute to allow handling without stress. Credit: NOAA Fisheries/Ruth Haas-Castro

A scientist in orange lab gloves holds an adult salmon. Scales are being scraped from its mid-side, near the dorsal fin for later analysis. This salmon is about to be sold at a fish market in Greenland. — An adult salmon is scale-sampled before being sold at a fish market in Greenland. Credit: NOAA Fisheries/Ruth Haas-Castro

2. Collecting Data from the Fish

We store the scales in an envelope with all the associated information written on it:

Date of sample
Location
Fish species and life stage
Fork length
Weight
Presence or application of tags or clips
Disposition (i.e., “rel” means released, but sometimes fish are retained for other research)
Any other pertinent notes

We later enter the data into a computer database.

Two small scale envelopes from the Atlantic Salmon Ecosystems Research Team’s Image Analysis Lab. The envelopes show basic data from a salmon field sample including the date, field site, length, and weight of the specimen. — Example of a fish scale envelope (2x3 inches) for the Atlantic Salmon Ecosystems Research Team’s Image Analysis Lab. Credit: NOAA Fisheries/Ruth Haas-Castro

3. Preparing Scales for Examination

We place the scales between two glass slides for viewing under a microscope.

Two labeled microscope slides are shown side by side. The left glass slide shows ten scales from a juvenile salmon caught on its way to sea. The slide on the right shows two larger scales from an adult salmon off the west coast of Greenland. — Scales pictured above left are from a juvenile salmon caught on their way to the sea (smolt). The two larger scales on the slide on the right are from an adult salmon caught in the ocean off the west coast of Greenland. Credit: NOAA Fisheries/Ruth Haas-Castro

4. Taking Images for Viewing and Computer Analysis

Our image analysis system consists of a microscope with a digital microscope camera, which is attached to a computer. We save scale images to the computer and then use image analysis software to measure scale features.

A lab technician sits at a computer, analyzing salmon scales. Two computer screens are shown, one of which has a magnified salmon scale. The microscope, fitted with a digital microscope camera, is next to the technician. — A lab technician analyzes salmon scales at an image analysis workstation. Credit: NOAA Fisheries/Ruth Haas-Castro

5. Reading Scales

From scales and scale images, we can read the age of the fish and whether it was born wild or in a hatchery. We can see how many years it spent in a river before migrating to the ocean as a smolt and how many years it spent as an adult salmon in the ocean.

A. Scale from a age-1 smolt	B. Scale from an age-2 smolt
C. Scale from an age-3 smolt	D. Scale from an age-1 hatchery origin smolt
E. Scale from an adult salmon, 3 river years, 1+ years at sea	F. Scale from an adult salmon, 3 river years, 2+ years at sea

A magnified salmon scale from a 3 year old smolt. A black line is drawn from the center of the scale outward. Red measurements denote the passing of time and growth. Blue lines show the annual growth. — This salmon scale is from a 3-year-old smolt. Using the image saved to the computer, we can draw a line transect on the scale to measure distances to and between scale features, helping us determine the life history of the specific fish. Credit: NOAA Fisheries/Ruth Haas-Castro

Results and Preliminary Results

Scales provide age and growth data. By looking at these data collected over a number of years, we can see trends that help us understand what is happening in the endangered Atlantic salmon populations we are studying.