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6 min read

Laboratory animal identification: choosing the right system

Do you work with lab animals? Animal colony managers and researchers understand the importance of having an effective animal ID system in place. Lab animals can be difficult -- sometimes impossible -- to distinguish visually.

Animal identification mistakes directly lead to a cascade of issues, including ruined experiments, months of setbacks, and replacement costs. All of this can be avoided with a strict, reliable animal tagging protocol that should be part of your laboratory information management system


Importantly, before purchasing or implementing an animal tagging method, verify which methods match your animal management plan. Failing to adopt a working system can result in legal problems with animal welfare organizations like the Institutional Animal Care and Use Committee (IACUC).

"Some fundamental requirements of animal laboratory research never change. Among the most basic prerequisites: You must be able to identify every animal. Without exception. Period." - Bio Metric Data Systems

First, there are many different types of identification techniques for different animals. Some lab animals can forgo tagging. For instance, researchers can visually identify zebrafish from differences in scale patterns. Since many studies utilize small rodents, the focus of this article is mouse tagging methods. Nonetheless, these methods work for most rodents and are adaptable to other species.


Types of Animal Tagging: Temporary vs Permanent

Temporary tagging methods are useful because they are minimally invasive, quick, inexpensive, and can be used on young mice. Permanent tagging methods, on the other hand, are a long-term solution for tracking mice and should be implemented when the mouse is about 3 weeks old. We suggest that your lab selects one of each method, purchases necessary supplies, trains all personnel, and uses strict, consistent implementation.

Quick tips:

  • Set up a temporary and permanent ID method and protocol for your animal colony. Always be consistent.
  • Permanently tag, microchip, or ear punch mice when they are about 21-26 days old.


Temporary IDs for mice


animal id
Rodents groom themselves frequently, so temporary ink marks only last 1-2 days


Sometimes, you will need a quick way to differentiate between mice. For instance, if an ear tag falls out, or if mice are too young to be permanently tagged. Safe, noninvasive, IACUC-approved temporary tagging methods include marking tails with a permanent marker (1-2 days or older), dropping food coloring on fur (1-2 days or older ), and shaving a patch of fur (1 + weeks old).

Things to consider for temporary identification:

  • Age of mouse

  • Condition of their fur coats

  • Type of fur or lack thereof. Shaving won’t be visible on nude or young mice.

  • Sharpie and food coloring don’t work well on black or agouti mice.

Permanent IDs for mice

There are several permanent animal ID solutions, each with different advantages. However, they all require various levels of user training, overhead costs for initial equipment (eg. tattoo gun), and technology (eg. barcode scanners).

Some methods work better for large colonies or certain strains of mice. For example, BL6 mice are more active and mean-tempered; therefore, they tend to not sit still while the researcher squints to read tiny numbers on a tag.

Things to consider for permanent identification:

  • Are the tags/chips autoclave safe?

  • How many different IDs are needed?

  • Will the colony be too large for IDing with a limited-variety method, like ear punches or tattoos?

  • Are the rodents passive enough to easily read a tag?

  • Will the researcher need a way for quick by-eye identification, such as color?

  • Are the tags easy to remove?


Classic lab animal IDs: earmarks and metal tags

If pricing is the main concern, several suitable, traditional, and inexpensive animal ID methods exist. IACUC-approved mutilation methods include ear hole punching, toe clipping, and tattooing. Essentially, the only costs are the instruments, ranging from $22 for an ear puncher to $13000 for a tattoo machine.

However, these methods can be limited and ambiguous. Earhole notches, punches, or old blurry tattoos can be hard to tell apart - which leads to new issues. Toe clipping offers a limited amount of unique mutilations.


animal id ear tag
Metal ear tag from Kent Scientific


Metal ear tags are a widely-used solution. Etched with unique numeric IDs, they are a less ambiguous identification method.

Common ear tags are 1 cm long. They require an applicator tool, as cheap as $30 from National Brand. The metal tags fit up to 6 digits and can be purchased for about $0.10 per tag, which is cheap enough that there is no need to ever re-use the same tag or number.


animal ID
Multi-color ear tags for lab animals from Stoelting


Smaller (3.5 mm), multi-color tags can also be purchased for about $10 per tag from Stoelting. Researchers can easily differentiate between these colorful tags without having to read the small numbers, which limits disturbing and handling the mice. Consequentially, though, these tags are less durable since they’re made from aluminum.


Advances in animal identification methods

Technology is advancing towards new ways to make lab animal identification faster and easier. Companies are finding ways to make data more organized and reduce opportunities for mistakes. Importantly, animal colonies require meticulous monitoring and record-keeping, animal by animal. Tracking animal records by hand can be tedious, especially for large colonies. Advances in tags in better data management practices.

QR codes


animal id ear tag
QR codes printed on bright, multi-color tags from RapID


Ear tags with QR codes instead of numbers are a solution for information management and tracking. With QR codes, each animal’s ID and history of information can be stored in a database, removing hand-written data collection. This tagging method is quite versatile, adaptable for researching animals from cattle to honey bees.

QR code ear tags for lab rodents are available in metal by National Band and Tag Company or multi-colored plastic by RapID. The QR codes arrive pre-engraved onto the tags. Specific applicators are available at low cost through the respective companies. When scanned, each tag links to a unique ID. Scanners read tags at distances of 1-2 inches, as demonstrated in these videos. The metal tags from National also include a alphanumeric code for by-eye identification. RapID tags are randomized and, consequently, the ID code cannot be specified. However, they come in 5 bright colors, which easily distinguishes mice in the same cage.


Another animal ID solution is through microchips, tiny RFID chips encoded with unique identification information. This method is attractive because it is reliable, permanent and minimally invasive. However, microchips reside internally, leaving no easy way to visually identify mice.

Further, the RFID transponders can passively monitor peripheral information. For example, some transponders also record body temperature, and others can track mouse movement over long periods of time. The requisite microchip injection and scanning equipment is initially thousands of dollars. However, the chips themselves can be purchased for as little as $7 each.

In sum, microchips are a great animal identification solution for large labs that can afford the initial overhead cost. Also, they are a unique data collection solution for projects needing a no-contact tracking method for temperature or activity.

P-chip by Pharmaseq

A commonly used microchip is the Pharmaseq P-chip tagging system. These chips store information and are read upon activation by a laser wand. Implanting P-chips into a mouse’s tail causes minimal pain or discomfort. It can take place when mice are as young as 2 weeks old. Microchips are versatile, working for rodents, fish, and even insects. For example, researchers successfully studied ants and bees by adhering P-chips to their backs like backpacks.


animal id
At 6mm long, the DigiTail tag by SensaLab is smaller than a grain of rice and can be implanted humanely into a mouse's tail.


UC and UCT from UI Devices

UI Devices manufacture a versatile line of microchips. What makes the UC chips stand out is that they they are programmable while maintaining a permanent, 16-digit ID. Another outstanding feature: the UCT line of microchips can even collect ulterior information, such as core body temperature, from the host. They are as inexpensive as $7 per microchip. The chips themselves are 8 mm long and encased in glass for longevity. RFID sensors can read chips up to 8 inches away, which minimizes handling and speeds up identification.

Digitail Tags by SensaLab

The Digitail Tag by SensaLab is the smallest read/write microchip, making it as painless and humane as possible. A further benefit of SensaLab is in their accessories. They sell a complete package of everything needed for microchip ID implantation and chip reading. The package is ergonomic, easy-to-use accessories, such as scanners and software, These tools make the DigiTail platform as streamline and easy to set up as possible.

Why modernize? 

It all comes down to this: easier, better treatment to the mice lead to better experiments and data. Technologies like microchips and colorful QR codes allow for passive, noninvasive data collection and better data management. To that end, less confusion and less handling lead to healthier, happier mice. This can greatly affect the outcome of expensive, live-animal experiments.

Further, these technologies expand what we can learn. For example, RFID transponders let researchers study mouse behavior in the dark. Another example, microchips and QR codes can be manufactured small enough to affix them to insects.

Additionally, a major benefit of using scanning technology for mouse identification is that it aids in data management. With advances in animal colony management software, scanning a digital ID code can instantly link a researcher to a particular datum entry out of the animal’s entire history. No more shuffling through papers or spreadsheets.

Though slightly more expensive and time-intensive to set up, digitizing records saves time in the long run and protects against costly and time-consuming mistakes. Further, upgrading colony management with software and specimen scanning is not only becoming a solution but quickly becoming the standard.

As technology expands, managing an animal colony with the help of technology for information acquisition and storage is the way to go.


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