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6 min read

Best Mouse Colony Management Software Options of 2020

Gathering all details methodically and meticulously is key for any lab animal experiment.

Lab animal colony management requires recording each meticulous detail. Every lab animal must be carefully tracked for successful experiments and humane treatment. A lab animal researcher’s worst nightmare? Putting together data for a project only to find insufficient details and notes. Lab animals are simply too expensive for repeating experiments.

Software to simplify lab animal colony management

Of course, this is essential for any type of research. However, animal research comes with added costs and regulations. At these high stakes, all data must be captured and saved. It is impractical or impossible to start a protocol over.

Since animal work is already time-consuming and tedious, there are innumerable reasons to try to simplify the process. Managing a mouse colony requires attention to regulations, organization policies, and best practices. A single misplaced cage,  cage card, treatment update form, or even animal from a tagging mistake can derail a protocol.

Unfortunately, since animal research projects are undoubtedly complicated, mistakes are all too easy. For instance, sometimes several researchers and techs are involved on a project together. Sometimes collaborations are between different labs or organizations. And sometimes data is stored in several locations. For example, weekly mouse mass may be stored in one place, breeding and housing information in another, and surgery information in a third. Currently, typical labs meticulously record data by a mixture of spreadsheets, cage cards, clipboards, and post-it notes to maintain an animal colony.

Want a way to simplify this? Animal colony management software is a solution. It is a way to both organize and manage all this precious data, boost project reproducibility and repeatability, and give colony managers some piece-of-mind. Ultimately, the goal of colony management software is to make your life easier!

Software Features to Consider:

  • Price
  • Importing software
  • Sharing capabilities
  • Multiple users in hierarchical roles (ex. lab manager versus tech)
  • Budgeting and tracking per diem costs
  • Accompanying app for phone/tablet
  • Reminders and Calendar Management Tools (IACUC protocol events or breeding reminders)
  • Built-in message system
  • Full Audit Trailing for compliance
  • Intuitive, sleek interface
  • RFID or barcode integration

Here are some lab mouse colony software features:

  • Automatically tracks and reports information, like breeding competence, cage per diem, pedigrees
  • Generates important features, like cage cards, schedules and calendars
  • Automatically audits the current colony status, such as number of animals, ages, and litters
  • Easy or automatically generates reports
  • Simplifies communication with built-in task management and assignment systems
  • Monitors usage and coherence to IACUC protocols
  • Integrates with QR-code labels and ear tags, smart cage racks, and automated genotyping services
  • Saves cost by alerting users about unused or old mice
  • Saves costs by simplifying plans and reducing unnecessary mice
  • Centralizes all information about an animal colony in a single program
  • Can import or export all data from/into excel spreadsheets
  • Saves time, helps you stay organized, and manages all the essential, precious data from your lab animals!


Mouse colony management software programs come with different combinations of these features and more. We reviewed the 5 the best software solutions for lab animal colony management to help you choose the right option.

This review primarily covers software for managing mice and other rodent colonies. However, many software options can manage other species as well.

The 5 Best colony management software options…

…and how to choose one for your lab

  1. Softmouse
  2. mLIMS
  3. Colony by Transnetyx
  4. MouseJ
  5. Mosaic Vivarium

1. Softmouse

softmouse is a leading animal colony management software
A Softmouse feature you will love? Never fill out a cage card again! Choose fields, such as DOB or strain, and pre-populate cage cards with saved mouse info.

Did you previously use a clunky or now unsupported colony software? Value dependability and tech support? Then Softmouse may be your best option.

Users of defunded software platforms who were left hanging can easily integrate their old data into the Softmouse platform.

Softmouse offers a Premium platform, with added customization features, and a more basic “FOREVER FREE” package. Find a feature comparison table here. The free package isn’t very useful as a stand-alone product. However, it allows labs to minimize cost. For example, a lab can pay for a single user license to manage the colony, while free account users can still do basic functions (such as imputing basic mouse information). Also, even if a research group stops paying for premium, they can still access their information through a free account.

“I have inputted genotype results for upwards of 50 mice at a time, and it takes less than 10 minutes.” -Softmouse user

Further, Softmouse has optimized platforms for labs, vivariums/mouse cores, breeding facilities, and biotech companies. Softmouse doesn’t come with fancy frills like some of the other software options. However, it is a supported, reliable option with all the functions needed for boosting efficiency, simplifying data management and saving time.

Some Softmouse features:

  • 24/7 IT help and extensive FAQ page
  • Per diem cost control
  • Centralizes data and standardizes data collection to simplify personnel turnover
  • Time-saving measures, such as batch mouse processing or one-click litter weaning
  • Calendar
  • Automatic email reminders for tasks
  • Integrated QR code tags
  • Learn more..

2. mLIMS

mLIMS is an established, well-used colony management software. It's based off a Lab Information Management Systems, or LIMS. Learn more about LIMS software here. This web-based solutions has plans for labs, institutions, and core animal facilities with tiered pricing. Compare plan features in this chart.


mLIMS generates many types of reports automatically, plus it runs on mobile platforms.


Want to collect data by a mobile device in the vivarium? One of the great strengths of the mLIMS program is its integration with mobile devices, such as iPads and mobile phones. In fact, they periodically offer a promotion giving new users a free iPad downloaded with mLIMS.

Another strength of mLIMS is its data reporting. mLIMS software automatically processes data to generate informative charts in just a few clicks. One example is it will rank mice dams by breeding performance. Every time a litter of pups is born, pup count and survival information can be added to the mLIMS database. At your request, the program sorts this information into a breeding performance report. This kind of report helps inform decisions on which females to breed or keep. Likewise, many such reports can be generated for other reasons, such as cage usage or strain survival.

“There are very few programs available like mLIMS, and these other few are either too complicated or too simple to use.” -mLIMS user

Some mLIMS features:

  • IACUC protocol integration
  • Easy to use accompanying app on tablet or phone
  • Calendar feature showing tasks and assignments on dates
  • Multiple user groups
  • Track pedigrees
  • Supports multiple species (mouse, rat, guinea pig, rabbit, etc.)
  • Cage card design
  • QR code scanning integration
  • Complex breeding tools
  • Customizable cage card fields and automatic cage card creation
  • Learn more…

3. Colony by Transnetyx


transnetetyx colony management interface
Colony is a sleek, drag-and-drop platform with a multitude of handy features


If you’re already using the Transnetyx genotyping service, consider choosing Colony, Transnetyx’s colony management software. Colony is a highly rated, intuitive, modern software solution. Transnetyx integrates genotyping reports into Colony to make data transfers as easy as possible.

Reminiscent of a MacOS-like platform, has a 'drag and drop' cage management feature for ease of use. They boast of easy assay integration capabilities along with collaborative sharing between labs. Altogether, Colony is best for MacOS users in a small-to-medium sized research group.

Some Colony features:

  • Drag-and-drop moves cages or mice
  • Accompanying iOS app for tablet or phone
  • Cloud-based
  • Integrated barcode scanning
  • Automated genotyping that merges with Transnetyx genotyping platform
  • Free
  • Highly customizable
  • Calendar and reminders
  • Can add multiple users to one lab
  • Learn more…

4. MouseJ


MouseJ animal colony management software
The MouseJ design will be incredibly intuitive for Microsoft users


Do you enjoy using a Microsoft software products? And, interested in recording the minimal, essential features? Then MouseJ may be the optimal software choice. The user interface of MouseJ is designed to look like a Microsoft program, with the same tool bar and same style for icons. For this reason, Microsoft users will find it incredibly intuitive. Further, MouseJ can export all information into an Excel sheet with one click.

MouseJ is best for smaller labs using Microsoft. Without complicated customizations and features, MouseJ is easy to learn and simple to use to retrieve key colony data. If you love Microsoft excel and want a similar interface for your colony management software, MouseJ is the way to go.

Some MouseJ features:

  • Reminders on a calendar
  • Import/export compatible with Microsoft Excel
  • Alerts about overcrowded cages
  • No personnel assignments or tasks, no messages
  • IACUC protocol integration
  • Learn more…

5. Mosaic Vivarium

mosaic vivarium a multi-lab colony management application
Mosaic Vivarium is best for multi-lab colony management


If you want a colony software that tracks billing and expenses, Mosiac Vivarium is what you’re looking for. While they offer a special price for single investigators, the strength of this platform is its billing, tracking, and communication between outside users, features which aren't as useful for a single lab. Unlike the other software options,  specializes in large labs, especially entire vivariums with multiple projects and investigators. Though it’s not free, plans are flexible and vary depending on usage.

Some Mosaic Vivarium features:

  • Supports barcodes/RFID
  • Adaptable for multiple species
  • Accounts can be online or locally installed
  • Billing feature
  • Tracks which mice are in which cages and automatically designs cage cards for printing
  • Integrated messenger system reduces emails and aid in delegating tasks and assignments
  • Generates and prints cage cards
  • Role-based security and controlled access
  • Flexible, tiered pricing
  • Learn more…

Getting started with a new colony management software:

Every colony manager already has an extensive data tracking program in place. This could be in the form of notebooks, excel spreadsheets, or files of folders. Transitioning to a different, computer-based system can feel like a daunting, overwhelming task.

For one thing, several options offer a trial period. As a result, users can import data and test the software before ever being charged. We suggest taking this trial period seriously and having all managers and techs in your lab try it out. This way, your lab can get the best sense of if the software is a good fit for your lab.

All in all, no matter how simple the software transition is, some things will need to be repeated. For instance, printing new cage cards, adding users, or filling out calendars and tasks. However, the time input will be quickly recovered by all the time saved by automating data management.

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