Use animal objects to capture In Vivo study data. Create new cages and animals, assign identifiers, randomize animals into groups, and track their data over time. Perform actions on individual animals or manage them in bulk from the colony or a study.
Manage cages and animals in the colony
Create animals and cages, as well as record associated metadata and print cage cards, from within the colony. Animals must always be created and stored inside of a cage. Cages and animals can be managed from within the colony or within specific study to varying degrees. The colony view is the best place to see the cages and animals across all studies in the tenant. In addition, the colony is the only place to manage cages and animals that are not yet assigned to a study. When creating cages and animals, you may opt into recording extra, custom metadata about the objects to further record important information relevant to cages or animals.
Create cages and animals in the colony
- Navigate to the Colony section
- Click Add new
- Specify the number of cages to be created
- Click Add cages
- Specify the animal population per cage
- Click Add metadata to add optional custom cage metadata fields (e.g., location, rack)
- Click Next
- Enter animal details:
- Sex and DOB are required
- Species and Strain automatically appear, but are not required
- Click Add metadata to add optional custom animal metadata fields
- Click Next, then Create to finalize Cage and Animal creation.
Note: Using copy-and-paste functionality in the table-based sections during this process can help expedite data entry. Use the corner of a cell to drag-fill a column, or select the column header to select the entire column for bulk paste functionality.
Manage cages in the colony
In the Colony tab under the Cages header, you can select one or more cages with the checkboxes to take bulk actions to manage, edit or delete cages.
Manage cages
- Click Bulk actions and select Manage Cages from the menu
- Choose what action you’d like to take
- To edit the cage attributes or print labels, click on the … icon and select the option from the menu that fits what you need to do
- To change the name of a cage, click Rename
- To print the cage card for the selected cage, click Print label
- To delete the cage, click Delete and type DELETE to confirm the permanent deletion
- To add an animal, click Add animal to add a new animal to the cage
- If you’ve opened multiple cages, drag-and-drop animal boxes between cages to move animals between cages
- To create cages, click Create cages to create new empty cages
- To edit the cage attributes or print labels, click on the … icon and select the option from the menu that fits what you need to do
Note: you cannot delete a cage if there are animals in it.
Edit cage details
- Click Bulk actions and select Edit cage details from the menu
- Click on the cage name to rename the cage
- Click Add metadata to edit or add optional custom cage metadata fields (e.g., location, rack).
- Click Save to save the updates
Note: It is not possible to record custom metadata for Cages when creating new Cages in this process, however you can update or add custom metadata retroactively following the Edit cage details process. It is not possible to record custom metadata for Animals when creating new Animals in this process, however you can update or add custom metadata retroactively following the Edit animals details process.
Manage animals in the colony
- Navigate to the Colony tab
- Select the Animals header
- Select one or more Animals using the checkboxes
- Click Bulk actions >
- Assign identifiers to edit or add new animal identifiers
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Edit animal details to rename animals or update animal metadata
- Click on the animal name to rename the animal
- Click into the desired metadata to add or edit the animal metadata
- Click Add metadata to edit or add optional custom animal metadata fields
- Click Save to save the updates
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Move Cage to move the animal into an existing cage.
- Search for and click on the desired destination cage
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Mark as deceased to mark an animal as deceased.
- Specify the Deceased date, Deceased reason, and any relevant Additional comments related to the deceased event
- Click Save
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Delete to permanently delete animals
- Type DELETE
- Click Delete Animals
Note: See specific sections below for details on how to take each action listed above.
Print cage cards in the colony
- Navigate to the Colony tab
- Select the Cages header
- Click ‘…’ to the right of a cage name
- Select Print label to print the cage card
Note: Tenant Admins customize the label contents from the Manage Teams page.
Manage cages and animals in a study
Relative to the colony, many more actions can be executed on cages and animals from within their corresponding study. You can create cages and animals, record associated metadata, and perform a wide variety of study-specific actions such as measurement capture and randomization into groups. The containing study for a cage is the premier location to manage cages and animals, when possible. When creating cages and animals, you may opt into recording extra, custom metadata about the objects to further record important information relevant to cages or animals.
Adding cages and animals to a study
- Navigate to the Study
- Select the Cages section
- Select Add >
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Quick create cages to create a designated number of empty cages in the study
- Note: It is not possible to record custom metadata for Cages when creating new Cages in the Quick create cages process, however you can update or add custom metadata retroactively following the Edit cage details process
- Assign cages from Colony to assign existing cages to the study from the Colony
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Create cages with animals (recommended) to create new Cages and new Animals, and automatically associate them to the Study
- Note: see Creating cages and animals in the colony section for details on how to execute this process
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Quick create cages to create a designated number of empty cages in the study
Manage cages in a study
- Navigate to the Study
- Select the Cages section
- Click on the cage name to rename the cage, or click ... and select Rename
- Click the Add animal button to quickly add a new animal to the cage
- Drag-and-drop animal boxes between cages to move animals between cages
- Click Add to create new cages and/or animals
- Note: see Adding cages and animals to a study section for details on how to execute this process
- Click ... and select Print label to print the cage card for the selected cage
- Click ... and select Delete > type DELETE to permanently delete the cage
Print cage cards in a study
- Navigate to the Study
- Select the Cages section
- Click … to the right of a cage name
- Select Print label to print the cage card
Note: Tenant Admins customize the label contents from the Manage Teams page.
Manage animals in a study
- Navigate to the Study
- Select the Animals section
- Select one or more Animals using the checkboxes
- Click Bulk actions >
- Assign identifiers to edit or add new animal identifiers
- Randomize to groups to begin the randomization process for the selected animals
- Add to group (manual) to manually assign animals into a designated group
- Set tracking date to assign the animal a tracking date
- Set disease induction date to assign the animal a disease induction date
- Update sex to edit the animal’s sex
- Update DOB to update the animal’s date of birth
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Recage to reassign the animal into a net new cage
- Note: it is not possible to recage the animal into an existing cage from this option.
- Move to another study to move the animal to a different existing study
- Collect samples to collect samples from the animal
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Edit animal details to rename animals or update animal metadata
- Click on the animal name to rename the animal
- Click into the desired metadata to add or edit the animal metadata
- Click Add metadata to edit or add optional custom animal metadata fields
- Click Save to save the updates
- Remove from group to remove the animal from its assigned group
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Mark as deceased to mark an animal as deceased
- Specify the Deceased date, Deceased reason, and any relevant Additional comments related to the deceased event
- Click Save
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Delete to permanently delete animals
- Type DELETE
- Click Delete Animals
View an animal profile in a study
- Navigate to a Study
- Navigate to the Animals section
- Select any animal name from the animal table to view animal-specific information
- Use the tabs along the top to view information related to the animal:
- The Overview tab shows a summary of the animal profile, including relevant metadata and latest measurements captured
- The Alerts tab displays the animal’s alert history, including the user whose action triggered the alert, the date and time the alert was triggered, the type of alert, the alert conditions, the date and time the alert was resolved (if applicable), and the user who resolved the alert (if applicable). Active alerts may be resolved or unresolved from this page
Once users no longer need to be informed of an alert, it should be resolved. Once an alert is resolved it will only be displayed in the Alerts tab of the animal profile. It will not be included in the alert filter in the animal table or in workflows. Examples of when to resolve an alert include:
- A study milestone has been met. For example, tumor size is sufficient for enrollment into the study and the animal has been assigned to a study group
- A welfare issue has been resolved. For example, a body weight decrease occurred, the animal's diet was changed, and the animal’s body weight has increased
- Note: In this case, it would be desirable to set up a recurring alert so that the user would be alerted if the same body weight decrease issue occurred again later in the study
- A study endpoint has been reached. For example, an animal exceeded a study endpoint threshold or welfare threshold and the animal was euthanized
- The Observations tab displays the animal’s observation history. New observations may be added to the animal from this page
- The Samples tab displays all samples collected from this animal. New samples may be collected from this page
- The Dosing tab displays the animal’s dosing history. Doses may be deleted from this page
- Use the Actions button to:
- Edit animal metadata
- Add the animal to a group or remove the animal from a group
- Set or edit the animal’s tracking date
- Set or edit the animal’s disease induction date
- Move the animal to a new cage
- Mark the animal as deceased
- Delete the animal
- Use the measurement dropdown at the top right to view the measurement history and a summary measurement graph for the selected measurement for the animal
- Select Next along the top to move to the next animal profile
Edit animal details from the animals section
- Navigate to a Study
- Navigate to the Animals section
- Select one or more Animals using the checkboxes
- Click Bulk actions > Edit Animal details
- Click on the animal name to rename the animal
- Click into the desired metadata to add or edit the animal metadata
- Click Add metadata to edit or add optional custom animal metadata fields
- Click Save to save the updates
Assign animal identifiers
Note: Animal identifiers can be assigned when directly interacting with animals or when working with animals in a workflow. For details on how to assign animal identifiers within a workflow, see How to configure and use Workflows.
- Navigate to the Animals page in a Study or the Animals tab in the Colony
- Click Bulk actions > Assign identifiers to edit or add new animal identifiers
- Click into the applicable identifier cell (Name, Ear, Tail, Tag, Donor) and enter in the desired value to manually adjust an animal identifier
- Optionally copy-and-paste from external spreadsheets or order forms, or from within the table, to speed up manual identifier assignment
- Use Bulk assign IDs for to assign animal identifiers automatically
- Specify the identifier to be assigned using the first dropdown (Name, Ear, Tail, Tag, Donor)
- Specify the desired pattern to be followed (Repeating or Sequence)
- The Repeating pattern will cycle through the specified identifier values once per cage
- The Sequence pattern will increment through the specified alphabetical prefix and numerical postfix across cages
- Click Bulk assign
- Repeat as desired for each animal identifier
- Click Save
- Note: Toggle auto-save on to automatically save values as they are entered
- Click into the applicable identifier cell (Name, Ear, Tail, Tag, Donor) and enter in the desired value to manually adjust an animal identifier
| Type | Example Identifier Values | Cage #1 Output (5 Animals) | Cage #2 Output (5 Animals) |
| Repeating | 1, 2, 3, 4, 5 | 1, 2, 3, 4, 5 | 1, 2, 3, 4, 5 |
| Sequence | A; 001 | A001, A002, A003, A004, A005 | A006, A007, A008, A009, A010 |
Record a measurement from the animal profile in a study
- Navigate to a Study
- Navigate to the Animals section
- Select any animal name from the animal table
- In the top right corner of the screen, use the measurement dropdown to select the measurement type to be added
- Select Add new
- Specify the date taken
- Complete the applicable measurement fields
- Select Save
Mark animals as deceased
To mark an animal as deceased from the animal profile in a study:
- Navigate to a Study
- Navigate to the Animals section
- Click on the desired Animal Name
- Click Actions > Mark deceased
- Specify the Deceased date for the animal
- Select a reason
- Enter any additional comments
- Click Save
Mark animals as deceased in bulk
- Navigate to a Study
- Navigate to the Animals section
- Select one or more Animals using the checkboxes
- Click Bulk actions > Mark as deceased
- Specify the Deceased date for the animal
- Select a reason
- Enter any additional comments
- Click Save
Note: Deceased animals are locked from editing but can still have samples created belonging to them.
Unmark an animal as deceased
- Navigate to a Study
- Navigate to the Animals section
- Click on the desired Animal Name
- Click Actions > Undo in the blue information box titled Marked as deceased at the top of the page
- Select the cage which the animal should be added to
Update the details of an animal’s deceased event
- Navigate to a Study
- Navigate to the Animals section
- Click on the desired Animal Name
- Click Actions > Edit
- Update the desired fields
- Click Save
Delete animals from within a study
To delete an animal from the animal profile in a study:
- Navigate to a Study
- Navigate to the Animals section
- Click Actions > Delete
- Type DELETE into the field
- Click Delete animals to delete the animals
Delete animals in bulk
- Navigate to a Study
- Navigate to the Animals section
- Select one or more Animals using the checkboxes
- Click Bulk actions > Delete
- Type DELETE into the field
- Click Delete animals to delete the animals
Set critical study dates for animals within a study
Benchling In Vivo utilizes several key dates to effectively track, analyze, and manage animal studies, including Tracking Date and Disease Induction Date. These dates are set individually per animal, allowing for staggered enrollment studies. Though technically optional, either Disease Induction Date or Tracking Date must be set in order to ensure the animal’s inclusion in graphs, analysis, and group summary data exports, including the Prism report. Below is an example study with critical animal dates set.
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Study Start Date: June 25, 2025 (Baseline health checks begin)
Purpose: Marks the official beginning of the study.
Usage: Used for scheduling tasks such as initial animal setup, baseline measurements, and recurring health checks. Not used for graphing.
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Disease Induction Date: July 1, 2025 (Tumor implantation event)
Purpose: Records the date when the disease was induced in the animals.
Usage: Used as a reference point in data analysis and graphing.
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Tracking Date: July 15, 2025 (Randomization and treatment begins)
Purpose: Marks the start of tracking measurements after animals are assigned to study groups and receive first treatment, reference baseline for % change and analysis calculations.
Usage: All measurements taken on this date are set as the baseline for further group comparisons. This MUST be assigned to all animals to be included in graphs and exports.
Set and view the tracking date for animals
The Tracking Date is the specific date from which Benchling In Vivo begins using measurements for visualization and analysis. It is typically set by the user to represent the date of the first treatment or randomization for an individual animal. Benchling In Vivo uses the Tracking Date in the following ways:
- Measurements taken on the tracking date serve as the baseline for calculating percentage changes and further analysis.
- Provides flexibility to initiate tracking from the first measurement, treatment, or any desired critical date, such as when tumors reach a specific volume.
Set or update the tracking date for animals from the animal section in a study
- Navigate to the Study
- Select the Animals section
- Select one or more Animals using the checkboxes
- Click Bulk actions > Set tracking date
- Specify the desired date
- Click Save
Set or update the tracking date for animals from the animal profile in a study
- Navigate to a Study
- Navigate to the Animals section
- Click on the desired Animal Name
- Click Actions and select Set tracking date from the menu
- Specify the desired date
- Click Save
View the tracking date for animals from the animal section in a study
- Navigate to the Study
- Select the Animals section
- View the Tracking date column in the table
View the tracking date for animals from the animal profile in a study
- Navigate to a Study
- Navigate to the Animals section
- Click on the desired Animal Name
- View the Tracking date row in the table
Set and view the disease induction date for animals
The Disease Induction Date is meant to record the date when the disease or symptoms under investigation were induced in the animal (e.g., implantation date). Benchling In Vivo uses the Disease Induction Date in the following ways:
- Data from the disease induction date are compared to the data on the tracking date, establishing the baseline for comparison between initial measurements and subsequent data points.
- Graphs can plot data as “Days Post Disease Induction,” and measurements before the tracking date can be either included or excluded in graphs and exports. This setting is applied from the Treatment groups page in a study.
Set or update the disease induction date for animals from the animal section in a study
- Navigate to the Study
- Select the Animals section
- Select one or more Animals using the checkboxes
- Click Bulk actions and select Set disease induction date from the menu
- Specify the desired date
- Click Save
Set or update the disease induction date for animals from the animal profile in a study
- Navigate to a Study
- Navigate to the Animals section
- Click on the desired Animal Name
- Click Actions > Set disease induction date
- Specify the desired date
- Click Save
View the disease induction date for animals from the animal section in a study
- Navigate to the Study
- Select the Animals section
- Select Show > Disease induction date
- View the Disease induction date column in the table
View the disease induction date for animals from the animal profile in a study
- Navigate to a Study
- Navigate to the Animals section
- Click on the desired Animal Name
- View the Disease induction date row in the table
Assign animals to study groups
Animals can be added to study groups manually or via the randomization tool for a balanced study design. Study groups must already be created to assign animals to groups manually or via the randomization tool. Manual assignment works well if balanced designs are not a priority for the team or if no baseline metrics are collected in In Vivo. Randomization via clustered or block methods is best suited for studies where a balanced design using one or many metrics is required for data integrity. Exclusion criteria in randomization can be manually adjusted, which is a powerful tool to further refine the metrics of the selected animals especially if a large cohort of animals is being drawn from.
Manually assign animals to and remove animals from groups
- Navigate to a Study
- Navigate to the Animals section
- Select one or more Animals using the checkboxes
- Click Bulk actions > Add to group (manual)
- Select the desired group
- Repeat the process for each desired group
Manually assign an animal to a group from the animal profile in a study
- Navigate to a Study
- Navigate to the Animals section
- Select the desired animal name from the animal table
- Click Actions > Add to group
- Select the desire group
Manually remove animals from groups from the animals section in a study
- Navigate to a Study
- Navigate to the Animals section
- Select one or more Animals using the checkboxes
- Click Bulk actions > Remove from group
- Click Remove from group
- Repeat the process for each desired group
Manually remove an animal from a group from the animal profile in a study
- Navigate to a Study
- Navigate to the Animals section
- Select the desired animal name from the animal table
- Click Actions > Remove from group
- Click Remove from group
Randomize animals into groups
Note: You must record at least one measurement for each animal before randomizing it into a group.
- Navigate to a Study
- Navigate to the Animals section
- Select one or more Animals using the checkboxes
- Click Bulk actions > Randomize to groups
- Specify the desired behavior for measurements used in randomization:
- Use latest measurements: This option uses the most recent measurement values recorded for each animal, regardless of when those measurements were taken. This means that measurement dates may vary across animals.
- Specify a date: This option requires you to choose a specific date for measurements that will be used for all animals. Animals are automatically excluded if they do not have measurement data recorded on the chosen date.
- Enter in the desired number of animals to be randomized to each group
- Each group can hold up to the animal capacity specified when the groups were originally created
- Select Next
- Review the automatically defined exclusion criteria
- Optionally update based on a specific measurement metric (e.g. body weight) or target mean.
- To update the metric, click on the Exclude by dropdown menu and select the desired metric.
- To update the Target mean, deselect the check box next to Target mean and enter a target mean to be achieved during randomization.
- When this is entered, animals will automatically be excluded while attempting to hit the target mean value with the remaining animals.
- Note: This is an especially powerful feature if you have a large cohort of animals and a large number of animals that can be excluded. If you have a small cohort, or you are excluding a small number of animals, it can be difficult to achieve a target mean.
- Review the box and whisker plots and associated analytics.
- The top plot (grey) displays a pre-exclusion overview of the animals based on the selected metric.
- The bottom plot (blue) displays a post-exclusion overview of the animals based on the selected metric.
- If desired, manually override the excluded animals
- Scrolling to the bottom of the screen
- Select Show Animals
- Select or deselect animals using the checkboxes. As you add or remove animals, the plots and analytics will automatically update.
- If you would like to revert any changes, click the Undo Changes button in the blue banner at the top of the page.
- Optionally update based on a specific measurement metric (e.g. body weight) or target mean.
- Select Next
- An information panel will appear for animals that do not have tracking dates assigned, offering a shortcut to set tracking dates for the applicable animals. For more information on tracking dates, see Set critical study dates for animals within a study below
- Choose and execute one of the following randomization methods:
Block Randomization is for allocating animals into groups based on a single metric. This is a deterministic method of allocating animals to groups based on one metric. The best case outcome is generated by rank ordering the animals by metric and assigning them sequentially to evenly sized groups. Only one single outcome is possible and so you can only click randomize one time. This method is best suited for balanced group sizes, though it can be performed with unbalanced group sizes. If you are allocating animals across groups of differing capacities consider using clustered randomization and selecting a single metric instead.
- Benchling In Vivo orders animals from smallest to largest based on the selected metric.
- Benchling In Vivo separates animals into blocks. The size of these blocks is equal to the number of treatment groups in the study. For example, if there are 5 groups, the 5 animals with the smallest measurement will be in block 1, the next 5 animals will be in block 2, and so forth.
- Benchling In Vivo sequentially allocates animals to each group starting in block 1.
- Animal 1 (smallest measurement) – Group 1
- Animal 2 – Group 2
- Animal 3 – Group 3
- Animal 4 – Group 4
- Animal 5 – Group 5
- Benchling In Vivo reverses the assignment order when a new block is reached.
- Animal 6 – Group 5
- Animal 7 – Group 4
- Animal 8 – Group 3
- Animal 9 – Group 2
- Animal 10 – Group 1
- Benchling In Vivo repeats this process until all animals have been allocated to a group.
- If the number of animals assigned to each group is different, animals are allocated until the smaller groups are filled, and then the remaining animals are allocated to the groups with space remaining. This naturally assigns animals with the largest measurement to the larger groups and explains why uneven groups should be avoided when using block randomization.
- Benchling In Vivo sequentially allocates animals to each group starting in block 1.
To execute Block randomization
- Select I am randomizing by one metric
- Click Randomize
Note: you can only randomize once when using block randomization as the same results will always be produced.
Clustered Randomization is a non-deterministic method of allocating animals into groups based on multiple metrics and attributes (ex. sex, DOB) simultaneously. This is a bias free allocation using k-means clustering.
- Benchling In Vivo arranges animals into cohorts:
- If no attribute is selected, Benchling In Vivo always creates one cohort.
- If an attribute is selected, Benchling In Vivo organizes animals into cohorts based on the number of options available for the selected attribute (ex. If sex is selected as the attribute, the animals will be separated into 2 cohorts: male and female.)
- Within each cohort, Benchling In Vivo uses k-means to separate animals into clusters based on the selected measurements. Up to three measurement fields can be used at the same time.
- Benchling In Vivo determines an initial cohort capacity for each group by taking the capacity of the group and dividing it by the total number of cohorts (ex. A group capacity of 30 animals divided by 2 cohorts gives an initial cohort capacity of 15)
- Benchling In Vivo selects the first cluster and allocates the first animal from that cluster to a group at random. Benchling In Vivo then cycles through the groups until no animals remain in the cluster.
- Benchling In Vivo repeats this process for the remaining clusters until it has assigned each animal to a group. If there is uneven cohort sizing (ex. if there are more males than females), Benchling In Vivo may be unable to achieve the initial cohort capacity for all groups.
- Benchling In Vivo repeats this process for the next cohort.
- After this process, some animals may remain in the last cohort. Benchling In Vivo allocates these animals at random to groups with space remaining until the capacity of each group is achieved. This may happen for a number of reasons including uneven group sizing and uneven cohort sizing.
To execute Clustered randomization
- Select I am randomizing by one or more metrics and/or an attribute
- Specify any desired attribute (Sex, Donor ID, or Date of birth)
- If more than one attribute is required for randomization (ex. Sex and DOB), perform two separate randomizations
- Navigate to the Study
- Navigate to the Animals section
- Apply a filter to the animals table to select for one option of one attribute (ex. Female)
- Select all animals in the filtered table using the checkboxes
- Click Bulk actions > Randomize to groups
- Complete randomization for these animals using DOB as the attribute
- Repeat steps 1-4, however filter for the alternate option of the attribute previously filtered on (ex. Male)
- Repeat steps 5 and 6
- If more than one attribute is required for randomization (ex. Sex and DOB), perform two separate randomizations
- Select any desired metric(s)
- Click Randomize
- Note: you can re-randomize when using clustered randomization until the desired distribution is achieved
- Optionally use the summary table at the bottom of the page to review the distribution of animals across the groups
- The Population column shows the number of animals assigned to the group
- The selected Metric column shows the SD or SEM per group for the metric (depending on the group setting).
- Toggle the Show median button to display the median values per group
- The P-value under the Metric header represents the ANOVA-calculated P-value for the differences in means across groups. Click the i button to see the ANOVA table
- Click the carrot icon next to a group to see the names of the animals assigned to each group
- Click Finish to assign the animals to groups.
- To recage animals based on group assignment, see the Recaging animals and follow the Via Recage within a Study instructions.
Move animals between cages and studies
Recage animals into new or other existing cages to ensure digital alignment with actual cages in the vivarium. You can house up to 15 animals in a single cage at a time in Benchling In Vivo. You may transfer entire cages of animals within a study to other studies in the tenant, though only select data will transfer.
Recage animals
Via drag-and-drop within a Study
- Navigate to a Study
- Navigate to the Cages section
- Click and hold the animal, and drag and drop it into a different cage.
Via Recage within a Study
- Navigate to a Study
- Navigate to the Animals section
- Select one or more Animals using the checkboxes
- Click Bulk actions > Recage
- Specify the naming strategy to be used
- Cage number: Cages are named using an autoincrementing number per study (e.g. Cage 1, Cage 2, Cage 3)
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Group number: Cages are named using alphanumerics based on the group number and the quantity of cages needed for animals within the same group
- Cages are named 1A, 2A, 3A, etc. if each group is placed within one cage
- Cages are named 1A, 1B, 1C, 2A, 2B, etc. if each group is placed within more than one cage, with the letter distinguishing between the cages holding one group
- Cages are named Unassigned A, Unassigned B, etc. if animals being placed do not belong to a group
- If desired, assign new Animal IDs to animals during recaging
- Use the auto generate IDs feature to quickly assign IDs using a defined pattern (see Assigning animal identifiers for more information)
- Alternatively, manually type in desired IDs per animal
- Click on the cage name and enter in the desired name to manually rename cages
- Select Delete empty cages in study to automatically delete empty cages rendered from the recaging
- Note: this option permanently deletes any cages rendered empty from the recaging, along with all cage-related metadata. Manually transcribe or copy-and-paste any cage metadata from legacy to new cages if legacy metadata must be transferred. Do not delete legacy cages until metadata has been transcribed.
- Select Submit to complete recaging
- Benchling In Vivo automatically sends a Recaging report to the user’s email and uploads the report to the Attachments section of the study
Via bulk actions within the Colony
- Navigate to the Colony
- Select the Animals tab
- Select one or more Animals using the checkboxes
- Click Bulk actions > Move to cage
- Search for and click on the desired destination cage
Note: You can only move animals between cages in the same study. You cannot move animals that are not part of a study into cages that belong to a study.
Move animals between studies
Via bulk actions
- Navigate to a Study
- Navigate to the Animals section
- Select one or more Animals using the checkboxes
- Click Bulk actions > Move to another study
- Note: Recaging automatically includes all non-deceased animals from the same cages as the selected animals. Move any animals that shouldn't be in this list into new cages that are not being transferred. All groups, doses, alerts or tracking dates are removed in this process. Measurements, samples and observations will remain intact.
- Select Continue
- Select the destination study
- Note: You can only transfer cages between studies that share the same Preset
- Select Continue
- Select Confirm
Via Moving Animals feature
- Navigate to a Study
- Navigate to the Animals section
- Select one or more Animals using the checkboxes
- Click Bulk actions > Move to another study
- Review the selected animals
- Confirm that only the selected animals will be moved.
- Note: All groups, doses, alerts and tracking dates will be removed
- Select Continue
- Select the destination study
- Note: You can only select studies which you have WRITE access to
- Select Continue
- Confirm the measurement field mappings between your current study and the destination study.
- Map each measurement field in the current study to its corresponding field in the destination study
- If no equivalent measurement field exists in the destination study, select - Add to preset - to create the field in the destination preset. Benchling In Vivo automatically includes all calculated measurements and thus will automatically grey these fields out
- Select - Drop measurement - to ignore a measurement field and remove it from the transfer. Measurement fields can only be ignored if they are internal input fields that do not apply to a calculation of another measurement field in the new preset. Any measurement fields that do not have data recorded will not be shown in the list of fields to transfer as there is no data to transfer
- Note: Any existing data for fields marked as - Drop measurement - will be deleted for the animals being transferred
- Select Save.
- Select Take me to the new study to be rerouted to the destination study after confirming the measurement mapping and animal transfer
- Select Confirm to complete the animal transfer.
- Note: All groups, doses, alerts, tracking dates or dropped measurements will be permanently removed from the transferred animals. This action cannot be undone.
Frequently asked questions
Q: Can I assign multiple identifiers to one animal?
Yes, each animal can have up to five identifiers. Name is required and used as the primary reference across the study.
Q: Can I delete an animal after adding it to a study?
Yes, but you must first remove it from any study group.
Q: How can I associate a tag color as an animal identifier?
RapID Tags, color-coded QR codes on ear tags, offer a unique scannable ID system and allow for quick visual identification of an animal by its color. While RapID Tags don't automatically translate their color into Benchling In Vivo when scanned, you can manually record the color and tag IDs using the alternative identifier fields provided in In Vivo. The best way to do this is by using Assign IDs in Workflows, however this can also be accomplished using the assign animal IDs functionality from the animal table of a study.
- To use a color as an identifier, add the color to any of the five key name fields for each animal (e.g., name, ear). Colors can be assigned in bulk using the Repeating naming functionality described in Assigning animal identifiers
- Navigate to workflow
- In the General subsection, set the ID method to search by to the identifier field where the tag will be scanned in (e.g., Tag) and set the Display ID to the identifier field where color was added (e.g., name, ear)
- In the Measurement subsection, select Assign identifiers when taking measurements and set the identifier field to the identifier field where the tag will be scanned in (e.g., Tag)
- Set the After Saving field to Move to next animal
- Select Continue. An animal will be displayed based on its color identifier
- Pick up the corresponding animal in the vivarium and scan the animals tag to record the tag identifier
- Select Save
- Record any desired, set measurements (e.g., Bodyweight) as you usually would within Workflows
- Repeat steps 7 through 9 for the remaining animals
Q: I accidentally deleted a cage, animal or sample. How can I get it back?
You cannot un-delete an item in the user interface. Please reach out to Benchling Support (support@benchling.com) with all applicable information (study, the impacted item type/name/description, and the user who performed the action) if you need to restore a deleted item.