Benchling’s new animal and sample planning feature gives in vivo scientists a connected framework to design, organize, and execute studies from planning animals to collecting samples. It enables study teams to define how animals and samples will be tracked before work begins, ensuring consistency, traceability, and data integrity throughout every stage of the study.

Planned animals act as placeholders for animals you expect to use. They let you define IDs, group assignments, metadata, and sampling before animals arrive in your lab. Planned animals exist only within the study and do not sync to Benchling’s Registry or the colony.

Once animals are received and assigned to your study, you can create registered animals directly from the planned animals or map them at randomization or at any time post-hoc. Registered animals inherit the metadata defined on their planned counterparts and optionally replace names with planned IDs which sync to the Benchling Registry through the In Vivo Sync app.

With planned or registered animals in place, you can create a sampling plan that defines how and when samples will be collected. Sampling plans include planned sample groups that specify sample types, timepoints, and which animals or treatment groups they apply to. From these plans, you can generate planned samples which are digital representations of samples that can be linked to containers and labels for pre-emptive tube labeling.

When it’s time to collect samples, planned samples automatically convert to collected samples, carrying over all metadata and container associations. Samples that aren’t collected can be manually or automatically marked as cancelled, keeping study records clean and accurate.

This feature bridges the gap between study design and data capture, giving scientists a structured, auditable workflow from planning to collection while helping R&D teams reduce manual rework while maintaining confidence in their data.

Key definitions

• Planned animals: Placeholder animal IDs created during study setup. They represent animals expected to be registered later but not yet received. Planned animals help predefine groups, metadata, and sampling plans. They exist only within the study and do not sync to Benchling’s Registry.
• Registered animals: Animals that have been assigned to a study and received in the lab. Registered animals can be created from planned animals or created net new with group assignments. Once registered, they sync to the Registry through the In Vivo Sync app.
• Planned samples: Samples generated from a sampling plan before collection. Planned samples sync to the Registry through the In Vivo Sync app. They can be used to create containers and print labels, and appear globally in Benchling In Vivo with a sample status of Planned.
• Collected samples: Samples that have been physically collected. Planned samples automatically convert to collected samples during collection, preserving IDs and metadata. The sample status changes from Planned to Collected and this update is reflected in the Registry through the In Vivo Sync app.
• Cancelled samples: Samples that will no longer be collected. Cancelled samples retain their metadata but have their status set to Cancelled. They are automatically cancelled if a study is marked Complete or Cancelled, or if the related animal is deceased. This update is reflected in the Registry through the In Vivo Sync app.

Proposed user flow

1. Create a study: Define treatment groups, create planned animals, and set up your sampling plan.
   • Create treatment groups: Organize your study by treatment conditions. These groups define how planned and registered animals will be distributed.
   • Create planned animals: Generate placeholder IDs for animals you expect to use. Planned animals help you design studies before animal arrival and ensure team alignment.
   • Create a sampling plan: Standardize your study design with predefined sample groups, timepoints, and metadata. Assign planned sample groups to animals, groups, or treatment arms.
2. Create registered animals: Once animals are received and assigned to the study, convert planned animals into registered animals, or create new ones directly in Benchling.
3. Create planned samples: From your sampling plan, generate planned samples that sync to Benchling. These form the framework for container creation and labeling before collection.
4. Create containers and print labels: Manage containers directly in Benchling to ensure traceability and efficiency during sample collection.

Collect samples: As you collect, sample statuses automatically update from Planned to Collected, preserving sample lineage and metadata integrity across Benchling.

How to configure and use animal and sample planning

Update the In Vivo Sync app

The animal and sample planning feature must be paired with updates to the In Vivo Sync app to ensure newly available data fields are included in the sync to relevant entities in Benchling. To update the In Vivo Sync app to version 0.0.16:

1. Navigate to Benchling Bioresearch
2. Click Connections > In Vivo Sync app
3. Click on App Listing in the top right of the general plan
4. Click Upgrade
5. Once the update is complete, refresh the page and confirm the app version is 0.0.16

Planned animals do not sync to Benchling and therefore do not require any updates to the In Vivo Sync app.

To fully enable sample planning parity between In Vivo and the Registry, update the Sample schema in Benchling’s Registry with the following fields:

Note: These fields are system fields in In Vivo. They will automatically appear on samples in the tenant and will not be seen as custom metadata on the Sample schema in the glossary.

Once these fields are added to the Sample schema, configure the following field mappings in the In Vivo Sync app:

Create or update study forms

Study forms must be updated to include the new sections in order to enable animal and sample planning. 

1. Navigate to Manage Team > Studies > Forms
2. Select an existing form to edit or create a new form from scratch
3. Ensure the following sections are selected for inclusion:
   • Groups
     • Must be included if Plan animals, Register animals, or Sample Plan functionality is desired during study creation
   • Animals
   • Sample Plan

Note: It is most intuitive to have the sections immediately following one another in the following order: Groups, then Animals, then Sample Plan. 

Note: You cannot use the legacy section Cages and Animals in a study form when using the new Animals section.

Create planned animals 

In Benchling In Vivo, animals can have one of two statuses: planned or registered.

Planned animals represent animals that are expected to be registered within a study but have not yet been received in the lab or assigned to the study. They can only be viewed within the study in which they were created and do not sync to Benchling’s Registry through the In Vivo Sync app. Planned animals can only be created during initial study creation, but they can later be used to generate registered animals with the same animal ID and metadata defined at the planned animal level.

Registered animals are animals that have been assigned to a study and are typically already in the lab. They can be created directly during or after study creation, or generated from planned animals. Registered animals created from planned animals automatically inherit all metadata defined on the planned records, reducing the need for manual data entry. When created, registered animals sync to Benchling’s Registry through the In Vivo Sync app (if configured).

Note: You must create at least one treatment group before adding planned or registered animals during study creation.

Note: The study form must include the Animal section to enable animal planning. If the Animal section is missing or planned animals were not created during study creation, you will not be able to add planned animals afterward.

1. In study creation, navigate to the Animals section. Plan animals is selected by default
2. The table auto-populates with the total number of animals across all treatment groups (for example, if two treatment groups each have a capacity of 10 animals, 20 planned animals appear in the table)
   • [Optional] Remove rows to match the desired number of planned animals for the study

Note: You can remove animals from the table, but you cannot add new ones. If the the group capacity changes in the previous page, click Reset to ensure that the number of planned or registered animals also reflects this change.

3. Update the Planned Animal ID or Group column if needed
   • IDs auto-populate using the format Group Number – Animal Number
   • IDs can be manually edited at this stage and systematically updated once registered animals are created
4. Ensure the number of planned animals does not exceed the defined capacity for their treatment group
5. Complete the Sex field and optionally the Species and Strain fields
6. Click Add metadata to include any additional custom fields
7. Select Next and complete the remaining steps to create the study.

Note: Planned animals are only visible on the Planned Animals page within their study. They do not appear on the Colony page. Planned animals are assigned an Animal Number only after a corresponding registered animal is created.

Edit planned animals

1. In the desired study, navigate to the Animals tab and select the Planned Animals subtab
2. Select the checkboxes next to the planned animals you want to edit
3. Select Bulk actions > Edit planned animals

If a treatment group containing planned animals is deleted, those planned animals remain in the study but lose their group assignment. In the Planned Animals subtab, an error message appears in the top-right corner indicating that some animals are assigned to invalid groups.

You can resolve this by either:

• Deleting the affected planned animals,
• Reassigning them to valid treatment groups, or
• Leaving them unassigned if no group is needed.

Map registered animals to planned animals

If you’ve created registered animals directly within a study, you can later associate them with planned animals. Mapping registered animals to planned animals helps you track study progress and maintain a clear link between your study design and the animals actually used. 

Note: Animal mapping is based on the treatment group assignment. Registered animals must be assigned to a treatment group in order to be mapped to planned animals. A sampling plan that is assigned to planned animals cannot be executed until these have been mapped to registered animals. 

You should map registered animals to planned animals using one of two processes depending upon if you are using randomization to assign animals to groups or if you are assigning animals to groups manually.

If you are using randomization, map registered animals to planned animals within the randomization flow:

1. Proceed through randomization as usual up until clicking Finish (refer to the Randomize animals into groups help article for step-by-step instructions on randomizing animals into groups)
2. Toggle Proceed to mapping stage to the right of the Finish button
3. Select Next
4. [Optional] Toggle Overwrite animal names with planned IDs to rename the registered animals according to the Planned animal ID of their respective mapped animals
5. Select Finish

If you are assigning animals to groups manually, map animals from the Planned Animals subtab:

1. In the desired study, navigate to the Animals tab and select the Planned Animals subtab
2. Select Map animals to automatically identify registered animals and map them to applicable planned animals
3. Animals are mapped to planned animals using their treatment group as the matching key. Within each group, planned animal IDs are ordered by the numeric portion of the ID in ascending order (not string order).
   • For example: 001, 010, 100, 2, 3
4. Use the dropdown menu in the Planned Animal ID column to adjust which planned animal each registered animal is mapped to, if needed
5. Select Map animals to confirm and complete the mapping

Note: When registered animals are mapped to planned animals, metadata on the registered animal remains unchanged. The planned animal’s metadata also stays intact, even if it differs from that of the registered animal.

Create registered animals using planned animals

You can create registered animals in your study directly from planned animals. This process copies all predefined metadata and group assignments from the planned animals to create new, corresponding registered animals. Registered animals are automatically mapped to their planned counterparts and named using the planned animal ID.

To create registered animals for all planned animals:

1. In the desired study, navigate to the Animals tab and select the Animals subtab
2. Select Create animals > Create from planned animals
3. [Optional] Click Add metadata to add or update any custom animal metadata fields
4. Select Create animals to generate the registered animals

Note: No registered animals must be present in the study in order to create planned animals from the Animals subtab. You must register animals for all planned samples when operating from the Animals subtab.

To create registered animals for all planned animals, or a subset of planned animals: 

1. In the desired study, navigate to the Animals tab and select the Planned Animals subtab
2. Select the checkboxes next to the planned animals you want to convert into registered animals
3. Choose Bulk actions > Create from planned animals
4. Specify the number of animals housed per cage in the Animals per cage field
5. [Optional] Click Add metadata to add or update any custom animal metadata fields
6. Select Create animals to generate the registered animals

Note: You can create only one registered animal per planned animal. Once a registered animal has been created from or mapped to a planned animal, that planned animal can no longer be edited. 

Note: If the capacity of a treatment group containing planned animals is changed, the planned animals remain intact. However, you can only create registered animals up to the new capacity limit defined for the treatment group.

Create a sampling plan 

Note: You must have registered animals created before creating planned samples. 

You can create planned samples either during or after study creation.

• During study creation: Continue to the Sampling Plan section of the study form and follow the steps below.
• After study creation: Navigate to the Samples tab in the desired study, select the Sampling Plan subtab, and follow the same steps below.

1. Select Add planned samples
2. Choose the desired sample type using the Select sample type dropdown
3. If the selected sample type has a weight or volume metric, specify the appropriate unit using the Units dropdown
4. In the sample type table, each row represents a group of samples of the same type and details to be collected during the study from the same group of animals. Click + to add additional groups of the selected sample type.

Note: Create a separate sample group for each unique combination of sample type, timepoint, planned metric value, and custom metadata.

5. For each row (planned sample group), enter the following details:
   • Planned sample group name (required): Referencable, unique name for the grouping of sample types, timepoints or animals that the row represents so that users can later select it when creating planned samples or collecting samples
   • Timepoints (optional): Enter as a number followed by a unit (e.g., 60s, 5m, 2h, 3d). You can enter multiple timepoints per group.
     • Enter in the form of number followed by m (minutes), h (hours), or d (days)
     • Timepoints cannot be in increments smaller than 60 seconds
   • Key metrics (optional): Specify any relevant metric such as Volume or Weight. Use the dropdown beside the sample type for this table to confirm the unit. 
   • Additional metadata (optional): Add any required or custom sample metadata.

Note: Custom metadata fields and requirements are defined by your tenant admin in the glossary.

6. Select Add another sample type to plan additional sample types
   • Each sample type can only be selected once, but can include multiple sample groups
   • You can copy and paste fields between sample type tables to streamline setup
7. Select Next.

[Optional] Assign planned sample groups

You can assign planned sample groups to specific treatment groups, registered animals, or planned animals. This helps structure how samples will be collected during the study.

1. Choose how you’d like to assign planned sample groups:
   • Groups: assign to treatment groups
   • Registered animals: assign to specific registered animals
   • Planned animals: assign to specific planned animals
2. In the table on the left, check the boxes next to the groups or animal IDs you want to assign
3. In the table on the right, check the boxes next to the planned sample groups you’d like to assign
4. You can assign one or multiple planned sample groups to each treatment group or animal
   • Assigned groups appear in the planned sample group column of the left table
5. Repeat this process until all planned sample groups are defined
6. Select Next to save your sampling plan.

Create planned samples from a sampling plan

​​After a sampling plan is created, you can generate planned samples from registered animals using this plan. Planned samples are used to create containers and barcode labels ahead of sample collection, ensuring traceability and readiness during study execution.

1. In the desired study, navigate to the Samples tab and select the Sampling Plan subtab
2. Use the checkboxes to select the planned sample groups you want to create planned samples from
3. Select Bulk actions > Create planned samples
4. Review the list of planned samples that will be created, and optionally deselect any animals for which you don’t want to create planned samples
5. Select Create to create the planned samples

Once created, planned samples appear in the Samples tab of your study with a sample status of Planned. They are also visible from the global Samples page in Benchling In Vivo and are synced to Benchling’s Registry via the In Vivo Sync app, if enabled.

Note: Samples cannot be created from planned animals, all planned animals must be mapped to a registered animal before sample creation. 

Collect samples from a sampling plan

You can collect samples directly from a sampling plan. Any corresponding planned samples created in advance will automatically convert to collected samples, preserving all sample IDs and metadata. If a planned sample is already stored in a container in Benchling, the collected sample will remain linked to that same container.

1. In the desired study, navigate to the Samples tab and select the Sampling Plan subtab
2. Use the checkboxes to select the planned sample groups from which samples will be collected
3. Select Bulk actions > Collect samples
4. Review the samples to be collected, and optionally deselect any animals for which you don’t want to collect samples
5. Select Continue
6. Complete the Collection Date & Time field
7. Use the Comments box to record any relevant notes about the sample collection
8. Select Collect to finalize the collection

Note: If the metadata of a planned sample is updated before collection, the collected sample will reflect the updated metadata rather than the original metadata from the sampling plan.

Edit a sampling plan

You can edit an existing sampling plan to update planned sample groups or adjust sample details.

1. In the desired study, navigate to the Samples tab and select the Sampling Plan subtab
2. Select Edit in the top-right corner
3. Update the planned sample groups as needed

Note: Editing a sampling plan does not change metadata on existing planned samples.

• Planned samples created after the edit will reflect the updated metadata
• Samples collected after the edit will reflect the updated metadata
• Planned samples created before the edit will remain unchanged
• Samples collected before the edit will remain unchanged

Mark planned samples as cancelled

You can manually change the status of planned samples to Cancelled if they will no longer be collected.

1. In the desired study, navigate to the Samples tab
2. Select any samples with the Planned status
3. Choose Bulk actions > Cancel samples

Once cancelled, the sample status updates to Cancelled.

In addition to manual changes, samples with the status Planned are automatically updated to Cancelled when any of the following occur:

• The study is marked as Completed
• The study is marked as Cancelled
• The related animal is marked as Deceased

Uncancel cancelled samples

You can change a sample’s status from Cancelled back to Planned using a bulk action in the samples table.

1. In the desired study, navigate to the Samples tab
2. Select any samples with the Cancelled status 
3. Select Bulk actions > Uncancel samples

The selected samples will revert to a status of Planned.