Collect, view, and export data in In Vivo

Alex
Alex
  • Updated

Benchling In Vivo supports multiple methods for capturing and managing study data, including workflows, data tables, animal profiles, bulk imports, doses, and attachments. Tasks can also be configured and executed to streamline data collection, with progress tracked in the calendar or study schedule. Once data is collected, you can visualize results across animals and groups, generate summary tables and analyses, and export study data in multiple formats. Audit logs are available to track study modifications and support quality control.

There are a variety of ways to record data within Benchling In Vivo. You can use:

  • Workflows for guided, hands-free data entry
  • Data Tables for tabular study planning and data collection
  • Animal profile for recording bespoke data against a single animal
  • Import for bulk importing measurement data
  • Doses for recording doses in bulk in a tabular format
  • Attachments for associating files or links to a study

 

Collect data from task execution

If you have configured tasks for your study, you can streamline data capture by executing the tasks with pre-defined actions. You can execute tasks from the calendar outside of a study, or from the study schedule within a study. 

 

Collect data from your task calendar

  1. Click the Tasks icon in the blue navigation bar
  2. Click the task you want to perform
  3. Click Execute task
  4. You will be brought to a pre-configured workflow setup window. Follow the instructions in How to configure and use Workflows to adjust the set up as desired and begin capturing data
  5. Be sure to navigate back to the task and update the status as needed

 

Collect data from your study schedule

  1. In your study, click Schedule
  2. Hover over the relevant task icon and select the tasks you want to perform
  3. Click Execute tasks

  1. If more than one task is selected, confirm the order using drag and drop
  2. Click Continue

  1. Select animals by searching for their ID, scanning (if using supported devices), or clicking on the animal in the correct cage
  2. Follow the instructions in How to configure and use Workflows to adjust the set up as desired and begin capturing data

 

Updating task progress

You can track and update task progress from the calendar or schedule to keep studies on track.

Progress indicators

Click on the current status in the top right corner of a given task to change the status.

  • Mark tasks as To do, In progress or Done
  • Tasks marked as Done show a checkmark in the task calendar and study schedule views
  • Filter tasks by status in the task calendar view

Show all study tasks

  • By default, the schedule displays today’s tasks
  • To view all tasks, click Clear in the date picker
  • Overdue tasks are shown at the top right corner of the page. Click the indicator to display them

 

Import measurement data in bulk

You can import measurement values from .csv, .xls, and .xlsx files. A correctly formatted template can be downloaded from the Import section of each study. Only one calendar day of measurements can be imported at a time — to import multiple days, repeat the process with one file per day.

 

Format measurement data for bulk import

  1. In your study, click the Import subtab in the left navigation bar
  2. Click Download import template
  3. Fill in the template with your data. A valid file must:
    • Use the first row for headers
    • Include a column for animal identifier (name, tail, ear, tag, donor)
      • Animal identifiers must match existing animal identifiers in the study
      • Use a cage column if animal identifiers are not unique within the study
    • Include a column for at least one measurement field
      • List one animal per row, with each measurement in its own column
      • Use column names that exactly match Benchling measurement field names defined in the preset
      • Leave out units from measurement values
      • Contain only one day of measurements (date is selected during import, not in the file)
    • Have data in the first tab of the spreadsheet (Benchling defaults to the first tab for import)

 

Import measurement data in bulk

  1. In your study, click the Import subtab
  2. Select the Recorded date for the measurements
  3. Upload your data file (drag and drop, or browse your computer)
  4. Click Continue

  1. Map column headings from your file to In Vivo fields:
    • Fields mapped successfully show a green checkmark next to Automatically matched to the [Field name] field. Update the mapping using the field dropdown if desired. Click Confirm to accept or Ignore to skip.
    • Fields that fail to map show with a yellow exclamation mark next to Unable to automatically match to a field. Use the field dropdown to manually select a field, or choose Ignore. Click Confirm to accept.
    • Fields with incomplete cells show with a yellow exclamation mark next to X% ​​of your rows have a value for this column. The other data in the column can still be imported, but some animals will not have data for that field
    • All fields must be confirmed or ignored to proceed
  2. Click Review to see the import preview
    • Errors and warnings appear at the top of the page, with affected cells highlighted in red
    • You can toggle Only show rows with warnings or errors to simplify review
    • Errors must be fixed in the source file — you cannot edit the table during import
  3. Click Continue
  4. Review the summary and click Import data to complete the import

 

Visualize data

Benchling In Vivo makes it easy to visualize study data across animals and groups, so you can track results, spot trends, and make decisions faster.

 

Configure study-wide visualization settings

Settings for averages, variation, display colors, and reference dates are managed in the Treatment groups section of your study. These choices affect how data is graphed and analyzed throughout the study.

  1. In your study, click Treatment groups
  2. To set display colors:
    • Click Edit on the treatment table
    • Double-click the color next to a group
    • Choose a color from the picker or enter a hex code
    • Click Save

 

 

  1. In the table at the bottom of the Treatment groups page, choose how you would like to calculate averages:
    • Arithmetic (default): Standard arithmetic mean across animals
    • Geometric: Standard geometric mean across animals

 

  1. In the table at the bottom of the Treatment groups page, choose how you would like to display variation:
    • Standard deviation (default): Error bars show standard deviation
    • Standard error of the mean: Error bars show standard error of the mean
  2. In the table at the bottom of the Treatment groups page, set the Days Plotted to define what days the graphs are plotted using:
    • Post tracking date (default): The measurement collected on the tracking date for each animal will be the Day 0 data point
    • Post disease induction date: The measurement collected on the disease induction date for each animal will be the Day 0 data point
      • Toggle the Exclude data before tracking date option to hide measurements taken between each animals induction date and tracking date from graphs
  3. In the table at the bottom of the Treatment groups page, set the Control group dropdown to the study control group:
    • Click the dropdown menu below the Control group setting
    • Select a group
    • Click the X to clear the selection, or the dropdown to select a new group

 

View and customize study graphs

The Graphs section shows study-wide plots of measurements and survival metrics across time. You can customize graph type, axis, and data display.

 

Navigate graphs

  1. In your study, click Graphs
  2. Choose a Metric from the dropdown above the graph

 

  1. Select a graph type (caret icon, top-left of page)
    • Grouped (default view): Compare groups over time
    • Daily: Compare groups on a specific day
    • Spider: View individual animals over time
    • Survival: Kaplan-Meier survival curves

 

  1. Choose how to visualize data (top-right dropdown)
    • Absolute (default view): Plots raw values
    • Relative: Day 0 = 100%, subsequent measurements are relative
    • % Change: Percentage change from Day 0
    • Cumulative: Running total per animal

 

Note: You must set the relevant reference date per animal for data to appear on graphs. See How to manage animals for instructions.

Configure graph options

  1. In your study, click Graphs > Options
  2. Set y-axis scale: Linear (default) or Logarithmic
  3. Choose daily point plotting
    • Mean (default): Mean of animal data points for each group on each day
    • Median: Median of animal data points for each group on each day
    • % dT/dC: Percent dT/dC values for each group on each day
    • % Inhibition: Percent inhibition values for each group on each day (e.g., tumor growth inhibition)
  4. Update variation display (default variation settings follow the study-wide configuration)
    • Standard deviation
    • Standard error of the mean

Add or remove groups

  • Open the Groups dropdown and check/uncheck groups (all selected by default)
  • Double-click a group name in the legend to isolate that group

Zoom in on a graph

  • Zoom in: Click and drag diagonally across a graph area. Double-click to reset
  • Cross-section: Drag vertically or horizontally to zoom into one axis. Double-click to reset
  • Amend axis range: Click and drag on x- or y-axis to adjust values. Double-click to reset

Download a graph

  1. In your study, click Graphs > Options
  2. Select Download as image

Note: Visual changes (like zooming) will appear in the download.

 

Temporarily exclude data points

Sometimes a single outlier can skew group averages and make it harder to interpret trends. You can temporarily exclude data points from graphs and analyses without deleting them from your study.

  1. In your study, click Graphs
  2. Scroll below the graph to the tabular data view
  3. Click a data point, then click Submit changes
    • Excluded points appear blue with a strikethrough
    • To restore, click the point again and click Submit changes

 

Note: Excluded values will not be used when calculating group means or related analysis. Excluded points are reversible. They remain in exports but won’t be used for group means or analysis

 

Create summary tables and perform analysis

As each study progresses, you can generate summary tables that contain a variety of analyses. These calculations are performed instantly and accurately to ensure correct interpretation of the data. Before you can use analysis, the following must be true:

  • Animals are assigned to Treatment Groups
  • Animals have tracking dates
  • A control group is set in the treatment groups page

 

Generate a summary table

Every study includes summary tables and analyses. Oncology studies include additional oncology-specific options

To create a summary table:

  1. In your study, click Graphs
  2. Click the Analysis subtab at the top of the page
  3. Click Options
  4. Select a summary table
    • Survival: Based on when animals are marked as deceased
    • Tolerance: Based on body weight only
    • Tolerance and Survival: Combines tolerance and survival calculations

 

  1. Select the desired Reference Date (tracking date or disease induction)
  2. Click Apply

If your study preset includes a measurement marked as tumor volume, you’ll have access to additional summary tables specific for oncology studies. See How to configure the In Vivo tenant for instructions on how to set a tumor volume measurement.

Additional summary table options include:

  • Efficacy: efficacy calculations
  • Efficacy Prophylactic: prophylactic efficacy calculations
  • Oncology Summary: Comprehensive efficacy analysis

When running oncology analyses, provide configuration inputs in the Options dropdown:

  • Measurement: Select the tumor metric
  • Target tumor volume: Set a tumor volume to calculate time-to-volume per group
  • Summary statistic: Choose mean or median for grouped-animal calculations
  • Analysis day: Number of days from the reference date to use for calculations
  • Reference date: Choose tracking date or disease induction date

After configuring the settings, toggle Set as default to save the current analysis and configuration options as the default for the study. When you revisit the analysis page, this table will be the default table shown.

 

Understand summary table columns

Survival calculations

  • Mortality (day of death): Count of animals marked deceased per day (e.g., 40, 2D47, 49, 2D50, 51, 2D52, 55). Days are shown relative to tracking date or disease induction date, depending on summary table options
  • Median day of survival: Median day of death for the group
    • = MEDIAN(DoD)
      • DoD = Day of Death
    • Depending on the display day defined in summary table options this will either show the day post tracking date or the day post disease induction date for each animal.
  • Min day of survival: Earliest day of death for the group
    • = MIN(DoD)
      • DoD = Day of Death 
    • Depending on the display day defined in summary table options this will either show the day post tracking date or the day post disease induction date for each animal.
  • Max day of survival: Latest day of death for the group
    • = MAX(DoD)
      • DoD = Day of Death
    • Depending on the display day defined in summary table options this will either show the day post tracking date or the day post disease induction date for each animal.
  • Percent increased life span (% ILS): Median survival gain in treatment vs. control groups
    • = (MDST - MDSC) / MDSC * 100
      • MDST = Median day of survival (treatment group)
      • MDSC = Median day of survival (control group)
    • Depending on the display day defined in summary table options, this will either show the day post tracking date or the day post disease induction date.
  • Survived to study end:Number of animals per group that survived to study completion (requires “survived to end of study” option to be selected when marking animals as deceased)

Tolerance calculations

  • Mean body weight change at nadir: mean of the greatest change in body weight from the day of nadir (day of greatest decrease from tracking date)
    • = (BW0 - BWN)/BW0 * 100
      • BW0 = Mean body weight at day 0 (tracking date)
      • BWN = Mean body weight at the day of nadir
  • Day of nadir: Day of greatest body weight decrease from tracking date for a group. This is not impacted by specifying a day for the analysis.
    • Depending on the display day defined in summary table options, this will either show the day post tracking date or the day post disease induction date
  • Day of mean weight recovery: Day that group body weight recovered to or increased above weight on tracking date
    • Depending on the display day defined in summary table options, this will either show the day post tracking date or the day post disease induction date.

Efficacy calculations

  • dT/dC: Change in tumor volume for treated vs. control groups
    • = (SS(TVday(t) - TV0(t)) / SS(TVday(c) - TV0(c)))*100
      • SS = Summary statistic: user defines either MEAN or MEDIAN in options
      • (t) = Treatment group
      • (c) = Control group
      • TV0 = Tumor Volume at day 0 (tracking date)
      • TVday = Tumor Volume at specified day
  • % Regression: Percentage tumor regression
    • = SS((TV0 - TVday)/(TV0) x 100)
      • SS = Summary statistic: user defines either MEAN or MEDIAN in options
      • TV0 = Tumor volume at day 0 (tracking date)
      • TVday = Tumor volume at specified day
  • Partial regression: Number of animals where minimum tumor volume < half of baseline
    • TVmin < (TV0 / 2)
      • TV0 = Tumor volume at day 0 (tracking date)
      • TVmin = Minimum volume after the tracking date
  • Complete regression: Number of animals where minimum tumor volume < 14 mm³
    • TVmin < 14 mm³
      • TVmin = Minimum volume after the tracking date

Efficacy prophylactic

  • T-C in days: Tumor growth delay (TGD; difference in time to target volume between treatment and control)
    • = TTRT -TTRc
      • TTRT = Time for treatment group to reach target value
      • TTRc = Time for control group to reach target value
  • % T-C: Percent tumor growth delay (% TGD).
    • = (TTRT -TTRc)/TTRc * 100
      • TTRT = Time for treatment group to reach target value
      • TTRc = Time for control group to reach target value

Oncology summary calculations

  • Fold change: Average fold change in tumor volume from the tracking date
    • = SS((TVday - TV0) / TV0)
      • SS = Summary statistic: user defines either MEAN or MEDIAN in options
      • TV0 = Tumor volume at day 0 (tracking date)
      • TVday = Tumor volume at specified day
  • Tumor growth inhibition: Percent inhibition relative to control
    • = 100 - dT/dC
    • = 100 - ((SS(TVday(t) - TV0(t)) / SS(TVday(c) - TV0(c)))*100)
      • SS = Summary statistic: user defines either MEAN or MEDIAN in options
      • (t) = Treatment group
      • (c) = Control group
      • TV0 = Tumor volume at day 0 (tracking date)
      • TVday = Tumor volume at specified day
  • Tumor volume on day:  Tumor volume on analysis day, using mean or median summary statistic
  • Time for tumor to reach target value: Days for group to reach specified target value, using linear regression
    • = SS(LR(PV, DTJ1: DTJ2, TVTJ1: TVTJ2))
      • SS = Summary statistic: user defines either MEAN or MEDIAN in options
      • PV = Predetermined Volume
      • T = Treatment
      • J1 = Day before target
      • J2 = Day after target
      • TV = Tumor Volume
      • LR = Linear Regression
      • D = Day

 

Export study data

You can export core study data at any time from the Export tab. You can email core study data to yourself or download it directly from the study. You can also export data tables, samples, observations, and summary tables directly from their respective sections in a study.

Export core study data

  1. In your study, click Export
  2. Use the checkboxes to select your desired reports
  3. Click download to download the files, or click Send to your email to receive an email with the files

Export formats include:

  • Raw study data: .xlsx file with a full animal-level dataset, including study, group, cage, animal, and treatment information. Each metric is on a separate sheet, with data points by collection date.
  • Study group report: .xlsx file with a group-level dataset, including study, group, cage, animal, and treatment details. Each metric is on a separate sheet, with summary statistics (mean, SD, SEM, median, MAD). Includes absolute and relative data sheets.
  • Prism report: .pzfx file for GraphPad Prism, containing group-level data. Each metric has absolute and relative datasheets. Survival data is included in a separate datasheet.
  • Study dosing: .xlsx file with a history of dosing events, viewable by study day or exact dosing date

Export samples

  1. In your study, click Samples
  2. Click Export to download a .xlsx of the sample table

Note: Filters applied to the table will affect which samples appear in the export

Export observations

  1. In your study, click Observations
  2. Click Export and choose:
    • All observations: .xlsx file with all recorded observations
    • Current selection: .xlsx file with observations visible after search and filters

Export data tables

  1. In your study, click Data tables
  2. Select the data table you want to export
  3. Click Export to download a .xlsx file of the full data table

Note: Only displayed values will be exported, underlying formulas will not be

Export a summary table

  1. In the Graph section of your study, generate a summary table
  2. Click Export to download a .xlsx file with the same analyses

 

Download an audit log

The In Vivo audit log gives you a detailed record of study modifications to support quality control and troubleshooting. It tracks created, updated, and deleted events for measurements, samples, observations, doses, and animal living status changes. By default, edits and deletions do not require users to entere a reason for change, but you can request that Benchling Support enable this requirement for your tenant. Reasons for change will then be captured in audit logs. Audit logs are only available in .csv format — PDF exports are not supported.

  1. In your study, click Export
  2. Click Generate audit log

You’ll receive an email with a download link once the log is ready. A .csv file will also appear in the Attachments section of your study. Each time you generate a log, a new .csv file is created.

 

Frequently asked questions

Q: Can I record more than one measurement of the same type per day per animal?

A: No, measurements are restricted to once per day per animal.

Q: Can I record more than one observation per animal per day?

A: Yes, additional observations can be recorded at any time.

Q: Can I edit a saved measurement?

A: Yes. Go to the Animal Profile, click the entry, and select Actions > Edit.

Q: What file format should I use for data import?

A: Use a .csv or .xlsx file with column headers and exact field name matches. 

Q: What types of graphs can I generate?

A: Grouped, Daily, Spider, and Survival graphs are available in the Graphs tab.

Q: What happens if animals are missing tracking dates?

A: Those animals will be excluded from graphs and analysis tables.

Q: How do I switch graph views to show individual animals?

A: Use the Spider plot to show individual animal lines instead of group means.

Q: Can I analyze data by disease induction date instead of tracking date?

A: Yes. Assign induction dates and select Days post disease induction in the option within the Treatment groups tab.

Q: How are mean vs median applied in tables?

A: You can toggle this in the Analysis tab.

Q: What does the Prism export contain?

A: A .pzfx file structured for GraphPad Prism. It includes groups, timepoints, and raw measurements.

Q: What happens to excluded data?

A: Excluded points are hidden from graphs and tables, but remain in the dataset. They can be re-included at any time.

Q: Why can’t I see my data?

A: If graphs are not displaying correctly, ensure:

  • Data points exist on the study for the selected metric
  • Animals have been assigned to groups
  • Animals have a tracking date and/or a disease induction date
  • All data points have not been excluded.

Q: What happens if no workflow is set for a task?

A: Tasks can still be executed manually without a linked task. 

Q: Are task statuses linked to completion of workflows?

A: No. Tasks and the fulfillment of a workflow are not linked and task statuses will not automatically update. Be sure to update task statuses after completing the actions.

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