How to import data into Benchling In Vivo

  • Updated

Many instruments, such as imagers and smart cages, produce a spreadsheet or CSV file containing the relevant results. These can be easily uploaded to Benchling In Vivo using the universal import feature.


File Formatting

Prior to starting, ensure that your data is in a format that will be recognised by Benchling In Vivo. We recommend keeping Animal IDs, Cage IDs and relevant metrics in columns, with each row representing a different animal. Make sure that the first row contains the heading for each column.


Use the "Download Import Template" button to generate an excel template pre-populated with animal and cage IDs.


Uploading Data

Click the Import button on the study navigation bar. This will open a screen that enables you to select the relevant file and assign a date. Benchling In Vivo can upload data from CSV, XLS and XLSX files. Once complete, click the Continue button to advance to the next stage.


Matching Columns

You now need to tell Benchling In Vivo what is contained within the columns of your spreadsheet. You will be presented with a series of boxes containing the headings from the first row and a preview of the first 3 animals in each. The software will attempt to automatically match these to a field in Benchling In Vivo; however, sometimes you may need to manually assign.


In the example below, the first column in the spreadsheet contained the heading "Tail Mark". In Benchling In Vivo, we simply use the term "Tail".


When you are happy that everything is matched correctly, click the Confirm button to validate each data column. You can also choose to ignore columns if you do not want to import particular data.


Note: If the animals in your study do not have unique IDs for the selected ID then you must also confirm a column for Cage name to ensure the measurements are mapped to the correct animals in your study.


We will display notifications relating to the data in each column to the right of each selection. This will alert you if data already exists on the selected date and the percentage of rows that contain a value.


Review your Data

After matching your columns, you can advance to the Review Import screen. This will show a summary of the data to be imported into Benchling In Vivo.


At this stage, we will flag errors and warnings.


Errors occur if:

  • The animal ID does not exist in the specified Cage.

  • The animal ID or cage ID do not not exist in the study.

  • Duplicate IDs have been used within the same Cage.

  • Mistakes in the data (for example text in a number field).

Importantly, rows containing errors will not be imported to Benchling In Vivo.


Warnings occur if:


  • There were empty fields in your spreadsheet.

  • Data has already been entered for the metric on that day.

Rows containing warnings can still be imported to Benchling In Vivo. If data has previously been entered it will be overwritten with the new value.


Import your Data

Finally, you will be presented with a review containing the number of rows to be imported, number of rows to be ignored and total warnings.


Click Import Data and everything will be uploaded to Benchling In Vivo.


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