Purpose 

To provide details about the necessary steps to implement the Beckman Coulter, Vi-Cell BLU connector for use with the Benchling Connect platform.

Introduction

The Vi-Cell BLU connector is a component used in the context of the Benchling Connect platform to parse data from Beckman Coulter, Vi-Cell BLU cell counters to an Allotrope Simple Model (ASM) and make those data available within the Benchling UI in the context of a Run.

The Benchling Connect, Vi-Cell BLU connector is a ‘file-based’ based connector, meaning that it processes text file exports generated by the Vi-Cell BLU instrument. The data within the file export is then accessed by Benchling Connect through the use of a ‘watched’ file directory on the local computer hosting a Benchling Gateway, which has been configured via a Connection from within Benchling.

In order to successfully implement the Beckman Vi-Cell BLU connector for use with the Benchling platform, there are several steps that need to be followed across both the Vi-Cell BLU and Benchling user interfaces. 

This guide details the steps to be taken in both applications in order to configure the integration. 

Steps within Vi-Cell BLU

The user should perform measurements following the Vi-Cell BLU Instructions for Use (PN C13232AH, March 2023).

The user is expected to enter Sample ID values within the Vi-Cell BLU UI that conform to entity identifiers within Benchling, either existing entity IDs or entities they wish to register upon processing of results.

Performing file export from Vi-Cell BLU

The user is expect to generate a .csv export from a ‘Sample Set’ as described in the Vi-Cell BLU Instructions for Use (IFU) or Vi-Cell BLU UI as shown below:

The user is then expected to place this .csv export file in a target directory which is specified during Connection configuration, when creating a Vi-Cell BLU Connection within the Benchling UI.

The user can specify this target directory for an individual Sample Set, by setting the directory path under the ‘Advanced Options’ (gear icon) on the Sample Set.

It is NOT RECOMMENDED that data to be ingested via the connector be exported via the ‘append results and export to’ within Run Options under the Settings menu as this concatenates all data generated overtime and thus could result in the creation of repeated measures when processed via the Lab Auto Run.

Steps within Benchling 

From within Benchling, a user must:

1. Enable the Vi-Cell BLU connector on the tenant [internal admin console]

2. Configure a Vi-Cell BLU Connection

3. Create a Result schema to structure the data to be recorded

4. Configure a Run schema to accept data from Vi-Cell BLU and records Results

For steps 1 & 2, please reference the Benchling Connect Installation Guide for details related to creating and installing a Gateway and configuring a Connection.

Create Result Schema for Vi-Cell BLU data

The Benchling Connect - Vi-Cell BLU cell counter connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the Vi-Cell BLU file export. The data is processed in a two step process; step one from  Vi-Cell BLU export to the .json based ASM, and step two from the ASM .json to a single sample file .csv file available for ingest to Benchling. 

Details about the Cell Counting ASM schema can be found here:

https://github.com/Benchling-Open-Source/allotropy/tree/main/src/allotropy/allotrope/schemas

The sample file can contain the following columns (if available within the data):

• model number
• file name
• software name
• ASM converter name - this refers to the connector that converted to original file to ASM
• ASM converter version
• analyst
• measurement identifier
• measurement time
• sample identifier
• device type
• detection type
• cell type processing method
• minimum cell diameter μm brightfield
  - note: ‘μm’ refers to unit and ‘brightfield’ to the detection type 
• maximum cell diameter μm brightfield
  -  note: ‘μm’ refers to unit and ‘brightfield’ to the detection type
• cell density dilution factor
• viability %
• viable cell density 10^cells/mL
• total cell count
• total cell density 10^6cells/mL
• average total cell diameter μm
• average live cell diameter μm
• viable cell count
• average total cell circularity
• average viable cell circularity

Sample file can be found here.

The example below shows a representative Result schema for data generated using a Vi-Cell BLU Connection. 

Configure Run Schema for Vi-Cell BLU data

The Run schema should specify that it will be using the Beckman Vi Cell BLU as the Connection schema.

If the data being imported from the Vi-Cell BLU already contains Benchling entity identifiers, it is not necessary to include any Run fields on the schema definition. It is also not necessary to configure an Input File since no data is being sent from Benchling to the Vi-Cell BLU.

Configuring the Output File Processor

The configuration of the Output File Processor is similar to that of other Runs. The Record Results should be specified as the ‘Benchling action’, and the ‘Result schema’ should be set as the schema created in the earlier step. 

It is also possible to specify the ‘default instrument data type’ returned by the connector that should be processed (with sample data being the only option in the context of cell counting). This step is optional - but it eliminates the need for the user to make this selection on each time a file is imported via a Run.

Lastly, it is necessary to perform the column mapping to assign the data being returned to the target Results schema. 

It is recommended to load sample data from an existing Connection to use for column mapping. Additionally, if the Result schema has not been previously defined, it may be done from this point as well. Alternatively, the column mapping may be manually if the desired columns are known.

The resulting column mapping will be shown in the Run schema.

Beckman Coulter, Vi-Cell BLU Connector Requirements

Revision History

2023/10 Initial Version

2024/06 

- Updated details regarding Gateway installation