Beckman Coulter, Vi-cell XR Cell Counter Configuration Guide

Purpose 

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

Introduction

The Vi-Cell XR connector is a component used in the context of the Benchling Connect platform to parse data from Beckman Coulter, Vi-Cell XR 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 XR connector is a ‘file-based’ based connector, meaning that it processes text file exports generated by the Vi-Cell XR 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 XR connector for use with the Benchling platform, there are several steps that need to be followed across both the Vi-Cell XR 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 XR

 The user should perform measurements following the Vi-Cell XR Instructions for Use (PN 383674BH, May 2022).

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

The processing of a single sample is referred to as a Run within the Vi-Cell XR software. An export containing data from multiple samples is referred to as a ‘Multi-Run’ file. The export of an individual Run is expected to be in a .txt format, while the export of a 'Multi-Run' file is expected to be in a .xlsx format.

Performing file export from Vi-Cell XR

The Vi-Cell XR connector is designed to process the ..txt or xlsx export generated by the Vi-Cell XR instrument.

Generating single 'Run' .txt export

To export an individual sample as a .txt file, the user should select ‘Export to text file’ on the Log in sample screen. This .txt file will follow the naming convention of <Sample ID>.txt

Generating a 'multi-Run' .xlsx export

A ‘multi-Run’ .xls export is created either selecting ‘Add to multi-run file’ within the Log in Sample UI or within the Run Options tab in under Preferences (shown below).

The user is expected to configure the parameters to be included in the multi-run file by selecting the available options within the Export tab under the Preferences (shown below). However, of the available options, only those listed are captured by the connector since these are defined within the cell counting ASM data model - Note the fields that are Required for connector function.

Parameters captured by connector:

• Sample ID (Required)
• Cell Type
• Minimum Diameter
• Maximum Diameter
• Dilution Factor
• Sample Date
• Total Cell Count (Required)
• Viable Cell Count
• Viability (Required)
• Total Cells /mL
• Viable Cells /mL
• Average Diameter
• Average Circularity
• Images

Configuration of Preferences within Vi-Cell XR

Whether a single-run or multi-run export is used, the file must be placed within the target directory which is specified during Connection configuration, when creating a Vi-Cell XR Connection within the Benchling UI.

The instrument can be configured to save to this directory automatically, by adding it to the Exported File path within Preferences > Directories

Within the Run Options, the Concentration exponent should be set to 10^6.

If the user desires to capture the serial number of the instrument used to perform the analysis, this needs to be populated within the Hardware tab under the Configuration menu (shown below).

Steps within Benchling 

From within Benchling, a user must:

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

2. Configure a Vi-Cell XR Connection

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

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

For details on completing these steps, please reference the Benchling Connect Installation Guide.

Data returned by Vi-Cell XR connector

The Benchling Connect - Vi-Cell XR cell counter connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the Vi-Cell XR file export. The data is processed in a two step process; step one from  Vi-Cell XR 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
• device serial number
• file name
• software name
• software version
• 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 - this corresponds to the ‘Cell Type’ in the XR interface
• 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
• viable cell count
• average total cell circularity
• image file - this is a record of the image file name, and not the image itself

Sample files can be found here.

Vi-Cell XR Connector Requirements

Revision History

2023/11/14

Initial Version

2024/05

- Corrected supported version from 2.4 and 2.6 to 2.04 and 2.06

2024/06

- Updated to reflect support for single-run .txt exports