Luminex, INTELLIFLEX Configuration Guide

The Benchling Connect, Luminex INTELLIFLEX data connector is a component used in the context of the Benchling Connect platform to parse data from Luminex INTELLIFLEX xMAP Analyzers to an Allotrope Simple Model (ASM) and make that data available within the Benchling UI in the context of a Run.

The Benchling Connect, INTELLIFLEX data connector is a ‘file-based’ based data connector, meaning that it processes .csv file exports generated by the Luminex INTELLIFLEX application. 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 Luminex INTELLIFLEX data connector for use with the Benchling platform, there are multiple steps that need to be followed across both the Luminex INTELLIFLEX and Benchling user interfaces. 

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

Steps within Luminex INTELLIFLEX Software

Executing an assay within the Luminex INTELLIFLEX software is referred to as a "Run".

Prior to running a Run, a user may (optionally) import a sample identifiers or Panel. 

To retrieve Run data from within Luminex INTELLIFLEX a user must:

(i) Generate the .CSV export which is compatible with the Benchling Connect, INTELLIFLEX data connector

(ii) Ensure that the file is placed with the watched directory configured via a Benchling Connection.

Importing sample identifiers to Luminex INTELLIFLEX Run

The Luminex INTELLIFLEX software annotates data based on sample identifiers.

To import a list of sample identifiers to a Run, the IMPORT utility in the PLATE CONFIGURATION/LAYOUT page should be used. The IMPORT utility expects a .CSV file with columns for:

For full details on Importing of sample identifiers to INTELLIFLEX, see pg. 50 of the Luminex INTELLIFLEX manual, under Import the Layout.

The file to be uploaded to the LAYOUT/IMPORT can be generated using the Input File Configuration within the Benchling Run. 

Note: although INTELLIFLEX defines plate identifiers within the software, plate identifiers are not defined by importing the layout. As such, for tracking experimental results, it is recommended that the user sample identifiers within the INTELLIFLEX run correspond to entities registered within Benchling. 

Importing analyte panel to Luminex INTELLIFLEX Run

The Luminex INTELLIFLEX software annotates data based on sample identifiers.

To import a list of sample identifiers to a Run, the IMPORT utility in the PLATE CONFIGURATION/PANEL page should be used. The IMPORT utility expects a .CSV file with columns for:

For full details on Importing of sample identifiers to INTELLIFLEX, see pg. 55 of the Luminex INTELLIFLEX manual, under Import the Panel.

The file to be uploaded to the PANEL/IMPORT can be generated using the Input File Configuration within the Benchling Run.

Exporting data from Luminex INTELLIFLEX

There are 3 report types that can be exported from INTELLIFLEX:

• INTELLIFLEX .CSV

• INTELLIFLEX .XLSX

• xPONENT .CSV - backwards compatible export similarly formatted as export from xPONENT software

At this time, only the INTELLIFLEX .CSV and xPONENT .CSV are supported by the Luminex INTELLIFLEX connector.

In order to export data from Luminex INTELLIFLEX, the user should follow the instructions for Export to CSV or XLSX (pg. 78) of the INTELLIFLEX manual.

To do so the user should:

• Navigate to the Results page
• Chose the completed Runs, filtering by date range or plate name
• Select Export > Results > Export
• In the Save As dialog box, the user should choose the export destination for the .CSV file
  This destination should be folder specified in the Connection configured within Benchling
• Click Save
• In the Export Complete dialog box, click "Ok"

Steps within Benchling

From within Benchling, a user must:

1. Enable the Luminex INTELLIFLEX data connector on the tenant [internal admin console]

2. Configure a Luminex INTELLIFLEX Connection

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

4. Configure a Run schema for the Luminex INTELLIFLEX assay generate file for Import Layout or Import Panel utility (if desired) and to record Results

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

Configuring the Run - Annotating data via Plate entered as Benchling Run field

As noted above, it is recommended to annotate experimental data from Luminex INTELLIFLEX using sample identifiers recorded within the INTELLIFLEX Run via Layout.

However, if the user prefers to associate the data with a plate and well within Benchling, it is possible to do so by annotating the results with information from a plate entered into the Benchling Run itself. 

In order to use the plate barcode and plate well to associate the well-level measurements contained within the INTELLIFLEX file with the appropriate entity in Benchling additional Transform steps must be configured. Note that this method is only appropriate for ingesting INTELLIFLEX files with a single plate, if multiple plates are present then the sample identifiers should be entered directly in INTELLIFLEX as discussed above.

First an ‘Add Column’ step is needed to capture the barcode of the plate that is entered on the Run. Since this barcode value needs to be repeated for each row of the file, ensure that the ‘Consolidate results into single row’ option is selected.

Next a combination of a ‘Duplicate’ and a ‘Merge’ step are used to combine the plate barcode with the well coordinates from the file, to create a column containing the plate well information in the necessary ‘barcode:well-coordinate’ format. Together the Transform steps would appear as shown below.  

Data returned by Luminex INTELLIFLEX Data Connector

The Benchling Connect, Luminex INTELLIFLEX data connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the INTELLIFLEX file export. The data is processed in a two step process; step one from INTELLIFLEX export to the .json based ASM, and step two from the ASM .json to a .csv file available for ingest to Benchling.

These data are structured using the Allotrope Multi-Analyte-Profiling ASM data model. Details about the this ASM schema can be found here:

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

The data connector then converts the ASM to:

• well file .csv file - such that each row of the file represents a well of the plate - along with metadata about the experiment
• measurement file .csv file - such that each row of the file represents a measurement - along with metadata about the experiment
• analyte file .csv file - such that each row of the file represents an analyte measured - along with metadata about the experiment and statistics calculated

For the Luminex INTELLIFLEX, the well file will typically contain the following columns (if available within the data):

• Product Manufacturer
• Equipment Serial Number
• Firmware Version
• File Name
• UNC path
• Software Name
• Software Version
• ASM File identifier
• ASM Converter Name
• ASM Converter Version
• Analyst
• Analytical Method Identifier - name of protocol used in analysis
• Experimental Data Identifier
• Container Type
• Plate Well Count
• Measurement Identifier
• Measurement Time
• Sample Identifier
• Sample Role Type
• Description
• Location Identifier
• Well Plate Identifier
• Device Type
• Sample Volume Setting
• Dilution Factor Setting
• Gain
• Minimum Assay Bead Count Setting
• Assay Bead Count Total
• Assay Bead Identifier <Analyte Name> - repeated for each analyte measured
• Assay Bead Count <Analyte Name> - repeated for each analyte measured
• Fluorescence Median RFU <Analyte Name> - repeated for each analyte measured
• Additional Statistics <Analyte Name> - repeated for each analyte measured
  • Supported at present: Mean, Trimmed Mean, Coefficient of Variation, Standard Deviation, Trimmed Standard Deviation, Peak, Trimmed Peak, Trimmed Count, Net MFI, Avg Net MFI, Test Result, % Recovery, %CV of Replicates -- added if available within the data
• Error - List of error message per well (if applicable)

The measurement file will typically contain the following columns (if available within the data):

• Product Manufacturer
• Equipment Serial Number
• Firmware Version
• File Name
• UNC path
• Software Name
• Software Version
• ASM File identifier
• ASM Converter Name
• ASM Converter Version
• Analyst
• Analytical Method Identifier - name of protocol used in analysis
• Experimental Data Identifier
• Container Type
• Plate Well Count
• Measurement Identifier
• Measurement Time
• Sample Identifier
• Sample Role Type
• Description
• Location Identifier
• Well Plate Identifier
• Device Type
• Sample Volume Setting
• Dilution Factor Setting
• Gain
• Minimum Assay Bead Count Setting
• Assay Bead Count Total
• Assay Bead Identifier <Analyte Name> - repeated for each analyte measured
• Assay Bead Count <Analyte Name> - repeated for each analyte measured
• Fluorescence Median RFU <Analyte Name> - repeated for each analyte measured
• Additional Statistics <Analyte Name> - repeated for each analyte measured
  • Supported at present: Mean, Trimmed Mean, Coefficient of Variation, Standard Deviation, Trimmed Standard Deviation, Peak, Trimmed Peak, Trimmed Count, Net MFI, Avg Net MFI, Test Result, % Recovery, %CV of Replicates -- added if available within the data
• Error - List of error message per well (if applicable)

The analyte file will typically contain the following columns (if available within the data):

• Product Manufacturer
• Equipment Serial Number
• Firmware Version
• File Name
• UNC path
• Software Name
• Software Version
• ASM File identifier
• ASM Converter Name
• ASM Converter Version
• Analyst
• Analytical Method Identifier - name of protocol used in analysis
• Experimental Data Identifier
• Container Type
• Plate Well Count
• Measurement Identifier
• Measurement Time
• Sample Identifier
• Sample Role Type
• Description
• Location Identifier
• Well Plate Identifier
• Device Type
• Sample Volume Setting
• Dilution Factor Setting
• Gain
• Minimum Assay Bead Count Setting
• Analyte
• Analyte identifier
• Assay Bead Identifier
• Assay Bead Count
• Fluorescence Median RFU
• Additional Statistics  - repeated for each analyte measured
  • Supported at present: Mean, Trimmed Mean, Coefficient of Variation, Standard Deviation, Trimmed Standard Deviation, Peak, Trimmed Peak, Trimmed Count, Net MFI, Avg Net MFI, Test Result, % Recovery, %CV of Replicates -- added if available within the data
• Error

Sample files can be found here.

Configure Run Schema to employ Luminex, INTELLIFLEX Connection

The Run schema can be created from the menu under Feature Settings.

As part of the Run schema creation, the user should specify 'Luminex, INTELLIFLEX' as the Connection Schema.

Configure the Output File Processor

For details on configuring the Output File Processor within the Run schema, please refer to these articles.

• Configure the Output File Config of a Benchling Connect Run
• Configure the Output File Processor to Create New Entities
• Configure the Output File Processor to Capture Results

Luminex INTELLIFLEX Data Connector Requirements

* This is the version of the INTELLIFLEX software with which the data connector has been developed and tested. The data connector may work with other versions of the INTELLIFLEX software, but that must be verified by the user.

Revision History

2024/09/17

Initial Version