Revvity Matrix, Configuration Guide

Purpose 

To provide details about the necessary steps to implement the Revvity, Matrix adapter for use with the Benchling Connect platform.

Introduction

The Revvity, Matrix  adapter is a component used in the context of the Benchling Connect platform to parse data from Matrix software to an Allotrope Simple Model (ASM) and make those data available within the Benchling UI in the context of a Run. The Matrix software is used in conjunction with the Cellaca MX imaging cell counters.

The Benchling Connect - Matrix adapter is a ‘file-based’ based adapter, meaning that it processes CSV/XLSX exports generated by the Matrix software. 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 Matrix adapter for use with the Benchling platform, there are specific steps that need to be followed across both the Matrix software and Benchling user interfaces. 

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

Steps within Revvity, Matrix

From within Matrix, a user must:

1. 1. Click the Export button located at the bottom of the Results screen
   2. The Export dialog will be displayed
   3. Confirm the export Location 
   4. If necessary update this path* by clicking the Browse button, navigating to a folder on your Operating Computer or network, and clicking OK.
   5. Select Well Level CSV in the Data section
   Click Export and Print

Verifying Default Data File/Image Folder Locations

1. Expand the Exports area in the Results screen
2. Click the location link to open the export folder
3. Confirm the folder path* and the output type is set to CSV

*The user is expected to configure the file export path to match the directory specified during Connection configuration within Benchling.

Note: The Revvity, Matrix software supports transmitted light and fluorescence cell counting measurements. At present, the Revvity, Matrix connector is only support transmitted light cell counting.

Steps within Benchling

From within Benchling, a user must:

1. Enable the Revvity, Matrix connector on the tenant [internal admin console]

2. Configure a Revvity, Matrix Connection

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

4. Configure a Run schema to accept data from Revvity, Matrix and records 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.

Creation of Result schema for Revvity, Matrix data

In order to record results returned via the integration a Result schema must be created. This can be done prior to configuration of the Run schema, or within the context of the Run schema Output File configuration. 

The Benchling Connect - Revvity Matrix adapter uses the Allotrope Simple Model (ASM) to structure the information parsed from the Matrix file export. The data is handled in a two step process; step one from Matrix .csv 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 Cell Counting 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 adapter then converts the ASM to:

• sample file .csv file - in which each row of the file represents a sample
• measurement file .csv file - in which each row of the file represents a measurement

For Matrix, the sample and measurement file will typically contain the following columns (if available within the data):

• Product Manufacturer
• Device Identifier
• Model Number
• Equipment Serial Number
• Software Name
• Software Version
• ASM converter name - name of adapter library
  
• ASM converter version - version of adapter library
  
• File Name
  
• Measurement Identifier
  
• Measurement Time
  
• Sample Identifier
  
• Detection Type
  
• Viability (cell counter)
  
• Total Cell Density (cell counter)
  
• Viable Cell Density (cell counter)
  
• Dead Cell Density (cell counter)
  
• Average Total Cell Diameter
  
• Average Live Cell Diameter (cell counter)
  
• Average Dead Cell Diameter (cell counter)
  
• Total Cell Count
  
• Viable Cell Count
  
• Dead Cell Count
  

Configure Run Schema to employ Matrix Connection

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

As part of the Run schema creation, the user should specify 'Revvity, Matrix' 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

Revvity, Matrix Connector Requirements

Revision History

2024/09/13

Initial Version

2024/10/14

Update for connector handling of CSV and XLSX files

2024/11/01

- Update guide to include handling for Cell Counting ASM-to-CSV to generate measurement file