Purpose 

To provide details about the necessary steps to implement the PerkinElmer, Envision data connector for use with the Benchling Connect platform.

Introduction

The PerkinElmer Envision data connector is a component used in the context of the Benchling Connect platform to parse data from Envision plate readers to an Allotrope Simple Model (ASM) and make that data available within the Benchling UI in the context of a Run.

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

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

Steps within PerkinElmer, Envision

From within PerkinElmer Envision, a user must:

 (i) configure a csv file export compatible with the Benchling Connect, PerkinElmer Envision data connector

(iii) ensure that the file is placed with the watched directory.

Supported Measurement Methods 

The EnVision allows users to perform experiments using different Measurement Methods including: Measurement (endpoint), Kinetic Measurement, Scan Measurement (area scan), and Wavelength Scan (spectral scan). At present the Benchling Connect - EnVision data connector is only capable of processing data recorded from endpoint measurements.

Measuring multiple plates

The Envision allows users to measure multiple plates per protocol. 

The Benchling Connect, EnVision data connector supports the processing of multiple plates per file. However, before exporting file with multiple plates it is highly recommended that the user update the barcode used within EnVision to correspond within plate barcodes used in Benchling. The plate names provided in EnVision may correspond to existing plate barcodes in Benchling, or may represent barcodes they intend to register as part of the processing of the file. Failure to do so will present challenges for associating the experimental data with the plate and associated entities within Benchling after the fact.

The user should reference section 15.2 - Barcode reading of the EnVision User Manual (Rev E, p.194)

Exporting data from Envision  

The user should configure the export of data as part of their acquisition protocol following the steps detailed section 7.4.2 - Output Settings of the EnVision User Manual (Rev E, p.74).

The File name should be updated such that the target folder corresponds to the same folder used when configuring the  Connection within Benchling. 

The data should be exported as a .csv file using “Export format: Plate 2”. 

Caution: while the Output Settings default to “Use system list separator”, ensure that a comma separator is used in the export file. 

Steps within Benchling  

From within Benchling, a user must:

1. Enable the PerkinElmer Envision data connector on the tenant [internal admin console]

2. Configure a PerkinElmer Envision Connection 

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

4. Configure a Run schema to accept data from PerkinElmer Envision and record results

For steps 1 - 4, please reference the Benchling Connect Installation Guide for details related to creating and installing a Gateway and configuring a Connection.

Data Returned by the PerkinElmer Envision

The Benchling Connect -  PerkinElmer Envision data connector supports the multi-mode plate reader functionality of Envision. Multi-mode plate readers are instruments that are capable of performing Absorbance, Fluorescence, and Luminescence measurements.

These data are structured using the Allotrope Plate Reader ASM data model (BENCHLING/2023/09). 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 Benchling Connect - PerkinElmer Envision data connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the Envision file export. The data is handled in a two step process; step one from Envision export to the .json based ASM, and step two from the ASM .json to a well file .csv and measurement file .csv available for ingest to Benchling. The well file is structured such that each row of the file represents a well of the plate; and the measurement file is structured such that each row of the file represents a measurement.

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

• Device Identifier
• Model Number
• Equipment Serial Number
• Software Name
• Software Version
• ASM converter name - name of data connector library
• ASM converter version - version of data connector library
• File Name
• Measurement identifier*
• Measurement Time
• Analytical Method Identifier - Protocol ID
• Experimental Data Identifier - Assay ID
• Well Plate identifier - this refers to the plate barcode
• Location identifier - this refers to the well position
• Sample Identifier - this defaults to “<Well Plate Identifier> <Location Identifier>” when the plate map is omitted
• Plate Well Count - number of wells
• Container Type 
• Compartment Temperature
• Detection Type - this will refer to Absorbance, Fluorescence, or Luminescence
• Detector Wavelength Setting* - where applicable
• Detector Bandwidth Setting* - where applicable
• Excitation Wavelength Setting* - where applicable
• Excitation Bandwidth Setting* - where applicable
• ‘Measurement’ - this column header will vary depending on the modality: absorbance, fluorescence, or luminescence - e.g absorbance_mAU
• ‘Calculated Results’ - this column header will vary depending on the label used for the Calculation 

* In cases of experiments measured at multiple wavelengths, these columns will be duplicated and will be annotated with a number for each measurement.  

Sample files can be found here.

PerkinElmer Envision Data Connector Requirements

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

Revision History

2024/04/08

Initial Version

2024/09/03

Update link to referenced schemas in Github

2024/09/18

Added Github testdata link