Revvity, Kaleido Configuration Guide

Purpose 

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

Introduction

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

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

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

Steps within Revvity, Kaleido

From within Revvity, Kaleido a user must:

(i) Perform a csv file export compatible with the Benchling Connect, Kaleido data connector 

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

Supported Measurements, Modes 

The instruments used in conjunction with the Kaleido software, such as the EnSight plate reader offer multiple acquisition technologies, including: absorbance, fluorescence (including FRET and Alpha), luminescence, imaging, and label-free. The Benchling Connect, Kaleido data connector  is capable of processing data from absorbance, fluorescence, luminescence, and imaging; but not label-free measurements.  The Kaleido software allows users to perform experiments using different Measurement Modes including: Single (endpoint), Kinetic, Well Scan (area scan), and Excitation or Emission Scan (spectral scan). At present the Benchling Connect, Kaleido data connector  is only capable of processing data recorded from Single (endpoint) measurements

Measuring multiple plates

Kaleido allows users to measure multiple plates per run of a Protocol. 

The Benchling Connect, Kaleido data connector  supports the processing of multiple plates per file. In all cases it is highly recommended that the user provide barcodes within Kaleido which correspond to plate barcodes used in Benchling, but especially so when performing experiments with multiple plates.

The Kaleido software supports the capture of barcodes affixed to the plate (using the integrated barcode scanner on the instrument), the manual entry of barcodes, or the creation of a virtual barcode which follow the convention of "V-YYYY-MM-DD HH:MM:SS".

The plate barcodes provided in Kaleido may correspond to existing plate barcodes in Benchling, or may represent barcodes they intend to register as part of the processing the file. The plate names used in Kaleido will appear within the "well plate identifier" column in the data returned to Benchling (discussed below). Failure to do so will present challenges for associating the experimental data with the plate and associated entities within Benchling after the fact.

Exporting data from Kaleido

The user should configure the data export as part of the Post Processing Sequence during Protocol Setup.

As part of the Post Processing Sequence the user can enable an automatic export of results following completion of the measurement(s). The user should click the [+] button and select Export to file from the pop-up menu to add an EXPORT operation. 

From this view the following parameters will be displayed in the Content Area where the can configure format and target location of the export. 

Of the available export formats, only the CSV_PLATE format is compatible with the Benchling Connect, Kaleido data connector . 

Steps within Benchling

From within Benchling, a user must:

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

2. Configure a Kaleido Connection

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

4. Configure a Run schema to accept data from Kaleido 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.

Create Result Schema for Kaleido data

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

The Benchling Connect - Revvity, Kaleido data connector supports the multi-mode plate reader plus imaging functionality functionality of Kaleido. Multi-mode plate readers are instruments that are capable of performing absorbance, fluorescence, and luminescence measurements - while some models have been extended to support automated microscopy.

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 data connector then converts the ASM to a well file .csv file which is structured such that each row of the file represents a well of the plate; and a measurement file .csv, in which each row of the file represents a measurement.

The well file and measurement file can 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 Signature
• Experimental Data Identifier - Measurement Signature
• 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, Luminescence, or Optical-Imaging
• Detector Wavelength Setting* - where applicable
• Detector Bandwidth Setting* - where applicable
• Excitation Wavelength Setting* - where applicable
• Excitation Bandwidth Setting* - where applicable
• Magnification Setting* - where applicable
• Exposure Duration Setting* - where applicable
• Illumination Setting* - where applicable
• Transmitted Light Setting* - where applicable
• Fluorescence Tag Setting* - where applicable
• Auto Focus Setting* - where applicable
• ‘Measurement’* - this column header will vary depending on the modality: absorbance, fluorescence, or luminescence - e.g absorbance_mAU
• Image File Name* - where applicable
• 'Image Feature'(s) - these column header(s) will vary depending on the label used for feature(s) derived from images.
• ‘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.

In order to create the Result schema directly from Kaleido sample data, the Result schema can be configured as part of the Run schema creation (discussed below).

Configure Run Schema to employ Kaleido 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 Kaleido' 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

Example Kaleido Data

Refer to the example files in the repository below if you would like to test this configuration pattern with demonstration data. 

https://github.com/Benchling-Open-Source/allotropy/tree/main/tests/parsers/revvity_kaleido/testdata

Revvity, Kaleido Data Connector Requirements

* These are the versions Kaleido with which the data connector has been developed and tested. The adapter may work with other versions of Kaleido, but that must be verified by the user.

Revision History

2024/03/20

Initial Version

2024/09/03

Update link to referenced schemas in Github

2024/09/18

Added Github testdata link