Cellular Technology Limited (CTL), ImmunoSpot Configuration Guide

Purpose

To provide details about the necessary steps to implement the CTL ImmunoSpot connector for use with the Benchling Connect platform.

Introduction

The ImmunoSpot connector is a component used in the context of the Benchling Connect platform to parse data from ImmunoSpot software to an Allotrope Simple Model (ASM) and make those data available within the Benchling UI in the context of a Run. The ImmunoSpot software is used in conjunction with CTL’s line of ImmunoSpot Analyzers.

The Benchling Connect - ImmunoSpot connector is a ‘file-based’ based connector, meaning that it processes text file (.txt) exports generated by the ImmunoSpot software suites (Single-Color (SC), Double-Color (DC), Fluoro-X). The data within the file export is then accessed by Benchling Connect through the use of a ‘watched’ file folder on the local computer hosting a Benchling Gateway, which has been configured via a Connection from within Benchling.

In order to successfully implement the ImmunoSpot connector for use with the Benchling platform, there are specific steps that need to be followed across both the ImmunoSpot software and Benchling user interfaces. 

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

Steps Within the ImmunoSpot Software

Within the ImmunoSpot software, users have the option of specifying where the spot counting results data should be stored. Users can also determine the types of output files should be generated by the counting process. Below we will outline the steps to perform for exporting text files compatible with the ImmunoSpot data connector.

1. From within the ImmunoSpot software suite window (SC, DC, or Fluoro-X), select the Preferences settings.
   
2. The ImmunoSpot Preferences window will open. Navigate to the Counting tab 
   
   
   
   
3. Set the Default plate location to the same folder that will be used when configuring the Connection within Benchling, 'watched' folder. It is recommended to place these folders within the C:\Users\Public\Documents folder since this location does not require Administrative rights to create new files and folders.

    

4. In the Plate Data to Save section, ensure that the Text file is selected to be saved. The ImmunoSpot connector will only process the .txt, Text file output. 
   
   
5. Click the Save and Exit button to save all changes
   
   Plates run by the software will generate the selected output files following counting. Users should ensure that the output text file from the Count mode are within a plate data folder/counted folder. The ImmunoSpot data connector will expect to parse result data files (.txt) within these sub-folders of the 'watched' folder.

ImmunoSpot Export File Structure

ImmunoSpot provides a specified file structure for storing exported files from the software. By default, the software will export data to a separate folder per plate measured, with three sub-folders for Scan, Count, and Quality Control each for different data generated during the analysis workflow. The Scan subfolder will contain raw image files that are processed by Count and Quality Control steps. Count and Quality Control sub-folders will contain a .txt file - each with the same user defined name. The ImmunoSpot connector will only process the .txt file returned to the counted folder, while the other sub-folders may be present in plate data folder these will not be parsed by the connector.

Measuring Multiple Plates

The ImmunoSpot software allows for users to obtain spot counts from multiple plates in a single run. Results from each of the plates is then by default exported into a separate export plate folders, with file paths such as the following:

C:\Users\Public\Documents\Plate1\counted\Plate1.txt

C:\Users\Public\Documents\Plate2\counted\Plate2.txt

Plates may be grouped together prior to spot counting within an Experiment folder containing multiple plate sub-folders, such as the following:

C:\Users\Public\Documents\Experiment1\Plate1\counted\Plate1.txt

C:\Users\Public\Documents\Experiment1\Plate2\counted\Plate2.txt

The spot counting results and image files produced by the software will always be exported to separate sub-folders, respective of the assay plate.

Steps within Benchling

From within Benchling, a user must:

1. Enable the CTL, ImmunoSpot data connector on the tenant [internal admin console]
   
2. Configure a ImmunoSpot Connection
   
3. Create a Result schema to structure the data to be recorded
   
4. Configure a Run schema to accept data from ImmunoSpot 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 ImmunoSpot data

The Benchling Connect - CTL ImmunoSpot data connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the ImmunoSpot file export. The data is handled in a two step process; step one from ImmunoSpot .txt 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 Plate Reader ASM data model. Note, while the CTL ImmunoSpot is typically referred to as an ELIspot Analyzer, the data can be effectively modeled as plate reader with optical imaging capabilities.

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 connection then converts the ASM .json to a well file .csv, in which 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.

For ImmunoSpot, the well file 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 data connector library
• ASM converter version - version of data connector library
• File Name
• Measurement Identifier*
• Measurement Time
• Sample Identifier
• Device Type
• Detection Type - This refers to ‘optical-imaging’
• Container Type - this refers to ‘well plate’
• Plate Well Count - number of wells
• Location Identifier - this refers to the well and spot position
• Well Plate Identifier - this refers to the plate barcode
• 'Image Feature'(s) - these column header(s) will vary depending on the label used for feature(s) derived from images.

* Note that in the case of the well data file, these columns will be duplicated and annotated with a number for each measurement.

Sample files can be found here.

Configure Run Schema to employ ImmunoSpot Connection

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

As part of the Run schema creation, the user should specify 'CTL ImmunoSpot' 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

CTL ImmunoSpot Connector Requirements

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

Revision History

2024/04/10

Initial Version

2024/09/04

Add link to referenced schemas in Github

2024/09/18

Added Github testdata link