Running Colony Detection

This topic assumes that there is an instance of the PIXLClient object called pixl. If this is not the case, please see the Connecting To The PIXL topic.

The Colony Detection workflow is a key feature of the PIXL. This workflow is made up of the following key steps:

The Colony Detection workflow is triggered by the client.
A source plate is requested by the PIXL.
The source plate is loaded into the PIXL by the client.
PIXL images the source plate and then detects and filters the colonies that should be picked.
PIXL reports the workflow has finished and returns any captured data.

The Colony Detection workflow is broken down into a flow diagram that can be viewed here.

From a clients point of view the following need steps need to be implemented in order to run a Colony Detection workflow:

Subscribe to the RequiredPlateInteractionsChanged event on the PIXLClient to receive plate change requests.
Call the RunColonyDetectionWorkflow method on the PIXLClient to trigger the Colony Detection workflow with a specified Project Template. Project Template's can be created on the PIXL's UI software.
Respond to RequiredPlateInteractionsChanged events with the PlateLoaded method on the PIXLClient to notify the PIXL of all plates that have been loaded.

For further examples on how to manage plates please see the Loading And Swapping Plates, Removing Plates, and Handling Plate Requests topics.

Whenever there is a pending plate interaction it can be cancelled by calling the Abort method event on the PIXLClient.

Once the workflow has been triggered and all plates loaded the PIXL will run the workflow. By providing the name of a Project Template the settings the PIXL uses to create the run the workflow can be adjusted. If an empty string is provided the last used Project Template is used.

Available Project Templates can be viewed by checking the AvailableColonyDetectionProjectTemplates property on the PIXLClient class.

Running the Colony Detection workflow with the last used Project Template	Copy Code
pixl.RunColonyDetectionWorkflow("ID1234", string.Empty);

The Colony Detection workflow returns an instance of the RunColonyDetectionWorkflowCommandResponse class, which contains information on the status of the finished operation as well as all data captured relating to the workflow.

Running the Colony Detection workflow and displaying all captured data on the Console	Copy Code
// Run the workflow. var result = pixl.RunColonyDetectionWorkflow("ID1234", string.Empty).Result; // Display the result. Console.WriteLine(result.Result.Message.ToString()); // Display the local tracking base path. Console.WriteLine($"Tracking base: {result.TrackingPath}"); // Display the program ID. Console.WriteLine($"Program ID: {result.ProgramInformation.ProgramID}"); // Use a StringBuilder to concatenate all information to display. var stringBuilder = new StringBuilder(); // Concatenate colony information. for (var i = 0; i < result.ProgramInformation.ColonyInformation.Length; i++) { var colony = result.ProgramInformation.ColonyInformation[i]; stringBuilder.AppendLine($"---{i + 1} of {result.ProgramInformation.ColonyInformation.Length}:"); stringBuilder.AppendLine($"------ID: {colony.ID}"); stringBuilder.AppendLine($"------Name: {colony.Name}"); stringBuilder.AppendLine($"------IsSelected: {colony.IsSelected}"); stringBuilder.AppendLine($"------SectorID: {colony.SectorID}"); stringBuilder.AppendLine($"------X: {colony.X}"); stringBuilder.AppendLine($"------Y: {colony.Y}"); stringBuilder.AppendLine($"------Area: {colony.Area}"); stringBuilder.AppendLine($"------Diameter: {colony.Diameter}"); stringBuilder.AppendLine($"------Brightness: {colony.Brightness}"); stringBuilder.AppendLine($"------AverageRed: {colony.AverageRed}"); stringBuilder.AppendLine($"------AverageGreen: {colony.AverageGreen}"); stringBuilder.AppendLine($"------AverageBlue: {colony.AverageBlue}"); stringBuilder.AppendLine($"------Redness: {colony.Redness}"); stringBuilder.AppendLine($"------Greenness: {colony.Greenness}"); stringBuilder.AppendLine($"------Blueness: {colony.Blueness}"); stringBuilder.AppendLine($"------ProximityToClosest: {colony.ProximityToClosest}"); } // If there were no colonies add an entry to inform the user of this. if (result.ProgramInformation.ColonyInformation.Length == 0) stringBuilder.AppendLine("---None"); // Display pinning header. Console.WriteLine("Colonies:"); // Display colony information. Console.WriteLine(stringBuilder.ToString());

Running the Colony Detection workflow and displaying all captured data on the Console

Copy Code

// Run the workflow.
var result = pixl.RunColonyDetectionWorkflow("ID1234", string.Empty).Result;

// Display the result.
Console.WriteLine(result.Result.Message.ToString());

// Display the local tracking base path.
Console.WriteLine($"Tracking base: {result.TrackingPath}");

// Display the program ID.
Console.WriteLine($"Program ID: {result.ProgramInformation.ProgramID}");

// Use a StringBuilder to concatenate all information to display.
var stringBuilder = new StringBuilder();

// Concatenate colony information.
for (var i = 0; i < result.ProgramInformation.ColonyInformation.Length; i++)
{
    var colony = result.ProgramInformation.ColonyInformation[i];
    stringBuilder.AppendLine($"---{i + 1} of {result.ProgramInformation.ColonyInformation.Length}:");
    stringBuilder.AppendLine($"------ID: {colony.ID}");
    stringBuilder.AppendLine($"------Name: {colony.Name}");
    stringBuilder.AppendLine($"------IsSelected: {colony.IsSelected}");
    stringBuilder.AppendLine($"------SectorID: {colony.SectorID}");
    stringBuilder.AppendLine($"------X: {colony.X}");
    stringBuilder.AppendLine($"------Y: {colony.Y}");
    stringBuilder.AppendLine($"------Area: {colony.Area}");
    stringBuilder.AppendLine($"------Diameter: {colony.Diameter}");
    stringBuilder.AppendLine($"------Brightness: {colony.Brightness}");
    stringBuilder.AppendLine($"------AverageRed: {colony.AverageRed}");
    stringBuilder.AppendLine($"------AverageGreen: {colony.AverageGreen}");
    stringBuilder.AppendLine($"------AverageBlue: {colony.AverageBlue}");
    stringBuilder.AppendLine($"------Redness: {colony.Redness}");
    stringBuilder.AppendLine($"------Greenness: {colony.Greenness}");
    stringBuilder.AppendLine($"------Blueness: {colony.Blueness}");
    stringBuilder.AppendLine($"------ProximityToClosest: {colony.ProximityToClosest}");
}

// If there were no colonies add an entry to inform the user of this.
if (result.ProgramInformation.ColonyInformation.Length == 0)
    stringBuilder.AppendLine("---None");

// Display pinning header.
Console.WriteLine("Colonies:");

// Display colony information.
Console.WriteLine(stringBuilder.ToString());

It is recommended that all plates should be removed from the PIXL when it finishes a workflow. After a plate has been removed call the PlateRemoved method on the PIXLClient to notify the PIXL of all plates that have been removed.

Reference

Getting Started

Managing Plates