Note: More details can be found on our main website : PIXL Command Line Detection - Singer Instruments
Introduction - Offline Detection
The offline detection application is a console application which can be used to run PIXL's colony detection algorithm outside the bounds of the software. It uses the same libraries as the PIXL software to perform this detection but does not require a real PIXL in order to perform the detection.
Contents
Installation
The offline detection software is bundled with the normal PIXL windows UI. The latest installer can be obtained by contacting technicalsupport@singerinstruments.com.
Setup
In order to maximise detection accuracy there is a small amount of setup required.
Guide rails
The PIXL uses plate holders which feature guide rails to accurately locate plates. The location of these guide rails may vary slightly between PIXLs. The PIXL can be calibrated by the user by selecting the 'Calibrate Camera' option from the 'Maintenance' menu. Each plate holder must be calibrated separately.
If positional accuracy is important then the PIXL capturing the source images must be calibrated and these settings must be updated on the PC running offline detection. To do this simply copy the file C:\Program Files\Singer Instrument Company Limited\PIXL\Configuration\HardwareConfiguration.xml from the PIXL to the same location on the PC running the offline detection program.
Agar depth
In order to correct perspective within the images the depth of the agar within the plate needs to be accounted for. It is worth noting that small differences in agar depth will have minimal impact on accuracy. When running the PIXL software an ultrasonic sensor is used. However, when running online this value can be specified in the template file.
The agar depth can be determined by manually measuring the depth of the agar, or can be pulled from the exported data.
Measuring manually
Measure from the internal bottom of the plate to the surface of the agar.
Pulling from export data
When the PIXL successfully completes a 'Colony Detection' workflow it will create a tracking folder. In that folder will be a file, SourcePlateColonySummary.tsv, that summarises the source plate. This has a field, SourcePlate_AgarDepth, that identifies the detected depth of the agar.
Specifying in a template
Once known the agar depth can be specified in the template file.
The root node ProjectTemplate has a child node Source. The Source node has an attribute AgarDepth. Agar depth is specified in millimeters and is a floating point number and can be any value greater than 0 and less than the internal depth of the plate.
<ProjectTemplate ...>
<Source AgarDepth="5" ...>
...
Running
In order to use the offline detection application, you need to call it in a batch script or similar.
Start "fullPath/SI.Software.Products.PIXL.OfflineDetection.exe" projectName imagePath templatePath
The offline detection works by creating a colony detection project on the PC. This means you first need to specify a project name.
The second argument you must pass is a path to the image that you are trying to analyse. This will be the image that the project uses for analysis.
Finally you must also pass a full path to the project template that you wish to use to create the project with. The colony detection project will use all settings from that template to analyse the image.
After this has finished you can find any output in the tracking directory which will be printed on the output window.
Program Exit codes
Success: 0
Image File Not Found: 1
Template File Not Found: 2
Invalid Image File: 3
Invalid Template File: 4
Invalid Project Name: 5
Other Error: 6
If you require more information please contact technicalsupport@singerinstruments.com for assistance.
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