Enabling saving Thumbnail Images on the MiniSeq

Thumbnail Images on the MiniSeq may be useful when troubleshooting run quality issues or for determining clustering efficiency. By default, the setting to save Thumbnail Images is not enabled on the MiniSeq, as these images increase run folder size and can cause runs to crash due to the increased strain on the hard drive. However, if users would like to enable the saving of thumbnail images for diagnostic purposes, follow the guidance below.

1. Close MiniSeq Control Software (MnCS).

2. Locate the following file:

• Windows 7:

  • C:\Illumina\MiniSeq Control Software\InstrumentShell.MiniSeqControlSoftware.Options.cfg

• Windows 10:

  • C:\ProgramData\Illumina\MiniSeq Control Software\InstrumentShell.MiniSeqControlSoftware.Options.cfg

    • The ProgramData folder may be hidden. To unhide files, select the View tab in the File Explorer window and ensure that "Hidden items" is checked.

1. Make a copy of the file, rename it to "InstrumentShell.MiniSeqControlSoftware.Options.BACKUP.cfg", and save it as a backup.

2. Open the original file and locate this line:

• 

1. Change false to true, and make sure that no additional characters or spaces are added or deleted.

2. Save the changed file.

3. Power cycle the instrument following the instructions in How to Power Cycle the MiniSeq.

• After following the steps above, the next run will save Thumbnail Images for each cycle.

• To disable Thumbnail Images, follow the above steps and change the argument back from true to false in step 5.

Additional considerations:

• Thumbnail Images will only be saved for Tiles 1 and 6 if this setting is enabled.

• Enabling this option does not retroactively add Thumbnails Images to past runs.

• When saving is enables, the Thumbnail Images are saved to:

  • [Run Folder]\Thumbnail_Images\L001\C[X.1] where X refers to the cycle number.

For any feedback or questions regarding this article (Illumina Knowledge Article #2032), contact Illumina Technical Support [e-mail].