Troubleshooting

Retrieving Log Files for Illumina Support

If you encounter a problem while using the Illumina StrataMap Image Tool, the Illumina support team may request a log file to help troubleshoot the problem. Follow the steps below to locate and send the correct log file from your system.

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Locate the Log File

The application creates a new log file every day. These files are named using the format YYYY-MM-DD.log and are stored in a system folder on your computer.

On Windows

1. Open File Explorer.
2. In the address bar, paste the following path and press Enter:

   %APPDATA%\Illumina StrataMap Image Tool\logs\

3. Find the file named:

   YYYY-MM-DD.log

   Replace YYYY-MM-DD with the date the issue occurred.

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On macOS

1. Open Finder.
2. Press Cmd + Shift + G to open the “Go to Folder” dialog.
3. Enter the following path:

   /Users/<your username>/Library/Logs/Illumina StrataMap Image Tool/

4. Locate the file named:

   YYYY-MM-DD.log

   Replace <your username> with your macOS username and YYYY-MM-DD with the date the issue occurred.

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Send the Log File

Once you’ve located the log file:

1. Attach it to your support message.
2. Include a brief description of the issue and the steps that led to it.
3. Send the message with the log file.

ISIT stalls on a step

If processing stalls, close and restart the app. Your progress is saved up to that point.

Cloud Export Failure

In the event that the ISIT cloud export feature fails, use the following instructions to upload your OME-TIFF files directly to ICA for autolaunch or manual analysis. Additionally, you will need to create a corresponding sample sheet that contains the cloud locations of the OME-TIFF files.

1. After processing your images with ISIT, be sure to save the exports locally.
2. In a browser, navigate to your Core domain and enter the desired Project.
3. Upload the OME-TIFFs for all samples to Core using the user interface tool.

Where you decide to upload the OME-TIFFs is flexible. Choose a location that works for you.

1. Once the OME-TIFFs are successfully uploaded, save the URNs associated with each one:

   1. Select the name of the OME-TIFF to open the Data details.
   2. Find and copy the entire URN of each sample (note: the entire URN is longer than what appears here, so make sure to highlight as far as you can to the right to copy all characters):

      
2. On your computer, navigate to and open the samples_for_slide.csv that was locally exported from ISIT and is relevant to the slide you'd like to analyze.
3. Paste the URN associated with each OME-TIFF file into the CSV in the appropriate column.
4. Save the new CSV somewhere easily accessible on your computer.
5. In a browser, navigate to BSSH and create a sample sheet using the Run Planning Tool.

   1. When importing samples, use the "From this Computer" option.
   2. Upload the samples_for_slide.csv that was created in steps 5 through 7.
6. Proceed as you normally would with autolaunch or manual launch.

Registration failure

To enable image registration, the software detects the tissue area and searches for fiducials around it. Registration can fail when the auto-generated tissue mask is substantially incorrect. In these cases, you can edit the mask to define the tissue area, then repeat image registration. To edit the mask, this select the edit icon next to a sample that failed registration

Most registration failures are not caused by an incorrect tissue mask. Editing the mask only helps when the tissue mask caused the failure. It is unlikely to help when the existing mask is mostly correct.