Scan repair

Requires a separate license

Purpose

Use Scan repair to continue a slide scan acquisition that was interrupted prior to completion, or to replace individual tiles that may have been affected by a camera or lighting issue without having to re-run the entire acquisition.

The workflow is designed to guide you through the process of aligning the image with the live camera feed of the tissue on the microscope and starting the repair acquisition.

Procedure

Before you start

If you are using the scan repair workflow to replace specific tile(s) within the slide scan image, you will need to determine the name of the tile image(s) before starting the workflow.

  1. Navigate to the folder where the individual tile images are saved and sort by date. They are located in a folder labeled with a 4 digit number (i.e. 0001, 0002, etc.), within the folder where the slide scan image was saved.

  2. Open each tile image file in Stereo Investigator to find the affected tile image(s).

  3. Take note of the tile image file name(s) that need to be repaired and delete them from the directory. The scan repair will replace the tile image files with new ones.

Click Scan Repair on the Acquire ribbon to get started.

Scan repair workflow steps

  1. Place reference point

    In this step you have the option to place or reset the placement of the reference point.

    The reference point needs to be in the exact location it was at the time of the slide scan acquisition.

  2. Align tracing

    Use this step if a tracing was created to define slide scan acquisition area that can help with alignment to the live camera feed.

  3. Load repair data

    Click Browse to repair directory and select the folder that contains the individual tile images, and the AssemblyData and RepairData text files. This folder, labeled with a 4 digit number (i.e. 0001, 0002, etc.), is located in the folder where the slide scan image was saved.

  4. Pick image for alignment

    Use this step to pick an area on the slide scan image that will help with alignment to the live camera feed.

  5. Define scan region

    This step defines the area around the original slide scan region. This ensures that the microscope will not navigate outside of the defined region for safety of the objective and slide.

  6. Align image with live

    This step is used as the final alignment between the live camera feed and the slide scan image to be repaired.

    Accurate alignment of the slide scan image and the live camera feed in the X and Y axes, as well as adjusting the focus position of the live camera feed to match the focus position of the image, is critical in performing a successful slide scan image repair.

    Alignment of the live camera feed and the slide scan image is performed using the Blend tool which is automatically enabled.

  7. Auto-align image with live

    This step is used to automatically align the image and the live camera feed in the Z axis. This ensures that the focus of the repair tile images will align with the focus of the original slide scan image.

  8. Start the repair

    1. Adjust the microscope focus to just below the bottom Z position of the of the slide scan image.

    2. Click Set safe lower limit to ensure the microscope will not navigate below this set Z position for the safety of the objective and slide.

    3. Click start the repair.