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Scan Mode Extended Depth of Field (EDF)
Scan Mode

Information in this article applies to:

  • uScope Navigator V4.5 and Later

Article ID: NSC1206 — Created: 21 Aug 2019 — Reviewed: 22 Aug 2019

Summary

uScope Navigator v4.5 adds support for EDF (Extended Depth of Field) image composition. This support is composed of several processes:

  1. Multi-Layer Scanning (Image Stacking)
    This process involves selecting the region to scan as well as the depth of focus and number of layers to capture. Scanning multiple focus levels for each field increases the scan time proportionately.
  2. EDF (Extended Depth of Field) Compositing
    This process involves selecting the best-focused parts of each layer from an image stack and combining them into a single image where everything is in focus. This process is may be time-consuming depending on the perormance of your PC.
  3. Stitching the Composite EDF Images
    After creating the EDF image set for the multi-layer scans, the composite images must be analyzed to determine the required overlap and offset for stitching.
  4. Creating a Whole Scan Image
    And finally, a whole slide image of the EDF image set is created.

These tasks are described in details in the following sections.

More Information

Creating EDF images requires an additional software license. Please contact our sales department for more information.

Multi-Layer Scanning

Multi-Layer Scanning or Image Stacking involves taking several images at each scan field position at different focus points. Different power objectives have different depth of field (the thickness of the specimen that is in focus without moving the objective). Higher power objectives have narrower depth of field (less of the specimen is in focus) while lower power objectives have wider depth of field (more of the specimen is in focus).

In any case, extremely thick specimens (for example, 100 microns) require focus adjustment to see a clear, sharp image.

Image Stacking accomplishes this by capturing an image at regular focus layers for the thickness of the specimen.

Creating EDF Images

The Extended Depth of Field (EDF) algorithm combines the best focused parts of several images and creates a composite image where everything is in the best focus available from the stack of individual images.

Stitching EDF Images

After each field image is processed by the EDF algorithm, the are stitched and combined into a large, whole scan image using the standard algorithm used by the uScope Navigator Application.

Creating a Whole Scan Image

Creating a Whole Scan Image is accomplished as it is for a normal single-layer scan.

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