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Set up

Slide scanning workflow—step 1

Data file location

Select a location to save the data associated with the scan.

 

Acquisition type

Select the desired scan type.

Closed2D slide scan

Appropriate when only one image plane is desired.

Closed3D slide scan

Appropriate when more than one image plane is needed to create an image stack. This is generally suitable for higher magnifications, but can be used at lower magnification as well (3D is only available if you purchased the 3D slide scanning module.)

 

Multichannel acquisition

If you haven't set up the parameters for the acquisition, use the Multichannel setup button to access the settings.

This option is disabled when select brightfield as the slide type.

Make sure that the Multichannel box is NOT checked if this is a single channel acquisition.

 

Slide type

Make sure you select the correct type. This will affect the options available for background correction.

 

Scan type

ClosedScan inside contour only

Use only closed contours.

Processes tiles included in the contour that was drawn. The image may have rough, jagged borders but it will quicker and the file size will be smaller.

ClosedScan a rectangle around the contour
  • A rectangle is generated that contains the entirety of the contour. All fields within this rectangle are scanned and included in the final output image. The final image doesn't have rough edges but acquisition time and file size are increased.
    • ClosedScan in grid

    Use to define the area to be scanned as a set number of fields of view in a rectangular grid. This option requires that you be positioned at the top left corner of the region to be scanned; the current field of view is the first one scanned.

    Test the settings over a 3x3 grid before performing the full acquisition to ensure that the background image is satisfactory, that the trim and blend are appropriate, and to determine whether a stage delay is needed. This will save you considerable time!