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General Interest Whole Slide Scanner Terminology
General Interest

Information in this article applies to:

  • uScope Navigator (All Versions)

Article ID: NGN1263 — Created: 18 Jul 2019 — Reviewed: 6 Dec 2020

Summary

There are a number of terms associated with slide scanning. We have compiled the following list to help you quickly get up to speed with whole slide scanning.

Details

  • Browsing
    The act of interactively viewing a specimen on a glass slide. This includes moving the stage and focusing the objective while adjusting the illumination and viewing the image of the field on the computer screen. It is analogous to using a desktop microscope.
  • CPL or Cross Polarized Light
    On a polarizing microscope, an analyzer angle of 90°.
  • Deep Zoom or Deep Zoom Image
    A pyramidal image format that uses layers of tiles at various resolutions to produce an efficient viewing format for very large resolution pictures. Each layer in the pyramid is half the resolution of the layer immediately below it, ending with a top layer this is a single pixel.
  • Deep Zoom Tile
    A square image (typically 256×256 pixels) that is used in a mosaic to composite a deep zoom layer image. Starting at the top layer of the Deep Zoom Pyramid, the number of tiles for each layer are 1, 4, 16, 64, 256, and so on.
  • Device Settings File
    The device settings (or device configuration) file is an XML file that contains all the settings for a specific uScope device. Each device settings file is unique and specific to a particular device.
  • EasyScan Image
    See SZI Image.
  • EDF or Extended Depth of Field
    The process of analyzing multiple images of the same subject at different focal points; determining the best focused parts of each image; and creating a new, composite image where everything possible is in best focus. Refer to Extended Depth of Field (EDF) for more information.
  • Field
    The field (or field of view) is what is seen through the objective of the uScope without moving in the X or Y direction.
  • Field Image
    The image captured of the field viewed through the objective without moving in the X or Y direction.
  • Filter
    An image processing filter (or filter sequence) like brightness, contrast, or gamma that can be applied to the overview or objective images. uScope Navigator can also apply filters to Whole Scan Images. Refer to uScope Navigator Filters for more information.
  • Flat Field or Flat Field Processing
    The process of compensating for light and dark areas of an image. An image captured through the objective should be consistently lit from edge to edge. However, variations in the camera, lens, and illuminator as well as lens alignment cause gradients that must be "flattened" to produce a perfect image.
  • Flat Field Image
    An image that is captured in air (not through a glass slide) that is used for Flat Field Processing.
  • Image Stacking
    See Multi-Layer Scanning.
  • MPP or Microns Per Pixel
    A measurement of the size of a square pixel in an image. This value can be used to calculate the size of objects in the image based on their size in pixels.
  • Multi-Angle Scanning
    The process of capturing multiple polarized images at different analyzer angles. Refer to Scanning Multi-Angle Regions for more information.
  • Multi-Layer Scanning
    The process of capturing multiple images for each field at different focus levels. These images may be used to provide virtual focus or to composite EDF (extended depth of field) images. Refer to Scanning Multi-Layer Regions (Image Stacking) for more information.
  • Multi-Region Scanning
    The process of scanning multiple regions of interest on a single slide.
  • NA or Numerical Aperture
    A number that characterizes the range of angles over which the objective can accept light—the acceptance cone. Calculated as NA = n sin θ where n is the index of refraction (1.0 for air, 1.33 for water) and θ is the half-angle of the cone of light. Low NA is associated with a low-power objective while high NA is associated with a high-power objective.
  • Objective Image
    A picture of the point of the slide directly under the objective.
  • Overview Image
    A picture of the scannable part of the slide. The overview image is not a high-resolution image. It is used to easily select a region of the slide for scanning.
  • Pixel Mapping
    This refers to the number of microns per pixel (MPP) for images captured by the objective camera. It may also refer to images captured by an overview camera. See MPP./li>
  • Point of Interest
    A single field. Typically referenced when browsing a slide.
  • Program Settings File
    The program settings file is an XML file that contains the settings for the uScope Navigator application. It is stored in the C:\ProgramData\Microscopes International\uScopeNavigator4\Settings folder.
  • ROI or Region of Interest
    A bounded area of the slide (usually) containing part or all of the specimen. When scanning a slide, the region of interest is the area of the slide that is scanned.
  • Scan Field
    The image (or images) captured of the field viewed through the objective for each stage position in the X and Y axes. There are multiple images captured for a single field when Z-stacking.
  • Scanning
    The act of (automatically) acquiring images of the fields in a region of interest and combining (stitching) them into a final, composite image that can be viewed at a later date or shared remotely.
  • Stage
    The platform that holds or contains a slide for scanning. The stage moves in the X (in and out of the uScope) and Y (left and right in the uScope) directions.
  • SVS Image
    A type of whole scan image made popular by Aperio in the early 2000's.
  • SZI Image
    A type of whole scan image popularized by EasyScan. Basically, it is a Deep Zoom image in an uncompressed ZIP file container. Refer to What are EasyZoom (SZI) Images? for more information.
  • Tiled TIFF
    A sub-format of the TIFF (Tagged Image File Format) image format that support image mosaics composed of regular-sized tiles. Refer to What are Tiled TIFF (SVS) Files? for more information.
  • Whole Scan Image
    The composite, stitched image that is created from a scanned region of interest. There are a number of different file formats for whole scan images. uScope Navigator can create whole scan images in Deep Zoom, SVS, and SZI file formats. Refer to What are "Whole Scan Images"? for more information.
  • WSI
    Whole Slide Imaging is a term for high-speed/high-resolution digital image acquisition of a specimen on a glass microscope slide and storage in a format that may be viewed later on a computer or tablet.
  • Z-Stacking
    See Multi-Layer Scanning.

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