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uScope Navigator (Scan)

Scan Folder Structure
uScope Navigator (Scan)

Article ID: NSC1074
Created: 16 Oct 2017
Reviewed: 10 Dec 2017

Information in this article applies to:

  • uScope Navigator V4.0 and Later

Question

What is the file folder layout for a scanned slide job?

Answer

When you scan a slide with the uScope Navigator application, you must enter a job name (folder name) for the scanned images. This folder is created (by default) in the C:\Images\ subdirectory.

Images Folder

All scanned slides (regions of interest) are saved in job folders in <ImagesFolder> which defaults to: C:\Images\. You can change the default <ImagesFolder> on the Program Options — Application Preferences tab.

Typically, the images folder appears as follows:

C:\Images
      Job1
      Job2
      Job3
         uS-Overview.jpg
         uS-Key.jpg
         uS-ScanInfo.xml
         JobInfo.xml
         DZCombine.xml
         MIDZ.html
         TiledTIF
         Deepzoom-unfiltered
            uS-Overview.jpg
            uS-Key.jpg
            DZThumbnail.jpg
            DZThumbnail_sq.jpg
            DZInfo.xml
            DZViewer.xml
            DZOutput.xml
            DZOutput_files

Job Folder

When you create a new job <JobName>, all files for that job are stored in <ImagesFolder>\<JobName>\.

After scanning, the job folder contains the following files:

  • uS-Overview.jpg
    This image file is the overview image of the whole slide. It is captured by the overview camera as a single, high-definition image. The scanned region of interest is outlined in green.
  • uS-X???Y???.jpg or .png
    These files are the individual fields captured while scanning the region of interest. Each image is saved in standard definition (960x540) or high definition (1920x1080) format.
  • uS-ScanInfo.xml
    This XML file contains information about the scan.
  • uS-Key.jpg
    This image file is a composite of the individual fields. It is not full image resolution. it is only intended to be a guide to associating a particular field to a position in the scanned region.
  • JobInfo.xml
    This XML file contains information about the job.
  • DZCombine.xml
    This XML file contains the image overlap adjustment data that is required to properly overlap field images into a seamless mosaic.

The following folders are created in each job folder:

  • TiledTIF Folder
    This folder contains Tiled TIFF (SVS) images created for the region scan.
  • Deepzoom-* Folders
    These folders contain deep zoom image sets created by the uScope Navigator application. The suffix is the name of the filter used to create the deep zoom image. If no filter is used, the suffix is "unfiltered".

DeepZoom Folders

Each deep zoom image you create is saved in its own folder and is given a name of DeepZoom followed by the filter name selected for the deep zoom image. The folder is named DeepZoom-unfiltered if no filter is applied.

The deep zoom folder contains the following files:

  • DZOutput.xml
    This XML file is required by the deep zoom image viewer. If you plan to use another deep zoom image viewer, you need only this file and the DZOutput_files folder.
  • DZOutput_files folder
    This folder contains the deep zoom image pyramid that contains the individual tiles associated with each level of the deep zoom pyramid.
  • uS-Overview.jpg
    This is the image of the slide (minus the label) from the overview camera. The region scanned is outlined in green.
  • uS-Key.jpg
    This is an image of the region scanned (after it has been stitched). It is not a full-sized image.
  • DZThumbnail.jpg
    This image is a 3:2 (1800x1200) image of the constrained uS-Key.jpg image.
  • DZThumbnail_sq.jpg
    This image is a cropped square image (240x240) of the DZThumbnail.jpg image.
  • DZInfo.xml
    This XML file contains information about each scan. Information from this file is extracted by the deep zoom image viewer and used to create the info popup and to calculate image scale.
  • DZViewer.xml
    This XML file contains filter information for the deep zoom image viewer.

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