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uScope GX Multi-Angle Job Folder Structure
uScope GX

Information in this article applies to:

  • uScope Navigator V4.5 and Later

Article ID: GXA1201 — Created: 21 Aug 2019 — Reviewed: 6 Sep 2019

Summary

uScope Navigator v4.5 adds a new folder structure for Multi-Angle scans. Previous versions of uScope Navigator (v4.3 and earlier) did not include an automated method for scanning multiple polarizer angles of a specimen.

More Information

uScope Navigator v4.5 and later store a multi-angle scan as follows:

C:\Images
      Multi-Angle-JobName
         JobInfo.xml
         Angle01
            uS-Overview.jpg
            uS-Key.jpg
            uS-ScanInfo.xml
            uS-XxxxYyyy.(jpg|png)
            DZCombine.xml
         Angle02
            (same as Angle01 above)
         Angle03
            (same as Angle01 above)
         DeepZoom-unfiltered
            DZDirInfo.xml
            MIDZ.html
            Angle01
               MIDZ.html
               uS-Overview.jpg
               uS-Key.jpg
               DZThumbnail.jpg
               DZThumbnail_sq.jpg
               DZInfo.xml
               DZViewer.xml
               DZOutput.xml
               DZOutput_files
                  (Deep Zoom Pyramid Files)
            Angle02
               (same as Angle01 above)
            Angle03
               (same as Angle01 above)
         EasyZoom
            (EasyZoom (SZI) Images)
         SVS
            (SVS Images)
         Exports
            (Deep Zoom Exported ROI Images)

Job Folder

When you create a new multi-angle job <Multi-Angle-JobName>, all files for that job are stored in <ImagesFolder>\<Multi-Angle-JobName>\. The following files and folders are created in each job folder:

  • JobInfo.xml
    This XML file contains information about the job.
  • Angle?? Folders
    These folders contain the field images and scan data files for each selected polarizer angle.
  • 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".
  • SVS Folder
    This folder contains the SVS images for each scan angle.
  • EasyZoom Folder
    This folder contains the EasyZoom (SZI) images for each scan angle.
  • Exports Folder
    This folder contains ROI (region of interest) image files exported from the Deep Zoom image viewer.

Angle?? Folders

Each different angle scan is stored in a separate folder. After scanning, each angle 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-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.
  • uS-ScanInfo.xml
    This XML file contains information about the scan.
  • uS-XxxxYyyy.(jpg|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. Images are saved as JPG (lossy, compressed) or as PNG (lossless, compressed) depending on scan settings.
  • DZCombine.xml
    This XML file contains the image overlap adjustment data that is required to properly overlap field images into a seamless mosaic.

DeepZoom-??? Folders

Each time you create deep zoom images (with different filter settings) a new folder is created with the name DeepZoom followed by the selected filter. The folder is named DeepZoom-unfiltered if no filter is applied. The deep zoom folders contain the following files:

  • MIDZ.html
    This file is the deep zoom image viewer HTML file. It supports viewing single-angle scans as well as multi-region/angle/layer scans.
  • DZDirInfo.xml
    This XML file is the multi-scan directory information file that is required by MIDZ.html to figure out how to open a multi-region/angle/layer scanned image.
  • Angle?? Folders
    These folders contain the deep zoom images for each scanned angle.

DeepZoom Angle?? Folders

These folders contain the deep zoom images for each angle. They contain the following files:

  • MIDZ.html
    This file is the deep zoom image viewer HTML file. It supports viewing single-angle scans as well as multi-region/angle/layer scans. Launching the viewer from this folder allows you to view this angle only.
  • 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.
  • 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.
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