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Job Manager Multi-Region/Angle/Layer Job Folder Structure
Job Manager

Information in this article applies to:

  • uScope Navigator V4.5 and Later

Article ID: NJX1282 — Created: 20 Aug 2019 — Reviewed: 6 Sep 2019

Summary

uScope Navigator v4.5 introduces multi-scan jobs—a method of scanning slides with multiple regions, polarizer angles, or Z-stack layers. The job folder has been updated for scans with multiple regions and/or angles and/or layers so that all scans are stored in the specified job folder. Previous versions of uScope Navigator did not support multi-scan jobs.

The change to the folder structure for multi-scan jobs accommodates a new deep zoom image viewer that supports viewing all scanned regions, angles, and layers from a single viewer page.

Note
Regions, Angles, and Layers are stored in a nested, hierarchical folder structure that can get very deep and large. For example, three (3) regions of three (3) angles with three (3) layers would be 27 total scans (3×3×3).

If there are only Angles and Layers (no Regions), then the Region?? folders are not created. If there are only Regions and Layers, then the Angle?? folders are not created.

More Information

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

C:\Images
      Multi-Scan-JobName
         JobInfo.xml
         Region01
            Angle01
               uS-Overview.jpg
               uS-Key.jpg
               uS-ScanInfo.xml
               uS-XxxxYyyyZzz.(jpg|png) 
               DZCombine.xml
         Region02
            (same as Region01 above)
         Region03
            (same as Region01 above)
         DeepZoom-unfiltered
            DZDirInfo.xml
            MIDZ.html
            Region01
               Angle01
                  EDF
                     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)
                  Layer01
                     (same as EDF above)
                  Layer02
                     (same as EDF above)
                  Layer03
                     (same as EDF above)
               Angle02
                  (same as Angle01 above)
               Angle03
                  (same as Angle01 above)
            Region02
               (same as Region01 above)
            Region03
               (same as Region01 above)
         EasyZoom
            (EasyZoom (SZI) Images)
         SVS
            (SVS Images)
         Exports
            (Deep Zoom Exported ROI Images)

Job Folder

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

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

Region?? Folders

Each region is stored in a separate folder. After scanning, each region folder contains the following files:

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-XxxxYyyyZzzz.(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-region 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.
  • Region?? Folders
    These folders contain the Angle?? folders.
  • Angle?? Folders
    These folders contain the EDF and Layer?? folders.
  • EDF & Layer?? Folders
    These folders contain the deep zoom images for the composited EDF image and each layer of the scan.

DeepZoom Region??, Angle??, or EDF & Layer?? Folders

These folders contain the deep zoom images for each region, angle, or EDF/layer respectively. They contain the following files:

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