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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: 1 Sep 2020

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 used. If there are only Regions and Layers, then the Angle?? folders are not used.

Multi-Region Scans

A Region is a region of interest from a single slide. You may select multiple regions to scan. Each selected region is treated as a separate image. The uScope Deep Zoom image viewer provides a selector to choose which region to view. Refer to the following knowledge base articles for more information:

Multi-Angle Scans

An Angle is a different analyzer angle applied to a region of interest. Only the uScopeGX Polarizing scanner allows multi-angle scans. With the uScopeGX, you may select multiple angles to scan. Each selected angle is treated as a separate image. The uScope Deep Zoom image viewer provides a method to view each angle. Refer to the following knowledge base articles for more information:

Multi-Layer Scans

A Layer is a scan taken at a single focus point (the objective is not moved). Multi-Layer scans capture multiple focus points for each field in the region of interest. Each field is saved with a filename of XxxxYyyyZzzz where xxx and yyy are the field offset from the top-left corner (000-999) and zzz is the objective position (000-999). So all files named XxxxYyyyZ001 are at the same focus level. Each layer, when converted to a whole scan image, is treated as a separate image. The uScope Deep Zoom image viewer provides a method to view each layer. Refer to the following knowledge base articles for more information:

Combinations

You can create any combination of the above types of scans. For example:

  • A Multi-Region, Multi-Layer scan,
  • A Multi-Region, Multi-Angle scan,
  • or A Multi-Region, Multi-Angle, Multi-Layer scan.

As you can see, this can get out of hand and unwieldy very quickly. And, many of the combinations probably make little sense. But, they are all possible. You should be aware that combining the different scan types can quickly consume disk space.

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-Layer??.xml
               EDF
                  uS-ScanInfo.xml
                  DZCombine.xml
                  uS-XxxxYyyy.jpg
         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 (New in v4.5)
            (EasyZoom (SZI) Images)
         SVS (New in v4.5)
            (SVS Images)
         Exports (New in v4.5)
            (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 named Region01, Region02, and so on. After scanning, each region folder contains either the files (as listed under Angle?? Folders) for the region scan (if multiple angles are not used) or the Angle?? Folders.

Angle?? Folders

Each different angle scan is stored in a separate folder named Angle01, Angle02, and so on. After scanning, each angle folder contains the following files (if multiple layers are not used) or the EDF and/or Layer?? folders (depending on the type of scan).

  • 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)
    or
    uS-XxxxYyyy.(jpg|png)
    These files are the individual fields captured while scanning the region of interest. The Zzzz part of the filename is included for multi-layer scans only. 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-Layer??.xml
    These XML files contain image overlap adjustment data required to properly stitch field images into a seamless mosaic. One file is created for each layer in the scan.

EDF Folder

The EDF folder is created when an EDF layer is created during the Whole Scan Image generation process. This folder contains the composited EDF field images as well as xml data.

  • uS-ScanInfo.xml
    This XML file contains scan information about the EDF fields.
  • DZCombine.xml
    This XML file contains image overlap adjustment data required to properly stitch field images into a seamless mosaic.
  • uS-XxxxYyyy.jpg
    These files are the individual field images that are composited by the EDF software from the multi-layer images captured while scanning the region of interest. Each image is saved in standard definition (960x540) or high definition (1920x1080) format. EDF images are saved only as JPG (lossy, compressed).

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 composite 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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