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General Interest Multi-Layer Job Folder Structure
General Interest

Information in this article applies to:

  • uScope Navigator V4.5 and Later

Article ID: NGN1199 — Created: 21 Aug 2019 — Reviewed: 1 Sep 2020

Summary

uScope Navigator v4.5 adds a new folder structure for Multi-Layer (image stacking or Z stack) scans. Previous versions of uScope Navigator (v4.3 and earlier) did not include an automated method for scanning multiple layers of a specimen.

More Information

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

C:\Images
      Multi-Layer-JobName
         JobInfo.xml
         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
         Deepzoom-unfiltered
            DZDirInfo.xml
            MIDZ.html
            EDF (folder containing EDF field images)
               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)
         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-layer job <Multi-Layer-JobName>, all files for that job are stored in <ImagesFolder>\<Multi-Layer-JobName>\. The following files and folders are created in each job folder:

  • JobInfo.xml
    This XML file contains information about the job.
  • 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-XxxxYyyyZzz.(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-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
    This folder contains the field images and scan data files for the EDF (Extended Depth of Field) composite layer.
  • 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 the EDF scan and for each layer.
  • EasyZoom Folder
    This folder contains the EasyZoom (SZI) images for the EDF scan and for each layer.
  • Exports Folder
    This folder contains ROI (region of interest) image files exported from the Deep Zoom image viewer.

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-layer 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.
  • EDF Folder
    This folder contains the deep zoom images for the composited EDF image.
  • Layer?? Folders
    These folders contain the deep zoom images for each layer of the scan.

DeepZoom EDF & Layer?? Folders

These folders contain the deep zoom images for the EDF and for each scan layer. They contain the following files:

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