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:

• Scanning Multiple Regions
• Viewing Multi-Region Scans

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:

• Scanning Multi-Angle Regions
• Viewing Multi-Angle Scans

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:

• Scanning Multi-Layer Regions (Image Stacking)
• Viewing Multi-Layer (Image Stack) Scans

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
               DZCompute-Layer??.xml (New in v4.6)
               EDF
                  uS-ScanInfo.xml
                  DZCombine.xml
                  DZCompute.xml (New in v4.6)
                  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:

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).

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.

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:

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: