Information in this article applies to:
Article ID: NJX1282 — Created: 20 Aug 2019 — Reviewed: 1 Sep 2020
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.
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.
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:
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:
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:
You can create any combination of the above types of scans. For example:
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.
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)
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:
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.
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).
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.
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:
These folders contain the deep zoom images for each region, angle, or EDF/layer respectively. They contain the following files: