Information in this article applies to:
- uScope Navigator V4.5 and Later
Article ID: NJX1199 — Created: 21 Aug 2019 — Reviewed: 1 Sep 2020
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.
uScope Navigator v4.5 and later store a multi-layer scan as follows:
EDF (folder containing EDF field images)
(Deep Zoom Pyramid Files)
(same as EDF above)
(same as EDF above)
EasyZoom (New in v4.5)
(EasyZoom (SZI) Images)
SVS (New in v4.5)
Exports (New in v4.5)
(Deep Zoom Exported ROI Images)
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:
This XML file contains information about the job.
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.
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.
This XML file contains information about the scan.
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.
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.
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.
This XML file contains scan information about the EDF fields.
This XML file contains image overlap adjustment data required to properly stitch field images into a seamless mosaic.
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).
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:
This file is the deep zoom image viewer HTML file. It supports viewing single-layer scans as well as multi-region/angle/layer scans.
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:
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.
This is the image of the slide (minus the label) from the overview camera. The region scanned is outlined in green.
This is an image of the region scanned (after it has been stitched). It is not a full-sized image.
This image is a 3:2 (1800x1200) image of the constrained uS-Key.jpg image.
This image is a cropped square image (240x240) of the DZThumbnail.jpg image.
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.
This XML file contains filter information for the deep zoom image viewer.
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.