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Scan Mode Reducing Scan Disk Storage Space
Scan Mode

Information in this article applies to:

  • uScope Navigator V4.3 and Later

Article ID: NSC2332 — Created: 16 Oct 2020 — Reviewed: 20 Dec 2020

Symptom

Huge amounts of drive space are required for slide scans and the resulting images.

Cause

The space required for a job folder is caused by a number of factors including:

  • Required Job Files
  • Image Format for Source and Deep Zoom Images
  • Source Field Images
  • Whole Scan Images

uScope Navigator gives you control over most of these and provides methods to reduce or eliminate entire folders of images that are typically created.

Note
Whole Slide Scans, by their nature, consume a large amount of disk space. Consider that even small whole scan images, the ones that are only 10,000×10,000 pixels, are composed of 100 million pixels that are 24-bits or 3-bytes per pixel which makes the uncompressed image 300 MegaBytes in size.

Resolution

Before attempting to manually "fix" the large job folders that are created, it is best to have an understanding of the files that are created so you know which files are truly required and which files can safely be deleted to free-up drive space.

The above knowledge base article shows a job folder structure that appears as follows:

C:\Images
      Job1
      Job2
      Job3
         uS-Overview.jpg
         uS-Key.jpg
         uS-ScanInfo.xml
         uS-XxxxYyyy.(jpg|png)
         JobInfo.xml
         DZCombine.xml
         Deepzoom-???
            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)
         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)

Note
We recommend that the files shown above in RED should not be deleted.

Required Job Files

The following files in the job folder are required for proper operation of the uScope Navigator software and should not be deleted:

  • uS-Overview.jpg
    This image is the overview image of the slide that was scanned.
  • uS-Key.jpg
    This image is a thumbnail of the area of the slide that was scanned.
  • uS-ScanInfo.xml
    This XML file contains information about the slide scan including name and summary as well as
  • JobInfo.xml
    This XML file contains information about the job.
  • DZCombine.xml
    This XML file contains information about how the image fields are combined.

These files consume little space so there is nothing to gain by deleting them.

The source field images, on the other hand, consume a lot of disk space but are probably not worth deleting since they are the original source digital images of the scanned region of interest. However, you can reduce their size by saving them as JPG images.

Image Format for Source and Deep Zoom Images

When scanning, fields are saved as either JPG or PNG image files. While PNG images are lossless and have much more image detail, they are also very large when compared to JPG images (which are lossy). However, in many situations, the quality of JPG images is more than adequate.

If the field images (uS-XxxxYyyy) have the JPG file extension, then they are saved as JPG files. But, if the field images have the PNG extension, then they are PNG files. Setting the image format to JPG (as shown in the knowledge base article above) can save considerable disk space. See below for tips on reducing the size of jobs that are already scanned using the PNG file format.

This setting also applies to Deep Zoom images which are pyramidal image files that can get large and unwieldy very quickly. See What is a pyramidal image? for more information.

Source Field Images

One of the space-consuming components of the job folder is the uS-XxxxYyyy.jpg or uS-XxxxYyyy.png files. These are the source field images that are captured when scanning the selected region of interest. While these image do require a lot of disk space, they can be used to re-create any of the whole scan images (Deep Zoom, SVS, or EasyZoom). Most users choose to keep these images because if they are deleted, you must re-scan a slide to create any of the whole scan images.

Whole Scan Images

Whole scan images are created by stitching together the source field images. These images are large, contiguous pictures that can be viewed using a special viewer program. The Deepzoom-???, EasyZoom, and SVS folders contain the corresponding whole scan images. Un-needed whole scan image folders can safely be deleted. They can be re-created from the source field images and required job files listed above.

For example, if you created an SVS whole scan image and a Deep Zoom whole scan image, but you use only the SVS image, you can safely delete the Deepzoom folder and its contents.

How to Reduce the Size of PNG Scans

If you have an existing job that was scanned to PNG files, there are several things you can do to reduce the size of the job folder. Refer to the following knowledge base articles for more information.

How to Reduce the Size of JPG Scans

Attempts to shrink JPG scan files will ultimately reduce image quality which is undesirable. If you have an existing job that was scanned to JPG files, we would love to be able to give you some tips to reduce the size of the job folder.

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