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Slide scanner usage : guidelines and limitations

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Slide scanner usage : guidelines and limitations

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Disclaimer : Some of these remarks might apply either to the Zeiss Axioscan or to the Hamamatsu Nanozoomer, but it is generally a good idea to take them into account for any slide scanner project.


If the samples vary in any one of these categories:

  • Thickness of the slices
  • Layout of the cuts
  • Size of the cuts
  • Intensity / color of the staining

Fluorescence specific:

  • Number of fluorescent dyes
  • target of the staining used as reference

The profile will have to be updated and saved as a new variant or it will probably fail (not focused, over/underexposed, stitching failing).


The acquisition time depends on:

  • Number of sample / blade
  • Sample size / blade
  • Lens used
  • Exposure time (not important in BF)
  • Z Stack or not and EDF(extend focus) or not
  • Accuracy of the two focus maps

Each of these parameters can greatly vary the acquisition time, which can range from a few minutes to an hour or more per slide.

Finally if you want to change the objective used for the acquisition, you will also need to update most of the previous parameters of the scan profile.


  • The files are acquired in the .CZI format for the Zeiss Axioscan, and .NDPI format for the Hamamatsu Nanozoomer.
  • The typical file size ranges from 100 Mb to several Gb
  • Files exported in TIFF will usually see their size increased AND multiplied several times depending on the number of channels
  • It is thus key to minimize the size of the dataset to be acquired to avoid further analysis problems -> always prefer the minimum magnification that will answer your scientific question. For screening purposes, use the lowest magnification.
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