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.
SCAN PROFILE
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).
ACQUISITION TIME
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.
DATA SETS
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.
