I wanted to start a discussion on best practices for dealing with (large) slide scanner images.
We started scanning at high-resolution, which results in RGB images that are typically larger than 50.000 x 50.000 pixels.
At current I export (in our case from NIS-elements) huge standard RGB TIFFs (that won`t open easily in most software, since the single plane is larger than 2 to 31 pixels) and the fact that there is no resolution pyramid.
These files I then open in python as numpy array (with tifffile) and thought to resave as:
Uncompressed binned Tiffs (4x4, 8x8, 16x16), one RGB file per resolution.
The same as pyramid in a HDF5 file.
(…and maybe the file split up in overlapping (by 100 at each border) 1000x1000 patches)
Do you have any suggestion on what to keep in mind to ensure ideal cross-platform compatibility and performance?
The output files are primarily:
a) to hand over to our user to inspect them and make figures
b) as input for manual or ML-based analysis
I do not care much about the preservation of metadata at this stage (and if so preferably in a separate file).
Thanks a lot & Kind regards