Got damaged .tif from .svs

[HanyingYan]

Hi @cgohlke,

I have a series of .svs images that I would like to convert into .tiff. Most of them are small (less than 300MB) and I got .tif using your tifffile package without any problem.

image = tifffile.imread(svs_file)
tifffile.imwrite(tif_file, image, photometric='rgb')

However, there is one .svs file of size ~4GB. I first read with tifffile.imread and image is of size around 50GB. Then when I tried to write the .tif file, which ended up generating a damaged file that I couldn't open, without any error or warning message.

I wonder if you know what happened and what I can do to solve this issue.

Thank you!
Hanying

[cgohlke]

The 50 GB array is written in BigTIFF format as one contiguous segment. I don't think the file is corrupt (check if you can read it back with tifffile). Either the Preview app does not support the BigTIFF format or it has a size limit (e.g., to prevent DOS or RAM exhaustion).

[HanyingYan]

Thank you for your quick response! Yes, you are correct! The .tif generated is of size 54G and can be read back with tifffile. In this case, I think everything works fine and it's just Preview couldn't load image of this large size. Thanks :)

[cgohlke]

Btw, such large images are typically stored using compressed tiles (tiles=(512, 512), compression=...).

[HanyingYan]

Oh, I see. Let me give it a try! Thank you!