Closed GeorgeBatch closed 5 months ago
I checked, last_suffix
is ".tif", but is_tiled_tiff(slide_path)
is False
, so neither OpenSlideWSIReader
nor TIFFWSIReader
gets to be tried.
I checked what happens in is_tiled_tiff
when passing my slide_path
. In the try-except block, a tif
is successfully made with tif = tifffile.TiffFile(path)
, but tif.pages[0].is_tiled
is False
for my slide, so is_tiled_tiff(slide_path)
is False
.
Given that openslide
opens the image and successfully parses metadata, I think the requirement of is_tiled_tiff()
to be true is too strict.
Finally, I checked out the develop
branch with the tiatoolbox-dev
environment created and activated as described in the README. The results are the same, which is as expected since the relevant parts of the code did not change:
and
I made a workaround that I will make into a pull-request. Please let me know what you think of it:
Add an argument ignore_is_tiled_tiff: bool = False
to wsicore.wsireader.WSIReader.open()
:
https://github.com/TissueImageAnalytics/tiatoolbox/blob/b68c9ce21104a9153c078a6757d7f4b68dfa495a/tiatoolbox/wsicore/wsireader.py#L231-L236
if last_suffix in (".tif", ".tiff") and (ignore_is_tiled_tiff or is_tiled_tiff(input_path)):
@Abdol @shaneahmed, do you have an estimate of when you will release v1.5.2?
Hi @GeorgeBatch , we plan to make a release v 1.6.0 as soon as #825 or #716 are ready. Probably by end of July/early Aug.
@shaneahmed, thank you for the update!
Description
I have slides scanned with a Ventana DP200 scanner and saved as
.tif
files.What I Did
Open with tiatoolbox WSIReader and print the extracted metadata:
Result:
The result did not seem right, so I checked with
openslide
Result:
For some reason, instead of using
OpenSlideWSIReader
orTIFFWSIReader
,VirtualWSIReader
is used. I will investigate further and add my findings in the comments below.