import torch changes OpenSlide vendor detection (Philips WSI becomes generic-tiff)

[0820LL]

Operating system

Ubuntu 16.04.7 LTS

Platform

x86_64

OpenSlide Python version

openslide-python: 1.4.6

OpenSlide version

openslide=4.0.1

Slide format

TIFF

Issue details

I encountered a very strange issue where the import order of torch and openslide changes how OpenSlide detects the same WSI file.

The exact same Philips TIFF file is recognized correctly when openslide is imported first, but is detected as generic-tiff when torch is imported first.

This causes downstream applications (e.g. HoverNet) to fail because OpenSlide no longer exposes Philips-specific metadata such as openslide.mpp-x.

Environment:

Python: 3.12.13
openslide-python: 1.4.6
openslide: 4.0.1
torch: 2.12.1+cu126
OS: Ubuntu 16.04.7 LTS

Minimal Reproducible Example

Case 1 (works)

import openslide

slide = openslide.OpenSlide("patient_190_node_0.tif")

print(slide.properties["openslide.vendor"])
print("openslide.mpp-x" in slide.properties)

Case 1 Output:

philips
True

Case 2 (works)

import openslide
import torch

slide = openslide.OpenSlide("patient_190_node_0.tif")

print(slide.properties["openslide.vendor"])
print("openslide.mpp-x" in slide.properties)

Case 2 Output:

philips
True

Case 3 (fails)

import torch
import openslide

slide = openslide.OpenSlide("patient_190_node_0.tif")

print(slide.properties["openslide.vendor"])
print("openslide.mpp-x" in slide.properties)

Case 3 Output:

generic-tiff
False

The WSI file used

https://github.com/0820LL/openslide-python-issue-file/releases/download/1.0/patient_190_node_0.tif

[bgilbert]

How did you install OpenSlide and OpenSlide Python? It seems likely the third case is using Ubuntu 16.04's distro package of OpenSlide, which is 3.4.0 and doesn't support Philips TIFF. You can confirm which OpenSlide library has been loaded with something like

print(''.join([l for l in open('/proc/' + str(os.getpid()) + '/maps') if 'openslide' in l]))

and you can get a log of OpenSlide's format detection by setting the OPENSLIDE_DEBUG environment variable to detection.

Note that current versions of OpenSlide and OpenSlide Python aren't tested with Ubuntu 16.04 (and you had to install a newer Python to get OpenSlide Python to even work) so this may not be the last of your difficulties. I'd strongly encourage you to update to a newer OS.

[0820LL]

I installed OpenSlide and OpenSlide Python in a conda environment
I also installed python packages using uv add, so the .venv is the uv environment

Here is the conda environment

micromamba env export --from-history
name: 
channels:
  - conda-forge
dependencies:
  - openslide=4.0.1
  - pip
  - python=3.12
  - uv=0.11

prefix: "/data/lilin/hovernet_features/.venv_micromamba"

The output of the above code print(''.join([l for l in open('/proc/' + str(os.getpid()) + '/maps') if 'openslide' in l])) is

7faf9a992000-7faf9a99c000 r--p 00000000 08:11 127025017                  /data/lilin/hovernet_features/.venv_micromamba/lib/libopenslide.so.1.0.1
7faf9a99c000-7faf9a9c4000 r-xp 0000a000 08:11 127025017                  /data/lilin/hovernet_features/.venv_micromamba/lib/libopenslide.so.1.0.1
7faf9a9c4000-7faf9a9d5000 r--p 00032000 08:11 127025017                  /data/lilin/hovernet_features/.venv_micromamba/lib/libopenslide.so.1.0.1
7faf9a9d5000-7faf9a9d7000 r--p 00043000 08:11 127025017                  /data/lilin/hovernet_features/.venv_micromamba/lib/libopenslide.so.1.0.1
7faf9a9d7000-7faf9a9d8000 rw-p 00045000 08:11 127025017                  /data/lilin/hovernet_features/.venv_micromamba/lib/libopenslide.so.1.0.1
7faf9a9d8000-7faf9a9d9000 r--p 00000000 08:11 127112183                  /data/lilin/hovernet_features/.venv/lib/python3.12/site-packages/openslide/_convert.abi3.so
7faf9a9d9000-7faf9a9da000 r-xp 00001000 08:11 127112183                  /data/lilin/hovernet_features/.venv/lib/python3.12/site-packages/openslide/_convert.abi3.so
7faf9a9da000-7faf9a9db000 r--p 00002000 08:11 127112183                  /data/lilin/hovernet_features/.venv/lib/python3.12/site-packages/openslide/_convert.abi3.so
7faf9a9db000-7faf9a9dc000 r--p 00002000 08:11 127112183                  /data/lilin/hovernet_features/.venv/lib/python3.12/site-packages/openslide/_convert.abi3.so
7faf9a9dc000-7faf9a9dd000 rw-p 00003000 08:11 127112183                  /data/lilin/hovernet_features/.venv/lib/python3.12/site-packages/openslide/_convert.abi3.so

[bgilbert]

Is that also the output for the failing case? What does OPENSLIDE_DEBUG=detection produce in both the good and failing cases?

[0820LL]

Yes. Both the working case and the failing case were run in exactly the same environment.

The only difference between them is the import order:

Working case:

import openslide
import torch

Failing case:

import torch
import openslide

When openslide is imported first, the slide is correctly detected as philips and the Philips-specific properties (such as openslide.mpp-x) are available.

When torch is imported before openslide, the same file is instead detected as generic-tiff, and the Philips-specific properties are missing.

[0820LL]

I ran the cases with OPENSLIDE_DEBUG=detection. The outputs are attached below.
case 1 (works)

case 2 (works)

case 3 (fails)

[bgilbert]

Case 3 is definitely OpenSlide 3.4.0, which leads me to think you didn't actually check the library paths for that case as I asked you to.

[0820LL]

Sorry, I took another look at which underlying OpenSlide library was actually being loaded, and I found that they are indeed different.

When torch is imported before openslide, openslide-python ends up loading the system OpenSlide library (libopenslide.so.0.4.0) instead of the one in my Conda environment (libopenslide.so.1.0.1).

I'm still trying to understand why this happens. Specifically, why does importing torch first cause openslide-python to load the system libopenslide rather than the Conda version?

case 1

python debug_case1.py 
7f7f5b716000-7f7f5b720000 r--p 00000000 08:11 127025017                  /data/lilin/hovernet_features/.venv_micromamba/lib/libopenslide.so.1.0.1
7f7f5b720000-7f7f5b748000 r-xp 0000a000 08:11 127025017                  /data/lilin/hovernet_features/.venv_micromamba/lib/libopenslide.so.1.0.1
7f7f5b748000-7f7f5b759000 r--p 00032000 08:11 127025017                  /data/lilin/hovernet_features/.venv_micromamba/lib/libopenslide.so.1.0.1
7f7f5b759000-7f7f5b75b000 r--p 00043000 08:11 127025017                  /data/lilin/hovernet_features/.venv_micromamba/lib/libopenslide.so.1.0.1
7f7f5b75b000-7f7f5b75c000 rw-p 00045000 08:11 127025017                  /data/lilin/hovernet_features/.venv_micromamba/lib/libopenslide.so.1.0.1
7f7f5b75c000-7f7f5b75d000 r--p 00000000 08:11 127112183                  /data/lilin/hovernet_features/.venv/lib/python3.12/site-packages/openslide/_convert.abi3.so
7f7f5b75d000-7f7f5b75e000 r-xp 00001000 08:11 127112183                  /data/lilin/hovernet_features/.venv/lib/python3.12/site-packages/openslide/_convert.abi3.so
7f7f5b75e000-7f7f5b75f000 r--p 00002000 08:11 127112183                  /data/lilin/hovernet_features/.venv/lib/python3.12/site-packages/openslide/_convert.abi3.so
7f7f5b75f000-7f7f5b760000 r--p 00002000 08:11 127112183                  /data/lilin/hovernet_features/.venv/lib/python3.12/site-packages/openslide/_convert.abi3.so
7f7f5b760000-7f7f5b761000 rw-p 00003000 08:11 127112183                  /data/lilin/hovernet_features/.venv/lib/python3.12/site-packages/openslide/_convert.abi3.so

case 2

7fb17a47a000-7fb17a484000 r--p 00000000 08:11 127025017                  /data/lilin/hovernet_features/.venv_micromamba/lib/libopenslide.so.1.0.1
7fb17a484000-7fb17a4ac000 r-xp 0000a000 08:11 127025017                  /data/lilin/hovernet_features/.venv_micromamba/lib/libopenslide.so.1.0.1
7fb17a4ac000-7fb17a4bd000 r--p 00032000 08:11 127025017                  /data/lilin/hovernet_features/.venv_micromamba/lib/libopenslide.so.1.0.1
7fb17a4bd000-7fb17a4bf000 r--p 00043000 08:11 127025017                  /data/lilin/hovernet_features/.venv_micromamba/lib/libopenslide.so.1.0.1
7fb17a4bf000-7fb17a4c0000 rw-p 00045000 08:11 127025017                  /data/lilin/hovernet_features/.venv_micromamba/lib/libopenslide.so.1.0.1
7fb17a4c0000-7fb17a4c1000 r--p 00000000 08:11 127112183                  /data/lilin/hovernet_features/.venv/lib/python3.12/site-packages/openslide/_convert.abi3.so
7fb17a4c1000-7fb17a4c2000 r-xp 00001000 08:11 127112183                  /data/lilin/hovernet_features/.venv/lib/python3.12/site-packages/openslide/_convert.abi3.so
7fb17a4c2000-7fb17a4c3000 r--p 00002000 08:11 127112183                  /data/lilin/hovernet_features/.venv/lib/python3.12/site-packages/openslide/_convert.abi3.so
7fb17a4c3000-7fb17a4c4000 r--p 00002000 08:11 127112183                  /data/lilin/hovernet_features/.venv/lib/python3.12/site-packages/openslide/_convert.abi3.so
7fb17a4c4000-7fb17a4c5000 rw-p 00003000 08:11 127112183                  /data/lilin/hovernet_features/.venv/lib/python3.12/site-packages/openslide/_convert.abi3.so

case 3

7f85deecf000-7f85def16000 r-xp 00000000 08:02 39585890                   /usr/lib/x86_64-linux-gnu/libopenslide.so.0.4.0
7f85def16000-7f85df115000 ---p 00047000 08:02 39585890                   /usr/lib/x86_64-linux-gnu/libopenslide.so.0.4.0
7f85df115000-7f85df116000 r--p 00046000 08:02 39585890                   /usr/lib/x86_64-linux-gnu/libopenslide.so.0.4.0
7f85df116000-7f85df117000 rw-p 00047000 08:02 39585890                   /usr/lib/x86_64-linux-gnu/libopenslide.so.0.4.0
7f85e2b1d000-7f85e2b1e000 r--p 00000000 08:11 127112183                  /data/lilin/hovernet_features/.venv/lib/python3.12/site-packages/openslide/_convert.abi3.so
7f85e2b1e000-7f85e2b1f000 r-xp 00001000 08:11 127112183                  /data/lilin/hovernet_features/.venv/lib/python3.12/site-packages/openslide/_convert.abi3.so
7f85e2b1f000-7f85e2b20000 r--p 00002000 08:11 127112183                  /data/lilin/hovernet_features/.venv/lib/python3.12/site-packages/openslide/_convert.abi3.so
7f85e2b20000-7f85e2b21000 r--p 00002000 08:11 127112183                  /data/lilin/hovernet_features/.venv/lib/python3.12/site-packages/openslide/_convert.abi3.so
7f85e2b21000-7f85e2b22000 rw-p 00003000 08:11 127112183                  /data/lilin/hovernet_features/.venv/lib/python3.12/site-packages/openslide/_convert.abi3.so

[bgilbert]

What does os.environ.get('LD_LIBRARY_PATH') return before and after importing torch?

[0820LL]

I ran the code

import os
print(os.environ.get('LD_LIBRARY_PATH'))
import torch
print(os.environ.get('LD_LIBRARY_PATH'))
import openslide
print(os.environ.get('LD_LIBRARY_PATH'))

and got the result

None
None
None

[bgilbert]

I'm not sure why this is happening. On Linux, OpenSlide Python loads OpenSlide using ctypes.cdll.LoadLibrary(), so the behavior of that function ultimately dictates what happens here. PyTorch appears to monkey-patch that code, but in a way that I wouldn't immediately expect to cause the behavior you're seeing.

It seems likely that this issue is not caused by OpenSlide Python, so this issue tracker is not a good place to troubleshoot further. I'll close this issue for now. If you find some evidence that OpenSlide Python is misbehaving, feel free to follow up here. Good luck.

[bgilbert]

The other odd thing is that OpenSlide Python tries to load libopenslide.so.1 before it tries libopenslide.so.0. Whatever PyTorch is doing, it isn't just reordering the library search path, it's ensuring that OpenSlide 4.0.1 isn't found at all.