Alternatives to OpenSlide

[sarthakpati]

Is your feature request related to a problem? Please describe.
OpenSlide is (and probably will always remain) a pain to install and use because it needs the library files present and correctly loaded in the environment prior to any import.

Describe the solution you'd like
Look for alternatives to this for WSI I/O.

Describe alternatives you've considered
N.A.

Additional context
Post alternatives (and reasons why it is better than OpenSlide) as comments.

[sarthakpati]

1. tifffile: https://pypi.org/project/tifffile/

Pros:

• No additional libraries need to be installed, making the installation and usage very seamless and includes out-of-the-box support for Windows, Linux and macOS
• Conda installer available
• Support for (virtually) all formats supported by OpenSlide, barring a few proprietary ones

Cons:

• Not as well-known as OpenSlide
• Python <= 3.7 is not supported

[github-actions]

Stale issue message

[sarthakpati]

Keeping this open for future considerations.

[grenkoca]

@sarthakpati I'm currently working on OPM2 to make it more stable and simplify code. We might want to look into using PathML as a backend.

[sarthakpati]

I'm currently working on OPM2 to make it more stable and simplify code

Awesome-sauce!

We might want to look into using PathML as a backend.

Let's discuss about this, since we want to move away from open-slide, not add yet another (potentially complicated) dependency for patch extraction. 😛

[sarthakpati]

After #261 is merged, the OpenSlide requirements will be reduced to the following few (admittedly minor) items: https://github.com/CBICA/GaNDLF/search?l=Python&q=openslide

Could one of you take a crack at this?

[sarthakpati]

I think we have a winner with tiffslide, which is pretty much a drop-in replacement for OpenSlide using tifffile as the backend.

[ap--]

Hi @sarthakpati

I'd be super interested in your experience moving this project from openslide to tiffslide. Were there any issues you ran into or did everything work ootb?

Cheers,
Andreas 😃

[sarthakpati]

Thanks, @ap--. We will definitely let you know about our experience. Since I don't specialize in dealing with WSI on GaNDLF, I am waiting on feedback regarding my PR. 😄