Alternatives to OpenSlide about gandlf HOT 9 CLOSED

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 😃

from gandlf.

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. 😄

from gandlf.

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

from gandlf.

Stale issue message

from gandlf.

Keeping this open for future considerations.

from gandlf.

@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.

from gandlf.

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. 😛

from gandlf.

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?

from gandlf.

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

from gandlf.