Openslide python on Windows

[Adam Carvosso]

Hi Benjamin,

Thank you for the suggestion re: vips. It didn't spit it out in exactly the format I was expecting but It wasn't difficult to modify the slide viewer code to compensate.



-----Original Message-----
From: Benjamin Gilbert [mailto:bgilbert at cs.cmu.edu]
Sent: Sunday, 17 July 2016 3:32 PM
To: Adam Carvosso <adam.carvosso at utas.edu.au>
Cc: openslide-users at lists.andrew.cmu.edu
Subject: Re: Openslide python on Windows

On Thu, Jul 14, 2016 at 06:39:19AM +0000, Adam Carvosso via openslide-users wrote:
> I am attempting to install OpenSlide as it is a prerequisite for the
> New York University Virtual Microscope and the scripts that it takes
> advantage of for converting .svs files into other formats.  The
> project can be found
> here: https://github.com/evildmp/VirtualMicroscope (I am running
> Windows 7 currently).
>
> My current error is:
>
> "'module' object has no attribute 'OpenSlide'. "

Hi Adam,

The NYU SVS tiling script doesn't use OpenSlide Python: it uses pyOpenSlide, which is an older, unmaintained Python binding.  The script has other problems as well; for example, it tries to read the entire slide into memory, which doesn't generally work on 32-bit systems.

I'd suggest using VIPS instead.  It can read a slide file using OpenSlide and generate a Google Maps pyramid:

    http://libvips.blogspot.com/2013/03/making-deepzoom-zoomify-and-google-maps.html

Windows binaries:

    http://www.vips.ecs.soton.ac.uk/supported/current/win32/

--Benjamin Gilbert


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