SVS File Whole Slide Image Tiling

[Sied Kebir]

Dear John,

thank you so much! I have managed to get tiles from my .svs file. I have
two questions now:

A) Of the image tiles I got, many do not have any informative data, e.g.
showing the background for example. How can I remove those?

B) Some tiles are out of focus, is there a way to remove them as well?

Thanks again!

Best
Sied

Am Mi., 11. Dez. 2019 um 09:49 Uhr schrieb <jcupitt at gmail.com>:

> Hello Sied,
>
> On Wed, 11 Dec 2019 at 06:56, Angelos Pappas <angelos at smartcode.gr> wrote:
> > You can use vips to create Deep Zoom images using the following command:
> >
> > vips dzsave yourslide.svs yourdzdirectory
>
> dzsave will make a deepzoom pyramid by default, so a series of levels,
> with overlapping tiles at each one.
>
> It has quite a few options -- try:
>
>     vips dzsave yourslide.svs yourdzdirectory --overlap 0 --tile-size
> 512 --depth one
>
> And it'll only write the top layer (highest res) of the pyramid, tiles
> will be 512 x 512, and there will be no overlap. Use --suffix .png if
> you want PNG tiles.
>
> You can run it from Python with:
>
>     import pyvips
>     image = pyvips.Image.new_from_file("yourslide.svs")
>     image.dzsave("yourdzdirectory", overlap=0, tile_size=512, depth="one")
>
> There's a chapter in the libvips manual introducing dzsave:
>
> https://libvips.github.io/libvips/API/current/Making-image-pyramids.md.html
>
> You can also simply crop out tiles in Python:
>
>     import pyvips
>     image = pyvips.Image.new_from_file("yourslide.svs")
>     tile = image.crop(124878, 232445, 512, 512)
>
> John
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> openslide-users at lists.andrew.cmu.edu
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>
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