From jmather at mathworks.com  Fri Dec  6 12:19:55 2019
From: jmather at mathworks.com (Jeff Mather)
Date: Fri, 6 Dec 2019 17:19:55 +0000
Subject: Leanest OpenSlide possible
Message-ID: <38EE2F04-BCD2-4EDC-95B6-A88C76EF4FDC@mathworks.com>

Hi all,

I?ve just started looking into what might be involved to build something that links against OpenSlide. When I used homebrew to install OpenSlide on my Mac, I saw a lot of other libraries being fetched as well. Some made sense: libtiff, libjpeg, etc. Others puzzled me: cairo, freetype, little-cms, etc.

If my goal is simply to read raster data and file metadata, what?s the leanest set of additional libraries that I need? Eventually I?ll be building OpenSlide from source, and I?d like to link and redistribute as few libraries as possible.

(I haven?t dug deeply enough yet to know if it?s possible to reduce the footprint by only supporting a subset of the formats via build/config flags.)

Thanks!
Jeff
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From skycrazer at gmail.com  Tue Dec 10 13:21:25 2019
From: skycrazer at gmail.com (Sied Kebir)
Date: Tue, 10 Dec 2019 19:21:25 +0100
Subject: SVS File Whole Slide Image Tiling
Message-ID: <CAEgGdSfhBP6jCQzTqJSojuoJ55b3PEPeLd6ruLqg2RjCmXsNow@mail.gmail.com>

Hello there,

I am a completely new user of Openslide and hope to receive a response
nonetheless. I am using openslide for python. I am working with whole slide
histology images, that are usually huge in size. I would like to
automatically subdivide this whole slide image into many smaller chunks of
a fixed size, say 512*512 pixels. I have tried several approaches, any idea
on how to get there?

Many thanks

Sayed
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From angelos at smartcode.gr  Wed Dec 11 01:55:53 2019
From: angelos at smartcode.gr (Angelos Pappas)
Date: Wed, 11 Dec 2019 06:55:53 +0000
Subject: SVS File Whole Slide Image Tiling
In-Reply-To: <CAEgGdSfhBP6jCQzTqJSojuoJ55b3PEPeLd6ruLqg2RjCmXsNow@mail.gmail.com>
References: <CAEgGdSfhBP6jCQzTqJSojuoJ55b3PEPeLd6ruLqg2RjCmXsNow@mail.gmail.com>
Message-ID: <DB8PR01MB6518951E9B3219752230BE5FC85A0@DB8PR01MB6518.eurprd01.prod.exchangelabs.com>

You want to save them as separate images?
You can use vips to create Deep Zoom images using the following command:


vips dzsave yourslide.svs yourdzdirectory



https://jcupitt.github.io/libvips/API/current/Making-image-pyramids.md.html

________________________________
From: openslide-users <openslide-users-bounces+angelos=smartcode.gr at lists.andrew.cmu.edu> on behalf of Sied Kebir <skycrazer at gmail.com>
Sent: Tuesday, December 10, 2019 8:21 PM
To: openslide-users at lists.andrew.cmu.edu <openslide-users at lists.andrew.cmu.edu>
Subject: SVS File Whole Slide Image Tiling

Hello there,

I am a completely new user of Openslide and hope to receive a response nonetheless. I am using openslide for python. I am working with whole slide histology images, that are usually huge in size. I would like to automatically subdivide this whole slide image into many smaller chunks of a fixed size, say 512*512 pixels. I have tried several approaches, any idea on how to get there?

Many thanks

Sayed
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From jcupitt at gmail.com  Wed Dec 11 03:48:34 2019
From: jcupitt at gmail.com (jcupitt at gmail.com)
Date: Wed, 11 Dec 2019 08:48:34 +0000
Subject: SVS File Whole Slide Image Tiling
In-Reply-To: <DB8PR01MB6518951E9B3219752230BE5FC85A0@DB8PR01MB6518.eurprd01.prod.exchangelabs.com>
References: <CAEgGdSfhBP6jCQzTqJSojuoJ55b3PEPeLd6ruLqg2RjCmXsNow@mail.gmail.com>
 <DB8PR01MB6518951E9B3219752230BE5FC85A0@DB8PR01MB6518.eurprd01.prod.exchangelabs.com>
Message-ID: <CAGNS0RspuGMSJdXgc22xonqVPAN7Pysvj6E0AOn-3KZWSG2seQ@mail.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

From bgilbert at cs.cmu.edu  Wed Dec 11 15:20:52 2019
From: bgilbert at cs.cmu.edu (Benjamin Gilbert)
Date: Wed, 11 Dec 2019 15:20:52 -0500
Subject: Leanest OpenSlide possible
In-Reply-To: <38EE2F04-BCD2-4EDC-95B6-A88C76EF4FDC@mathworks.com>
References: <38EE2F04-BCD2-4EDC-95B6-A88C76EF4FDC@mathworks.com>
Message-ID: <CANioFnhFPjvWrYe7d4kAe-OticxBap=tDwDi+SxvEA5RRnChwA@mail.gmail.com>

On Fri, Dec 6, 2019 at 12:20 PM Jeff Mather <jmather at mathworks.com> wrote:

> I?ve just started looking into what might be involved to build something
> that links against OpenSlide. When I used homebrew to install OpenSlide on
> my Mac, I saw a lot of other libraries being fetched as well. Some made
> sense: libtiff, libjpeg, etc. Others puzzled me: cairo, freetype,
> little-cms, etc.
>
>
>
> If my goal is simply to read raster data and file metadata, what?s the
> leanest set of additional libraries that I need? Eventually I?ll be
> building OpenSlide from source, and I?d like to link and redistribute as
> few libraries as possible.
>

OpenSlide uses Cairo to render pixel data.  I'd guess FreeType and Little
CMS are being pulled in as indirect dependencies of Cairo.

OpenSlide itself doesn't have any optional dependencies, but some of _its_
dependencies do.  To get a rough sense of the minimal set (on Windows, at
least), see https://github.com/openslide/openslide-winbuild/.

--Benjamin Gilbert
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From bgilbert at cs.cmu.edu  Thu Dec 12 00:30:28 2019
From: bgilbert at cs.cmu.edu (Benjamin Gilbert)
Date: Thu, 12 Dec 2019 00:30:28 -0500
Subject: FYI: OpenSlide Buildbot shut down
Message-ID: <CANioFnj8x-=HvXrQQRHVonq+H+AFtEvmh6FKdBG3F06xcE05Gg@mail.gmail.com>

Hi all,

FYI, I've shut down the OpenSlide Buildbot that was running at
buildbot.openslide.org.  It's been essentially unmaintained for a while
now, including the worker nodes, and there's not a lot of commit traffic to
exercise it.  If there's any future interest in resurrecting it with a
newer version of the Buildbot software (or perhaps a different CI system),
the code is still available at
https://github.com/openslide/openslide-automation.

--Benjamin Gilbert
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From skycrazer at gmail.com  Tue Dec 17 13:08:00 2019
From: skycrazer at gmail.com (Sied Kebir)
Date: Tue, 17 Dec 2019 19:08:00 +0100
Subject: SVS File Whole Slide Image Tiling
In-Reply-To: <CAGNS0RspuGMSJdXgc22xonqVPAN7Pysvj6E0AOn-3KZWSG2seQ@mail.gmail.com>
References: <CAEgGdSfhBP6jCQzTqJSojuoJ55b3PEPeLd6ruLqg2RjCmXsNow@mail.gmail.com>
 <DB8PR01MB6518951E9B3219752230BE5FC85A0@DB8PR01MB6518.eurprd01.prod.exchangelabs.com>
 <CAGNS0RspuGMSJdXgc22xonqVPAN7Pysvj6E0AOn-3KZWSG2seQ@mail.gmail.com>
Message-ID: <CAEgGdSdXhqNy0+x4+1TBLM-j=GnA1g+B8oy21vJDea2siUk4+w@mail.gmail.com>

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
> _______________________________________________
> openslide-users mailing list
> openslide-users at lists.andrew.cmu.edu
> https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users
>
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From mark.d.zarella at gmail.com  Tue Dec 17 14:00:37 2019
From: mark.d.zarella at gmail.com (Mark Zarella)
Date: Tue, 17 Dec 2019 14:00:37 -0500
Subject: SVS File Whole Slide Image Tiling
In-Reply-To: <CAEgGdSdXhqNy0+x4+1TBLM-j=GnA1g+B8oy21vJDea2siUk4+w@mail.gmail.com>
References: <CAEgGdSfhBP6jCQzTqJSojuoJ55b3PEPeLd6ruLqg2RjCmXsNow@mail.gmail.com>
 <DB8PR01MB6518951E9B3219752230BE5FC85A0@DB8PR01MB6518.eurprd01.prod.exchangelabs.com>
 <CAGNS0RspuGMSJdXgc22xonqVPAN7Pysvj6E0AOn-3KZWSG2seQ@mail.gmail.com>
 <CAEgGdSdXhqNy0+x4+1TBLM-j=GnA1g+B8oy21vJDea2siUk4+w@mail.gmail.com>
Message-ID: <7DCB5AF3-A046-4837-896B-B44DFA80D5DB@gmail.com>

There are algorithms available online (I don?t know specifically where, maybe others can point to a direction) that can do both tissue-finding (request A) and focus detection (request B).? My suggestion is to perform the tissue-finding step at the level of the lowest-res image in the pyramid to speed up the I/O ? there?s no sense in reading a set of tiles that are ultimately blank and will be discarded anyway.? 

 

Focus detection has been done for a long time in various ways, although I believe Stumpe?s group at google published a preprint on this earlier this year that might be useful.? Not sure if they?ve shared the code or created an end-user function however.

 

 

From: openslide-users <openslide-users-bounces+mark.d.zarella=gmail.com at lists.andrew.cmu.edu> on behalf of Sied Kebir <skycrazer at gmail.com>
Date: Tuesday, December 17, 2019 at 1:08 PM
To: <jcupitt at gmail.com>
Cc: "openslide-users at lists.andrew.cmu.edu" <openslide-users at lists.andrew.cmu.edu>
Subject: Re: SVS File Whole Slide Image Tiling

 

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
_______________________________________________
openslide-users mailing list
openslide-users at lists.andrew.cmu.edu
https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users

_______________________________________________ openslide-users mailing list openslide-users at lists.andrew.cmu.edu https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users 

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From jcupitt at gmail.com  Tue Dec 17 15:14:09 2019
From: jcupitt at gmail.com (jcupitt at gmail.com)
Date: Tue, 17 Dec 2019 20:14:09 +0000
Subject: SVS File Whole Slide Image Tiling
In-Reply-To: <CAEgGdSdXhqNy0+x4+1TBLM-j=GnA1g+B8oy21vJDea2siUk4+w@mail.gmail.com>
References: <CAEgGdSfhBP6jCQzTqJSojuoJ55b3PEPeLd6ruLqg2RjCmXsNow@mail.gmail.com>
 <DB8PR01MB6518951E9B3219752230BE5FC85A0@DB8PR01MB6518.eurprd01.prod.exchangelabs.com>
 <CAGNS0RspuGMSJdXgc22xonqVPAN7Pysvj6E0AOn-3KZWSG2seQ@mail.gmail.com>
 <CAEgGdSdXhqNy0+x4+1TBLM-j=GnA1g+B8oy21vJDea2siUk4+w@mail.gmail.com>
Message-ID: <CAGNS0RsyCGq3U3_TS8sse7AoSUrh80Tps8h34EbjDkOOD6YFsA@mail.gmail.com>

On Tue, 17 Dec 2019 at 18:08, Sied Kebir <skycrazer at gmail.com> wrote:
> 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?

You don't need a fancy tissue detector for slides. I would just take
the histogram of each area and see if you have more than a few % of
non-white pixels.

As Mark says, start with the low-res levels and refine.

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

I've always just found the histogram and calculated the entropy. It's
easy to make a nice, normalized 0 - 100 number, and its very robust.
Again, you don't need anything fancy for slides.

John