From schao at g.harvard.edu  Fri Jul  5 16:46:10 2019
From: schao at g.harvard.edu (Sherry Chao)
Date: Fri, 05 Jul 2019 16:46:10 -0400
Subject: QPTIFF
Message-ID: <1747AA77-E21C-4864-B1F3-81C1BE47ECB7@contoso.com>

Is OpenSlide compatible with PerkinElmer slides (.qptiff)?

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From kent3737 at gmail.com  Sat Jul  6 13:07:32 2019
From: kent3737 at gmail.com (Kent Johnson)
Date: Sat, 6 Jul 2019 13:07:32 -0400
Subject: QPTIFF
In-Reply-To: <1747AA77-E21C-4864-B1F3-81C1BE47ECB7@contoso.com>
References: <1747AA77-E21C-4864-B1F3-81C1BE47ECB7@contoso.com>
Message-ID: <CAPP0wyjCYpAU1bQxiKfW-y79n2AwoU-eLJcBVAxoecZXMidNFw@mail.gmail.com>

My understanding is that OpenSlide is limited to three colors, which rules
out any qptiff files with fluorescence data. I don't know if OpenSlide will
read a brightfield (RGB) qptiff; they might read correctly as a generic
tiled tiff.

Kent Johnson
Akoya Biosciences

On Fri, Jul 5, 2019 at 4:47 PM Sherry Chao <schao at g.harvard.edu> wrote:

> Is OpenSlide compatible with PerkinElmer slides (.qptiff)?
> _______________________________________________
> 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 yoderj at gmail.com  Thu Jul 18 13:38:31 2019
From: yoderj at gmail.com (yoderj)
Date: Thu, 18 Jul 2019 12:38:31 -0500
Subject: deepzoom_server.py only shows black image
Message-ID: <CAD=bn-otppMWFPJEvaMz6XmCvxfc8ZAh-GChsZ070a7_v30LTQ@mail.gmail.com>

Hi,

I'm trying to get started with deepzoom_server.py.   I downloaded:

deepzoom_server.py
templates/slide-multipane.html

The app now runs without errors, and I can see the main screen (in black)
as well as information about my multilevel .tif file through the browse.
But I can't see the image. The same image loads and displays a thumbnail
just fine with this code:

slide = openslide.OpenSlide(tif)
thumb = slide.get_thumbnail((10000,10000))
thumb.show()


I'm looking at the whole slide image (wsi) pds_12_HE.tif from the zip
peso_training_wsi_1.zip
<https://zenodo.org/record/1485967/files/peso_training_wsi_1.zip?download=1>
 at
https://zenodo.org/record/1485967#.XS42g-hKg2z
in case that is helpful.

Any idea what I should do differently?

Thanks,
Josiah
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From bgilbert at cs.cmu.edu  Thu Jul 18 18:32:32 2019
From: bgilbert at cs.cmu.edu (Benjamin Gilbert)
Date: Thu, 18 Jul 2019 18:32:32 -0400
Subject: deepzoom_server.py only shows black image
In-Reply-To: <CAD=bn-otppMWFPJEvaMz6XmCvxfc8ZAh-GChsZ070a7_v30LTQ@mail.gmail.com>
References: <CAD=bn-otppMWFPJEvaMz6XmCvxfc8ZAh-GChsZ070a7_v30LTQ@mail.gmail.com>
Message-ID: <CANioFnib3GEZCmBS4BV0GwpDoSD_sEB38vPaqCww6hPLATtEGQ@mail.gmail.com>

On Thu, Jul 18, 2019 at 6:30 PM yoderj <yoderj at gmail.com> wrote:

> I'm trying to get started with deepzoom_server.py.   I downloaded:
>
> deepzoom_server.py
> templates/slide-multipane.html
>
> The app now runs without errors, and I can see the main screen (in black)
> as well as information about my multilevel .tif file through the browse.
> But I can't see the image.
>

You also need the static/ directory and contents.

--Benjamin Gilbert
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