From ssowmith94 at gmail.com  Fri Jun 12 12:55:09 2020
From: ssowmith94 at gmail.com (Sowrirajan Sowmithran)
Date: Fri, 12 Jun 2020 12:55:09 -0400
Subject: Question about readRegion on MIRAX files
Message-ID: <CAEb9AqPLKUN3oGUkmvKa5fNUZcgqw1N_3NV7tKnJOMO4OL8sLg@mail.gmail.com>

Good day all,

I am currently working with MIRAX files using OpenSlide library Interface
with MATLAB and in particular, I am using these to example files from the
OpenSlide demo website,

1) Mirax2-Fluorescence-2
2) CMU-1-Saved-1_2

On trying to apply the openslide_readRegion() function to get the desired
part (random area) of the data, I end up getting a dark image instead (all
0s). Does this have something to do with the MIRAX format or the region
being empty? If it is the later how do I determine which region has data
and display it?

Thanks in advance.

Regards,
Sowri
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From kwiechen1 at gmail.com  Sat Jun 13 04:07:59 2020
From: kwiechen1 at gmail.com (Kai Wiechen)
Date: Sat, 13 Jun 2020 10:07:59 +0200
Subject: Question about readRegion on MIRAX files
In-Reply-To: <CAEb9AqPLKUN3oGUkmvKa5fNUZcgqw1N_3NV7tKnJOMO4OL8sLg@mail.gmail.com>
References: <CAEb9AqPLKUN3oGUkmvKa5fNUZcgqw1N_3NV7tKnJOMO4OL8sLg@mail.gmail.com>
Message-ID: <CAFRUvvWnOkPJ4HvfX-zKtKMsQjaDZfVP2TPjYVhYYSHqzM_5Vg@mail.gmail.com>

Can you please provide sample code?

Best regards

Kai

Sowrirajan Sowmithran <ssowmith94 at gmail.com> schrieb am Fr. 12. Juni 2020
um 18:58:

> Good day all,
>
> I am currently working with MIRAX files using OpenSlide library Interface
> with MATLAB and in particular, I am using these to example files from the
> OpenSlide demo website,
>
> 1) Mirax2-Fluorescence-2
> 2) CMU-1-Saved-1_2
>
> On trying to apply the openslide_readRegion() function to get the desired
> part (random area) of the data, I end up getting a dark image instead (all
> 0s). Does this have something to do with the MIRAX format or the region
> being empty? If it is the later how do I determine which region has data
> and display it?
>
> Thanks in advance.
>
> Regards,
> Sowri
> _______________________________________________
> 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  Sat Jun 13 05:39:38 2020
From: jcupitt at gmail.com (jcupitt at gmail.com)
Date: Sat, 13 Jun 2020 10:39:38 +0100
Subject: Question about readRegion on MIRAX files
In-Reply-To: <CAEb9AqPLKUN3oGUkmvKa5fNUZcgqw1N_3NV7tKnJOMO4OL8sLg@mail.gmail.com>
References: <CAEb9AqPLKUN3oGUkmvKa5fNUZcgqw1N_3NV7tKnJOMO4OL8sLg@mail.gmail.com>
Message-ID: <CAGNS0RtbiM-BOhcaaXeKnWe5owmWZ-_a6tu4h5djwruS6hqJEQ@mail.gmail.com>

On Fri, 12 Jun 2020 at 17:57, Sowrirajan Sowmithran
<ssowmith94 at gmail.com> wrote:
> On trying to apply the openslide_readRegion() function to get the desired part (random area) of the data, I end up getting a dark image instead (all 0s). Does this have something to do with the MIRAX format or the region being empty? If it is the later how do I determine which region has data and display it?

0 means transparent (ie. the slide background colour), so you are
probably reading outside the image area. I would check the openslide
bounds:

                "openslide.bounds-x",
                "openslide.bounds-y",
                "openslide.bounds-width",
                "openslide.bounds-height"

And make sure you are inside them. You could also open the image file
in a viewer and note the position of some real pixels.

John

From D.R.Magee at leeds.ac.uk  Tue Jun 16 11:55:21 2020
From: D.R.Magee at leeds.ac.uk (Derek Magee)
Date: Tue, 16 Jun 2020 15:55:21 +0000
Subject: ICC Profiles in Aperio/Leica SVS
Message-ID: <DB6PR03MB31091127AC84344A9D9D1D20E09D0@DB6PR03MB3109.eurprd03.prod.outlook.com>

Hi,

Does anyone have any experience with ICC Profiles in Aperio/Leica SVS files? In particular which TIFF tag are they stored? I see there are various open libraries for dealing with them. I'm assuming it is simply a matter of extracting the profile from the TIFF, and processing the (RGB?) values?

BTW: My interest is some (a very small number of images) slides look very different in imagescope vs openslide based programs. I'm assuming this is ICC related (not a bug in the openslide colourspace conversion).

Thanks in advance

Derek
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From ssowmith94 at gmail.com  Sat Jun 27 20:36:41 2020
From: ssowmith94 at gmail.com (Sowrirajan Sowmithran)
Date: Sat, 27 Jun 2020 20:36:41 -0400
Subject: Question about readRegion on MIRAX files
In-Reply-To: <CAGNS0RtbiM-BOhcaaXeKnWe5owmWZ-_a6tu4h5djwruS6hqJEQ@mail.gmail.com>
References: <CAEb9AqPLKUN3oGUkmvKa5fNUZcgqw1N_3NV7tKnJOMO4OL8sLg@mail.gmail.com>
 <CAGNS0RtbiM-BOhcaaXeKnWe5owmWZ-_a6tu4h5djwruS6hqJEQ@mail.gmail.com>
Message-ID: <CAEb9AqPRLQ6cJtDXm45V7ZV4c7D=JdUokznTHqaJONryFGr+cA@mail.gmail.com>

Sorry for the late reply.

Much thanks Dr. Cupitt for your suggestion.

No matter what region I read for a MIRAX file I keep getting the dark
region only. On the other hand I have no difficulties with the svs file.
One additional question is how do I determine the tile-size and block size
of the MIRAX file. I knew from the post by Benjamin that
"CameraImageDivisionsPerSide"
= 4 means a 4x4 blocks but what is the actual size of this tile?

https://lists.andrew.cmu.edu/pipermail/openslide-users/2012-July/000373.html


Any help is much appreciated.

On Sat, Jun 13, 2020 at 5:40 AM <jcupitt at gmail.com> wrote:

> On Fri, 12 Jun 2020 at 17:57, Sowrirajan Sowmithran
> <ssowmith94 at gmail.com> wrote:
> > On trying to apply the openslide_readRegion() function to get the
> desired part (random area) of the data, I end up getting a dark image
> instead (all 0s). Does this have something to do with the MIRAX format or
> the region being empty? If it is the later how do I determine which region
> has data and display it?
>
> 0 means transparent (ie. the slide background colour), so you are
> probably reading outside the image area. I would check the openslide
> bounds:
>
>                 "openslide.bounds-x",
>                 "openslide.bounds-y",
>                 "openslide.bounds-width",
>                 "openslide.bounds-height"
>
> And make sure you are inside them. You could also open the image file
> in a viewer and note the position of some real pixels.
>
> 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 dagutman at gmail.com  Sun Jun 28 09:38:54 2020
From: dagutman at gmail.com (David Gutman)
Date: Sun, 28 Jun 2020 09:38:54 -0400
Subject: Question about readRegion on MIRAX files
In-Reply-To: <CAEb9AqPRLQ6cJtDXm45V7ZV4c7D=JdUokznTHqaJONryFGr+cA@mail.gmail.com>
References: <CAEb9AqPLKUN3oGUkmvKa5fNUZcgqw1N_3NV7tKnJOMO4OL8sLg@mail.gmail.com>
 <CAGNS0RtbiM-BOhcaaXeKnWe5owmWZ-_a6tu4h5djwruS6hqJEQ@mail.gmail.com>
 <CAEb9AqPRLQ6cJtDXm45V7ZV4c7D=JdUokznTHqaJONryFGr+cA@mail.gmail.com>
Message-ID: <CABGe6AGqx0y1+o8nkRvcRba1L+uwf8aZr-0iKM6cRpEohg-QKQ@mail.gmail.com>

Is the image dark or any chance the contrast and or max/min or window
settings are just set improperly?   With 12 or 16 bit images sometimes at
least in other formats I've seen it where the image range is set from 0 to
2x16 but the image is only hundreds or thousands of units bright.. so
basically everything looks black because the range is goofed..

On Sat, Jun 27, 2020, 8:38 PM Sowrirajan Sowmithran <ssowmith94 at gmail.com>
wrote:

> Sorry for the late reply.
>
> Much thanks Dr. Cupitt for your suggestion.
>
> No matter what region I read for a MIRAX file I keep getting the dark
> region only. On the other hand I have no difficulties with the svs file.
> One additional question is how do I determine the tile-size and block size
> of the MIRAX file. I knew from the post by Benjamin that "CameraImageDivisionsPerSide"
> = 4 means a 4x4 blocks but what is the actual size of this tile?
>
>
> https://lists.andrew.cmu.edu/pipermail/openslide-users/2012-July/000373.html
>
>
> Any help is much appreciated.
>
> On Sat, Jun 13, 2020 at 5:40 AM <jcupitt at gmail.com> wrote:
>
>> On Fri, 12 Jun 2020 at 17:57, Sowrirajan Sowmithran
>> <ssowmith94 at gmail.com> wrote:
>> > On trying to apply the openslide_readRegion() function to get the
>> desired part (random area) of the data, I end up getting a dark image
>> instead (all 0s). Does this have something to do with the MIRAX format or
>> the region being empty? If it is the later how do I determine which region
>> has data and display it?
>>
>> 0 means transparent (ie. the slide background colour), so you are
>> probably reading outside the image area. I would check the openslide
>> bounds:
>>
>>                 "openslide.bounds-x",
>>                 "openslide.bounds-y",
>>                 "openslide.bounds-width",
>>                 "openslide.bounds-height"
>>
>> And make sure you are inside them. You could also open the image file
>> in a viewer and note the position of some real pixels.
>>
>> 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 ssowmith94 at gmail.com  Sun Jun 28 17:28:41 2020
From: ssowmith94 at gmail.com (Sowrirajan Sowmithran)
Date: Sun, 28 Jun 2020 17:28:41 -0400
Subject: Question about readRegion on MIRAX files
In-Reply-To: <CABGe6AGqx0y1+o8nkRvcRba1L+uwf8aZr-0iKM6cRpEohg-QKQ@mail.gmail.com>
References: <CAEb9AqPLKUN3oGUkmvKa5fNUZcgqw1N_3NV7tKnJOMO4OL8sLg@mail.gmail.com>
 <CAGNS0RtbiM-BOhcaaXeKnWe5owmWZ-_a6tu4h5djwruS6hqJEQ@mail.gmail.com>
 <CAEb9AqPRLQ6cJtDXm45V7ZV4c7D=JdUokznTHqaJONryFGr+cA@mail.gmail.com>
 <CABGe6AGqx0y1+o8nkRvcRba1L+uwf8aZr-0iKM6cRpEohg-QKQ@mail.gmail.com>
Message-ID: <CAEb9AqMMCC0K-6MBmj5aRK+MWFyoaxDTGJcJTQRC_V==VfGx+w@mail.gmail.com>

Dear Dr. Cuppit & Dr. Gutman,

I am using the example MIRAX files from the OpenSlide Website,

https://openslide.org/demo/

Files:

CMU-1-Saved-1_2 <https://openslide.org/demo/#>
CMU-1-Exported <https://openslide.org/demo/#>

Looking from the Image format, the values I noticed before was uint32. I
cast these values to uint8 format to get the final image. While this worked
great for the svs, MIRAX seems to differ.
*Also, as mentioned earlier, I am trying to read "One Tile" out of the 4x4
tile structured blocks in level0. *I assumed the "DIGITIZER WIDTH" and
"DIGITIZERHEIGHT" as the size of a single tile. Not sure if this assumption
is correct or not.

In the meantime let me also approach the issue from the angle Dr. Gutman
pointed out, and try casting the output of the openslide_readRegion to an
8-bit/ 16-bit data.

Sowri

On Sun, Jun 28, 2020 at 9:39 AM David Gutman <dagutman at gmail.com> wrote:

> Is the image dark or any chance the contrast and or max/min or window
> settings are just set improperly?   With 12 or 16 bit images sometimes at
> least in other formats I've seen it where the image range is set from 0 to
> 2x16 but the image is only hundreds or thousands of units bright.. so
> basically everything looks black because the range is goofed..
>
> On Sat, Jun 27, 2020, 8:38 PM Sowrirajan Sowmithran <ssowmith94 at gmail.com>
> wrote:
>
>> Sorry for the late reply.
>>
>> Much thanks Dr. Cupitt for your suggestion.
>>
>> No matter what region I read for a MIRAX file I keep getting the dark
>> region only. On the other hand I have no difficulties with the svs file.
>> One additional question is how do I determine the tile-size and block
>> size of the MIRAX file. I knew from the post by Benjamin that "CameraImageDivisionsPerSide"
>> = 4 means a 4x4 blocks but what is the actual size of this tile?
>>
>>
>> https://lists.andrew.cmu.edu/pipermail/openslide-users/2012-July/000373.html
>>
>>
>> Any help is much appreciated.
>>
>> On Sat, Jun 13, 2020 at 5:40 AM <jcupitt at gmail.com> wrote:
>>
>>> On Fri, 12 Jun 2020 at 17:57, Sowrirajan Sowmithran
>>> <ssowmith94 at gmail.com> wrote:
>>> > On trying to apply the openslide_readRegion() function to get the
>>> desired part (random area) of the data, I end up getting a dark image
>>> instead (all 0s). Does this have something to do with the MIRAX format or
>>> the region being empty? If it is the later how do I determine which region
>>> has data and display it?
>>>
>>> 0 means transparent (ie. the slide background colour), so you are
>>> probably reading outside the image area. I would check the openslide
>>> bounds:
>>>
>>>                 "openslide.bounds-x",
>>>                 "openslide.bounds-y",
>>>                 "openslide.bounds-width",
>>>                 "openslide.bounds-height"
>>>
>>> And make sure you are inside them. You could also open the image file
>>> in a viewer and note the position of some real pixels.
>>>
>>> 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 nicolas at primaalab.com  Tue Jun 30 09:20:32 2020
From: nicolas at primaalab.com (Nicolas Pozin)
Date: Tue, 30 Jun 2020 15:20:32 +0200
Subject: openslide and multiprocessing
Message-ID: <CALd3aLFHx8LXO1e56Vra5X7ru8-a7XTcaer6YWgQJ=H_vZcGTA@mail.gmail.com>

Hi everyone,

I am using openslide python.
I have a simple code where :
- a slide is loaded
- the read_region function is called to get tiles at various levels and
locations.

When doing so it appears the code runs in parallel, several processes are
launched. This is not a behavior I expected as no part of my code is
parallelized.
Is it expected? and Is there a way to impose openslide operations to run on
a single proc?

Thanks in advance
Nicolas
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