From mathieu.malaterre at gmail.com  Tue Feb  5 02:31:10 2019
From: mathieu.malaterre at gmail.com (Mathieu Malaterre)
Date: Tue, 5 Feb 2019 08:31:10 +0100
Subject: Introduction to MIRAX/MRXS
In-Reply-To: <5DB02926-675B-4BA9-A9D1-CC0F59203F71@163.com>
References: <5DB02926-675B-4BA9-A9D1-CC0F59203F71@163.com>
Message-ID: <CA+7wUsxyXar0PEL2i1W2HUCaELJJ2NXccb-3EWZaFG0uQ5u75w@mail.gmail.com>

Hi Bingxue,

Welcome to OpenSlide mailing list.

On Mon, Feb 4, 2019 at 6:21 PM Bingxue GUO <gbx5885 at 163.com> wrote:
>
> Dear Madam/Sir,
>
> Sorry to bother you. My name is Bingxue GUO and I am currently working on a project which has to deal with the .mrxs file obtained from 3D HISTECH. Some problems have troubled us for days.
>  I?ve been looking around but can?t find any easy solution to open a .mrxs file (accompanied with some .dat files) with openslide. Could you give us some help, Great thanks in advance.

Sorry if this sound pedantic, but you may want to read at least once
the following document:

[How To Ask Questions The Smart Way]
http://www.catb.org/esr/faqs/smart-questions.html#easyreply

We are missing a lot of information in order to potentially help you
here (error message, possible dataset, environment...)

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



-- 
Mathieu

From dclunie at dclunie.com  Tue Feb 12 16:22:10 2019
From: dclunie at dclunie.com (=?UTF-8?Q?David_Clunie?=)
Date: Tue, 12 Feb 2019 21:22:10 +0000
Subject: What tissue and preparation were used for CMU-1 open slide example
References: <3b811c80-dccc-0e10-49c8-34069911ff98@dclunie.com>
Message-ID: <01000168e396b36e-d6605a5d-57a2-4115-b42a-bc8b4e299393-000000@email.amazonses.com>

Hi all

I am working on my TIFF (SVS) to DICOM converter and I was making
some samples that populate the specimen preparation description.

Since, like everyone else I start with the openslide CMU-1 sample,
I was wondering what tissue and anatomic location were used for
that slide.

Does anyone know/remember?

Thanks ... David

From taqil001 at fiu.edu  Mon Feb 11 19:48:29 2019
From: taqil001 at fiu.edu (Tasmia Aqila)
Date: Mon, 11 Feb 2019 19:48:29 -0500
Subject: Need help to install openslide
Message-ID: <CACYJ-+Qxnq2iFdoMJmNTWusV8t-kK-zmSXf+XiyOrJsSYN+Y_w@mail.gmail.com>

Hello,
I want to work with histomicstk package in python.It requires me to
install openslide first.Can you please help with the steps I should
follow for installing openslide on my windows??
thanks in advance.
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From marklund at stanford.edu  Fri Feb 15 17:53:00 2019
From: marklund at stanford.edu (Henrik Marklund)
Date: Fri, 15 Feb 2019 22:53:00 +0000
Subject: Is it possible to create/edit WSI using openslide?
Message-ID: <DM6PR02MB4891CF191DFF9C02117F3C8AB1600@DM6PR02MB4891.namprd02.prod.outlook.com>

Hi all,


I am new to the mailing list. I am using openslide and the python API working with .svs files. Apart from just reading slides, I was wondering if it possible to create a whole slide image from a set of patches using openslide. Ideally, I could be able to just edit an existing svs file directly: read a patch, edit the patch, update the svs with the new patch.


Best regards,

Henrik
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From D.R.Magee at leeds.ac.uk  Fri Feb 15 21:45:47 2019
From: D.R.Magee at leeds.ac.uk (Derek Magee)
Date: Sat, 16 Feb 2019 02:45:47 +0000
Subject: Is it possible to create/edit WSI using openslide?
In-Reply-To: <DM6PR02MB4891CF191DFF9C02117F3C8AB1600@DM6PR02MB4891.namprd02.prod.outlook.com>
References: <DM6PR02MB4891CF191DFF9C02117F3C8AB1600@DM6PR02MB4891.namprd02.prod.outlook.com>
Message-ID: <6fd476af-7f55-4929-b4f5-c377e09f86f5@email.android.com>

Unfortunately not. Openslide is a read only library. I'd recommend libtiff for writing svs (it's just a tiled tiff with a particular structure). If you search back through the mailing list archived I posted a c++ example. Not sure how you'd do it in python, but there may be libtiff bindings.

D.

On 15 Feb 2019 22:54, Henrik Marklund <marklund at stanford.edu> wrote:

Hi all,


I am new to the mailing list. I am using openslide and the python API working with .svs files. Apart from just reading slides, I was wondering if it possible to create a whole slide image from a set of patches using openslide. Ideally, I could be able to just edit an existing svs file directly: read a patch, edit the patch, update the svs with the new patch.


Best regards,

Henrik
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From mrissmann at yahoo.com  Fri Feb 22 11:41:22 2019
From: mrissmann at yahoo.com (Mark Rissmann)
Date: Fri, 22 Feb 2019 16:41:22 +0000 (UTC)
Subject: Introduction to MIRAX/MRXS
In-Reply-To: <CA+7wUsxyXar0PEL2i1W2HUCaELJJ2NXccb-3EWZaFG0uQ5u75w@mail.gmail.com>
References: <5DB02926-675B-4BA9-A9D1-CC0F59203F71@163.com>
 <CA+7wUsxyXar0PEL2i1W2HUCaELJJ2NXccb-3EWZaFG0uQ5u75w@mail.gmail.com>
Message-ID: <755174184.3504487.1550853682998@mail.yahoo.com>

 I haven't seen any posts regarding your actual troubles...

I am currently converting the .mrxs format. It really isn't any different that other formats unless you want to do anything special.
The only annoyance I have is trying to get rid of the boundary markings produced by the scanner.

-Markus

    On Monday, February 4, 2019, 11:31:54 PM PST, Mathieu Malaterre <mathieu.malaterre at gmail.com> wrote:  
 
 Hi Bingxue,

Welcome to OpenSlide mailing list.

On Mon, Feb 4, 2019 at 6:21 PM Bingxue GUO <gbx5885 at 163.com> wrote:
>
> Dear Madam/Sir,
>
> Sorry to bother you. My name is Bingxue GUO and I am currently working on a project which has to deal with the .mrxs file obtained from 3D HISTECH. Some problems have troubled us for days.
>? I?ve been looking around but can?t find any easy solution to open a .mrxs file (accompanied with some .dat files) with openslide. Could you give us some help, Great thanks in advance.

Sorry if this sound pedantic, but you may want to read at least once
the following document:

[How To Ask Questions The Smart Way]
http://www.catb.org/esr/faqs/smart-questions.html#easyreply

We are missing a lot of information in order to potentially help you
here (error message, possible dataset, environment...)

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



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