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mrxs format whole slide images

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mrxs format whole slide images

Isabelle Dupont
1 post
Hello,

I obtained mrxs whole slide images of mouse kidneys with a Mirax Scan, viewed with Mirax Viewer.
I want to use these images with ImageJ to make area measurements.
However, when I open these images in ImageJ, the resolution of these whole slide images changes to a bad quality.
Is there a way to use these mrxs format images in Image J with the resolution preserved ?

Thank you,

Isabelle

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Re: mrxs format whole slide images

ctrueden
1670 posts
Hi Isabelle,

> I obtained mrxs whole slide images of mouse kidneys with a Mirax Scan,
> viewed with Mirax Viewer. I want to use these images with ImageJ to
> make area measurements.

Lots of people want support for .mrxs, but it is not yet supported by
Bio-Formats (which is the most likely path to getting them working in
ImageJ/Fiji). See this ticket in the OME issue tracker for details:

http://trac.openmicroscopy.org.uk/ome/ticket/4121

The good news is that .mrxs will be supported eventually!

Regards,
Curtis


On Tue, Aug 13, 2013 at 11:34 AM, Isabelle Dupont <[hidden email]>wrote:

> Hello,
>
> I obtained mrxs whole slide images of mouse kidneys with a Mirax Scan,
> viewed with Mirax Viewer.
> I want to use these images with ImageJ to make area measurements.
> However, when I open these images in ImageJ, the resolution of these whole
> slide images changes to a bad quality.
> Is there a way to use these mrxs format images in Image J with the
> resolution preserved ?
>
> Thank you,
>
> Isabelle
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: mrxs format whole slide images

Vitali Khvatkov-2
17 posts
Hi Isabelle,

If it helps,   3DHistech / Zeiss Mirax digital slides are supported on
Simagis Live cloud servers.
You can get your free account here
http://host.simagis.com/live/register  and use your cloud workspace to
view, share, measure and analyze Mirax whole slide images.

There is number of web applications in the App Store that you can use (
http://live.simagis.com/applications)
You can also run ImageJ macros on Mirax Images on Simagis Servers but
only if you have private server, which is not free.

Regards,

--
Vitali Khvatkov
Smart Imaging Technologies Co.
---------------------------------------
www.simagis.com



Curtis Rueden wrote:

> Hi Isabelle,
>
>> I obtained mrxs whole slide images of mouse kidneys with a Mirax Scan,
>> viewed with Mirax Viewer. I want to use these images with ImageJ to
>> make area measurements.
>
> Lots of people want support for .mrxs, but it is not yet supported by
> Bio-Formats (which is the most likely path to getting them working in
> ImageJ/Fiji). See this ticket in the OME issue tracker for details:
>
> http://trac.openmicroscopy.org.uk/ome/ticket/4121
>
> The good news is that .mrxs will be supported eventually!
>
> Regards,
> Curtis
>
>
> On Tue, Aug 13, 2013 at 11:34 AM, Isabelle Dupont<[hidden email]>wrote:
>
>> Hello,
>>
>> I obtained mrxs whole slide images of mouse kidneys with a Mirax Scan,
>> viewed with Mirax Viewer.
>> I want to use these images with ImageJ to make area measurements.
>> However, when I open these images in ImageJ, the resolution of these whole
>> slide images changes to a bad quality.
>> Is there a way to use these mrxs format images in Image J with the
>> resolution preserved ?
>>
>> Thank you,
>>
>> Isabelle
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html