[ome-users] ome-users Digest, Vol 120, Issue 4

Tue Mar 10 10:08:52 GMT 2015

Thanks Will,

That all looks great and I will certainly try it. I'm quite new to slide
digitisation techniques, it's amazing how you can look for something and
not find it and once it's pointed out you can't believe you missed it.

Regards,

Brendan.

On 9 March 2015 at 12:00, <ome-users-request at lists.openmicroscopy.org.uk>
wrote:

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>    1. Re: Viewing and annotating large z-stacked tifs (William Moore)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 9 Mar 2015 10:17:11 +0000
> From: William Moore <will at lifesci.dundee.ac.uk>
> To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
> Subject: Re: [ome-users] Viewing and annotating large z-stacked tifs
> Message-ID:
>         <7FA92788-E3D4-4FFA-97CE-1B3DF3200650 at lifesci.dundee.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Brendan,
>
>  We don't know how to make your data work on ImageScope or NDPview since
> we're not familiar with these packages.
>
> Since you're asking this on the OME lists, our natural solution to your
> needs would be to suggest OMERO,
> https://www.openmicroscopy.org/site/products/omero
> which will import your ome.tiff images and generate tiled "image pyramids"
> for viewing in remote Java or Web clients.
> The Java desktop client can be used to add ROI annotations (which can also
> be viewed in the web client).
> If you want to send us an example file (upload at
> https://www.openmicroscopy.org/qa2/qa/upload/ - zip it if it helps)
> we can see how well OMERO handles it, or you can sign up for a demo
> account at
> https://www.openmicroscopy.org/site/support/omero5.0/users/demo-server.html
> .
>
> Other software that my be able to help you is
> http://www.ini.uzh.ch/~acardona/trakem2.html (ImageJ plugin) or
> http://catmaid.org/index.html (web-based annotation tool, lighter-weight
> than OMERO), although you'd have to find out from their docs or developers
> about how to get your data into them etc.
>
> Hope that helps,
>
>    Will.
>
>
>
> On 5 Mar 2015, at 18:45, Brendan Ffrench <ffrenchg at tcd.ie> wrote:
>
> > Dear ome-users,
> >
> > I am new to this mailing list and hope that someone may be able to
> advise me.
> > I am combining digitized slide images taken on a NanoZoomer (.ndpi
> files) with matched fluorescence images scanned on an epiflouresent
> microscope (.tif files).
> >
> > Using ImageJ, Bio-Formats and GIMP, I have managed to extract, align and
> stack the images (both .ndpi and .tif files) into a 4 level z-stacked .tif
> file. The full .tif files are approx. 9500x9500 pixels (1GB; I am happy to
> share a sample if it helps). I was hoping to use Bio-Formats (ImageJ) to
> export these stacked .tif files back into a format that could be viewed and
> annotated by whole slide viewing software such as ImageScope or NDPview.
> Any software that allows me to make annotations and track the areas viewed
> on a thumbnail would suit my needs.
> >
> > ImageScope can open these files but it is not is not representing the
> z-stacks correctly. I imagine this can be fixed by editing fields in the
> files' metadata. However, I do not know how to start going about this. I
> have also tried exporting as .ome and .ome.tiff but none of the viewing
> software I have can open these files.
> >
> > Any insights into this would be greatly appreciated. Alternatively,
> another strategy for viewing, tracking and annotating large z-stacked tifs
> would be very helpful.
> >
> > Regards,
> >
> > Brendan.
> >
> >
> >
> >
> > _______________________________________________
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> > ome-users at lists.openmicroscopy.org.uk
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> End of ome-users Digest, Vol 120, Issue 4
> *****************************************
>

-- 
Brendan Ffrench, PhD

Circulating Tumour Cell Group,
Pathology Research Lab,
Coombe Women's Hospital,
Dolphins Barn,
Dublin 8,
Ireland.

Dept. Histopathology,
Trinity College Dublin,
Ireland.

Tel: +353-1-4085675
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