[ome-users] OMERO Question

[Kenneth Gillen (Staff)]

Hi Eric,

Thanks for the heads up.

We’ve had a dig into the server logs and it looks you have hit a small bug with the particular images you were working with, one which we seem to be able to replicate.

As always, we’ll be improving OMERO and Bio-Formats with the fix, so thanks for the heads up.

All the best,

Kenny

--

Kenneth Gillen
OME System Administrator

Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
CTIR 2
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

Tel: +44 (0) 1382 388797
Skype: kennethgillen

http://www.twitter.com/openmicroscopy

From: "Eric Griffis (Staff)" <e.griffis at dundee.ac.uk<mailto:e.griffis at dundee.ac.uk>>
Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Date: Tuesday, 12 May 2015 23:04
Cc: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-users] OMERO Question

Hi All,

I've been having a lot of issues with nightshade tonight. Everything is taking a very long time.

Best regards,

Eric



Centre for Gene Regulation and Expression
College of Life Sciences
University of Dundee
MSI/WTB/JBC Complex
Dow Street
Dundee DD1 5EH
United KIngdom

+44 (0)1382 385118
e.griffis at dundee.ac.uk<mailto:e.griffis at dundee.ac.uk>
http://www.lifesci.dundee.ac.uk/groups/eric_griffis/GriffisLab/index.html



On 11 May 2015, at 12:57, "Balaji Ramalingam (Staff)" <b.ramalingam at dundee.ac.uk<mailto:b.ramalingam at dundee.ac.uk>>
 wrote:

Hi Eric,

Here are some workflows that might help your case,

  1.  Open both the stacks on ImageJ.
     *   Images on disk : (Plugins —> Bio-Formats —> Bio-Formats Importer) or
     *   Images on Omero Server : (Plugins —> OMERO —> login to OMERO) : Then open the image of interest.
  2.  Image —> Stacks —> Tools —> Concatenate. (This concatenates the two stacks).
  3.  Plugins —> Bioformats —> Bioformats Exporter (Export the concatenated file locally) : This should preserve the metadata, while writing out the stack as an ome.tiff.
  4.  Now import the ome.tiff into OMERO. This should hopefully preserve the image and the associated metadata, for later use (in OMERO.Figure).

**You can also do the following post concatenating the images,  (But this workflow has a bug, which will get looked into at the earliest)
Plugins—> OMERO —> Upload and save to OMERO : should save the stack to OMERO directly from ImageJ.

Requirements for the above workflows:

  1.  Bioformats_package.jar in your ImageJ/Plugins folder. (Can be downloaded from : http://downloads.openmicroscopy.org/bio-formats/5.1.1/)
  2.  Omero-ImageJ/Fiji plugin in your ImageJ/plugins folder.  (Can be downloaded from : http://downloads.openmicroscopy.org/omero/5.1.1/)

For more information on the above workflows please visit our help page,
http://help.openmicroscopy.org/imagej.html

Hope that helps,

Best,
Balaji

__________________
Mr Balaji Ramalingam
Software Developer
OME Team
College of Life Sciences
University of Dundee

From: "William Moore (Staff)" <W.Moore at dundee.ac.uk<mailto:W.Moore at dundee.ac.uk>>
Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Date: Sunday, 10 May 2015 22:33
To: "Eric Griffis (Staff)" <e.griffis at dundee.ac.uk<mailto:e.griffis at dundee.ac.uk>>
Cc: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-users] OMERO Question


Hi Eric,

 I can't tell you myself how to do this, but I know that someone on the team will, so I'm forwarding to the e-mail list, and we'll go from there…

  Cheers,

   Will.


On 8 May 2015, at 13:44, Eric Griffis (Staff) <e.griffis at dundee.ac.uk<mailto:e.griffis at dundee.ac.uk>> wrote:

Hi Will,

I have an issue with a dataset. I have a cell that was imaged until the end of a timelapse, and then I started a new timelapse. I would like to be able to concatenate these two images and have all of the metadata merge together. I can do the concatenation by exporting and then separately opening the images in FIJI. However, the saved image loses all of the metadata and is therefore more difficult to work with in Figure than I would like. Is there a better way?

Best regards,

Eric


Centre for Gene Regulation and Expression
College of Life Sciences
University of Dundee
MSI/WTB/JBC Complex
Dow Street
Dundee DD1 5EH
United KIngdom

+44 (0)1382 385118
e.griffis at dundee.ac.uk<mailto:e.griffis at dundee.ac.uk>
http://www.lifesci.dundee.ac.uk/groups/eric_griffis/GriffisLab/index.html





The University of Dundee is a registered Scottish Charity, No: SC015096


The University of Dundee is a registered Scottish Charity, No: SC015096

The University of Dundee is a registered Scottish Charity, No: SC015096
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