OMERO ImageJ links OME

[SUBSCRIBE IMAGEJ Marie-Laure B]

Hi,
I'm trying to figure out linkiings between imageJ and OME.

I had found two workflow :

1- OmeroImporter.jar associated to loci_tools
((from http://www.openmicroscopy.org/site/support/omero4/downloads))

2-  ome-tools.jar associated to loci_tools

In the first case, when I export image metadatas are not saved
In the second case, I don't reach Omero.

Is anybody use ImageJ and OME together ?

Thank you for your help.

Marie Laure

[Jean-Marie Burel (Staff)]

Hi Marie Laure

The omero plugin to use is OMERO.imagej-4.3.3.zip
You can grab it from
http://www.openmicroscopy.org/site/support/omero4/downloads
I guess you click on the wrong link
A new version (I.e. OMERO.insight as an ImageJ plugin) will be available
in the coming 4.4. Version

Jmarie


>


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

[SUBSCRIBE IMAGEJ Marie-Laure B]

Hi Jean-Marie,

Thank you for your answer.

This is my configuration :
- ImageJ 1.45s
- loci-tools (the trunk build available here :
http://loci.wisc.edu/bio-formats/downloads
http://hudson.openmicroscopy.org.uk/job/BIOFORMATS-trunk/lastSuccessfulBuild/artifact/artifacts/loci_tools.jar
-OMERO.imagej-4.3.3.zip
http://cvs.openmicroscopy.org.uk/snapshots/omero/OMERO.imagej-4.3.3.zip

1- I had imported lsm image from my desktop to OMERO (Omero.importer-Beta4.3.3.win)
I can see acquisition informations into omero.insight window.

2- In imageJ I open my image with the plugin : OMERO.imagej-4.3.3
-> OMERO/Import from OMERO :
In metadata, I can't see acquisition data.

3- I make some change into imageJ into this image. (Image Analysis step)

4- I save via the LOCI plugin : Bio-Formats Exporter as treated.ome.tif

5- I import this image from my desktop to OMERO (Omero.importer-Beta4.3.3.win)
I can't see acquisition information.

Could you explain me where I'm wrong ...

Thank you very much for your help

Marie Laure

[Jean-Marie Burel (Staff)]

Hi Marie-Laure

To open in ImageJ, an image stored in OMERO we use an OME-TIFF version of
the original data.
The current implementation of the OME-TIFF export does not write all the
metadata initially present in the original image. This is a limitation
that we are planning to address in a near future.

Nothing wrong with what you are doing.


Jmarie


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

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[Surya Reis]

Hello,

I'm trying to define the cytoplasmic to nuclear signal intensity ratio
per cell in a stack of images.

Is there an easy way to do this?

Thank you,

Surya




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[Thomas Boudier]

Hi,

If you can segment your nucleus and cell, use the 3d object counter to
have the mean (or whatever) value of your signal :

http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:3d_object_counter:start

Thomas


Le 19/06/2012 04:34, Surya Reis a écrit :

> Hello,
>
> I'm trying to define the cytoplasmic to nuclear signal intensity ratio
> per cell in a stack of images.
>
> Is there an easy way to do this?
>
> Thank you,
>
> Surya
>
>
>
>
> The information in this e-mail is intended only for the person to whom
> it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you
> in error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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