Open Microscopy Environment

Hi,

I would like to have more information about ways of linking imageJ and Omero.

I found an Imagej plugin to import images from OMERO
OmeroImporter.jar associated to loci_tools
((from http://www.openmicroscopy.org/site/support/omero4/downloads))

I had imported the raw image by OmeroImporter plugin.
Analyzed my images and then exported by loci/Bio format exporter the analyzed image.
And then import with OMERO.importer the analyzed image.

In OMERO, I didn't find a link between the raw image and the analyzed image.
Perhaps you have a better way to manage that ...

I would like to know if there is an other way to launch imageJ ?
Perhaps it is possible to launch imageJ from the OMERO.insight as a script ?

Thank you for your help.

Marie Laure

Hi,
To sum'up my question :
Is anyone know if there is an "OmeroExporter" plugin ?
Thanks
Marie Laure

Hi Marie-Laure

We currently have two ways to interact with ImageJ

* In the coming 4.4 version, the OMERO.insight client can be used as an imageJ plugin. You will start ImageJ and open images stored in omero either using the built-in viewer or an imageJ viewer.

* you also have the ability to use the "Open With" option. From OMERO.insight, right-click on an image, select ImageJ (or Fiji, firefox) by browsing your directories, select imageJ. The image stored in OMERO will open in ImageJ. You will have to do that only once.

In both cases, you must have the LOCI plugin under ImageJ/Plugin.

Note that the "Open With" option only works on Mac OS X in the 4.3. version and will be cross-platform in the coming 4.4. version


We are planning to have much closer interaction in a near future with imageJ, ImageJ2 etc.

Thanks
Jmarie

Hi Jean-Marie,

Do you know when the coming version 4.4 will be on line ?
... I'll try to find a mac to test it !

Thank you for your help

Marie Laure B

Hi Marie Laure

We are working hard to fix bugs so we can release fairly soon.
We will keep you posted.

Thanks for your interest.

Jmarie

Hi,

1/On mac,
When I import from the O.insight client, images are imported without the full path
I can open with "openwith" imageJ this image.

When I import from the O.importer client, we have the choose to import with or without the full path.
if image has been saved with the full path, it's not possible to open it : "openwith" by ImageJ.
if image has been saved without the full path, I can open it with image J "openwith"

With full path or without, the name of the image change. When we export a report, we have the ID and the name, but without the full path.

id name
1740 ...Imagej/Dot_Blot.jpg

As I understand, the easy, and best way to import images is to use O.insight.
The name of images is never with a fullpath and we can import different set of images without waiting the end of the previous import.

2/With the dropbox, the name of the image is full. So we can't open it with imageJ (frome O.Insight GUI)
Right ?

3/ In ImageJ, when you run the plugin OMERO/Import from OMERO, all images can be openable.


4/ From this page I have downloaded the omero 's plugin
http://www.openmicroscopy.org/site/support/omero4/downloads/?searchterm=download
I don't find as it is mentioned in this page
http://www.openmicroscopy.org/site/support/legacy/ome-server/imagej-plugin
Download from OME
Upload to OMERO


I hope, my message is not too long .... and is understandable.

Thank you for your help and answers.

Marie Laure

Hi Marie-Laure

Thanks for the information
We have improved the "open with" functionality so it now works on all platforms
We will add additional tests to make sure the problem with the path you described in your post is correctly supported.

As of 4.4, the actual importer will no longer be supported and you will also be able to use OMERO.insight as an ImageJ plugin.

Thanks for your feedback

Jmarie

Ok, thank you for your answer and more than anything for your good work !