[ome-users] OMERO - answer to your question on Facebook

[Petr Walczysko (Staff)]

Hi Christophe

Thanks for your answer.

1. We want to save back to OMERO the ROIs as you understood, not only for the images opened locally but also for the images opened from OMERO.

2. We want to do the same (as ad. 1 above) with the results (this is work in progress though which will not make it to the 5.1.0 release). We intend to attach the results as an attachment to the appropriate image which was opened/selected/analyzed in ImageJ.

    Would you please specify whether an attachment of results as a textfile would be sufficient or would you prefer pytables format ?

3. You can already now open images from OMERO directly in ImageJ using our plugin for ImageJ (see http://help.openmicroscopy.org/imagej.html#imagej5). This very plugin gets the new features which are partly presented on the YouTube video.

4. We are investigating the status of the Open With feature at the moment.

All the best
Petr

Dr. Petr Walczysko
OME-Team


On 23 Jan 2015, at 11:24, Christophe TREFOIS <christophe.trefois at uni.lu> wrote:

> Hi
>
> Well it is all about usability for me. If I tell a user to upload the image to OMERO, and then work on it from ImageJ, it would be great if some things could be saved in OMERO afterwards. For instance, the workflow you described where ROIs are updated could be quite nice.
>
> The idea is: do you use OMERO only for image storage or do you also use to hold your results? In the latter case, this is where 2-way sync will be the most important.
>
> Also as you mentioned, having ImageJ open directly from OMERO would be cool. Does this work already today? Also on the web ? There could be a menu -> Open with ImageJ, similar as there is a “Download as…” button currently. Small things like that are tremendous improvements in UX.
>
> Best,
>
> Dr Christophe Trefois, Dipl.-Ing.
> Technical Specialist / Post-Doc
>
> UNIVERSITÉ DU LUXEMBOURG
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>> On 23 Jan 2015, at 12:16, Petr Walczysko <pwalczysko at dundee.ac.uk> wrote:
>>
>> Hi Christopher
>> you wrote on Facebook a question concerning the feature upcoming in
>> OMERO 5.1 which will allow you to interoperate between IJ and OMERO
>> regions and more, see https://www.youtube.com/watch?v=S-xYKpatHBs
>>
>> Your question was:
>> “Is this also including updates? Eg what happens if I decide I want a
>> different ROI. Will it re-upload the image as "new" ?”
>>
>> The workflow you are asking about is still work in progress. We had in
>> mind following sequence:
>> - open the (already uploaded) image from OMERO in ImageJ, using the
>> plugin shown in video (just double-click on the thumbnail in the Insight
>> Data Manager shown in the video, this will open the image in IJ)
>> - draw a region in ImageJ
>> - save the region (BUT DO NOT RE-UPLOAD THE IMAGE)
>>
>> What is your particular workflow please ?
>>
>> Any details on it would be very helpful to us. We are wondering about
>> questions like
>> Do you want to rewrite the existing regions, or just add the new ones ?,
>> Do you insist on the combination of the workflow shown in the YouTube
>> video and the three point workflow I described above or are you happy to
>> reopen the image from OMERO ?
>>
>> Thank you very much for your feedback
>>
>> All the best
>>
>> Petr
>>
>> Dr. Petr Walczysko
>> OME-Team
>>
>>
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
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