[ome-users] splitting a multi-image series

[Damir Sudar]

Thanks Ola, this is the OpenSlide software on: http://openslide.org/ ,
right? I'll definitely look at that. And yes, I already suggested that they
look at ways to omit the label and thumbnail while scanning. I'm myself
also not familiar with the Aperio scanner software but they are.
Cheers,
- Damir

On Fri, Jun 5, 2015 at 3:32 PM, Aleksandra Tarkowska (Staff) <
A.Tarkowska at dundee.ac.uk> wrote:

>  Hi Damir,
>
>  It was nice to meet you in Paris.
>
>  We used Aperio software called OpenSlide to permanently remove label
> from raw data as making it invisible in OMERO is not enough (remember about
> download button).
>  I personally have never scanned slides but I am pretty sure there should
> be an option to choose not to scan label and/or thumbnail.
>
>  Kind regards
> Ola
>
>   From: Damir Sudar <dsudar at lbl.gov>
> Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
> Date: Fri, 5 Jun 2015 13:36:31 +0200
> To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
> Subject: Re: [ome-users] splitting a multi-image series
>
>  Thanks Petr. I've forwarded your suggestion to my user and let him
> decide whether that approach is adequate for him or not. I agree that
> covering the label-part of the slide before scanning is the most
> appropriate thing to do.
> - Damir
>
> On Fri, Jun 5, 2015 at 1:27 PM, Petr Walczysko (Staff) <
> p.walczysko at dundee.ac.uk> wrote:
>
>> Hi Damir
>>
>>  Thank you very much for your feedback.
>> You are right, the Move action will not help you in the workflow you are
>> describing, OMERO always forces you to Move the whole component into the
>> different group,
>> so I would not go this way anymore.
>>
>>  The best workflow I have for hiding parts of mulit-image series is to
>>
>>    - create a new dataset  (e.g. named "dump")
>>   - use in Web or Insight the Cut and Paste (right-click context menu) on
>> the images with labels to remove them from the vicinity of the other,
>> valuable (or unlabelled) multi-image series
>>   - Paste the images into the "dump" dataset
>>
>>  I realise now that this might not be sufficient enough for your user,
>> because probably a full covering/removal of the labelled images is asked
>> for (in my workflow above, the labelled images will
>> STILL be visible and accessible when you expand and browse the "dump"
>> folder ) but I am not aware of any better workflow at the moment, possibly
>> one of my colleagues might come up with
>> some better answer yet.
>>
>>  All the best
>>
>>  Petr
>>
>>  Petr Walczysko
>> OME Team
>>
>>
>>  On 5 Jun 2015, at 10:35, Damir Sudar <dsudar at lbl.gov> wrote:
>>
>>  Hi OME team,
>>
>>  Thanks for an extremely useful and fun User's Meeting this week.
>>
>>  During one of the sessions I had asked whether there was any way to
>> remove one of the components of a multi-image series (one of my users is
>> uploading Aperio .svs images and would like to remove the image of the
>> label because of concerns of it having identifiable patient info on it).
>> Anyway, in your answer it was very clear that actually removing is
>> impossible since all components are in the same image file in the repo so I
>> completely understand that. However, I think it was Josh who suggested that
>> it may be possible to make one of the components not visible and I thought
>> I had remembered that one could do so by moving that component to a
>> different group. I just tried and OMERO tells me very clearly that all
>> components must stay together in the same group. Was there some other way
>> to make one component of a multi-image series not visible?
>>
>>  I already suggested to the user that he could simply obscure the label
>> before scanning but alas, they have scanned ~1000 slides already .....
>>
>>  Thanks,
>> - Damir
>>
>>  --
>>   Damir Sudar - Staff Scientist
>> Lawrence Berkeley Laboratory / Life Sciences Division
>> One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
>> T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov
>>
>>  Visiting Scientist, Oregon Health and Science University
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>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>
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>>
>
>
>  --
>    Damir Sudar - Staff Scientist
> Lawrence Berkeley Laboratory / Life Sciences Division
> One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
> T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov
>
>  Visiting Scientist, Oregon Health and Science University
>    _______________________________________________ ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
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>


-- 
Damir Sudar - Staff Scientist
Lawrence Berkeley Laboratory / Life Sciences Division
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov

Visiting Scientist, Oregon Health and Science University
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